sRNA-seq_sample	RNA-seq_sample	data_type	tissue	age	stimulus	genotype	sequencer	Treatment_protocol					
SRR394315	SRR394319	single-end	cotyledon	20 days after flowering	profiling of cotyledons	cultivar Heinong44	Illumina Genome Analyzer IIx	Soybean seeds of Glycine max cultivar Heinong44 were respectively planted in the experimental station and growth chambers in Beijing on May. Soybean cotyledons were dissected from seeds of 20 days after flowering (DAF). Roots, stems, and leaves were harvested from the plants cultivated for 14 days in growth chambers.					
SRR5220387	SRR5220366	single-end	cotyledon	24 hours	24h-2,4-D,40 mg/l of 2,4 D medium, Embryo Initiation, 3-5 mm cotyledon, for embryo initiation	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220388	SRR5220369	single-end	cotyledon	24 hours	24h+2,4-D rep1,40 mg/l of 2,4 D medium, Embryo Initiation, 3-5 mm cotyledon, for embryo initiation	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220389	SRR5220370	single-end	cotyledon	24 hours	24h+2,4-D rep2,40 mg/l of 2,4 D medium, Embryo Initiation, 3-5 mm cotyledon, for embryo initiation	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220390	SRR5220371	single-end	cotyledon	24 hours	24h+2,4-D rep3,40 mg/l of 2,4 D medium, Embryo Initiation, 3-5 mm cotyledon, for embryo initiation	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220391	SRR5220372	single-end	embryo	6 weeks	6 wk globular rep1,40 mg/l of 2,4 D medium, Embryo Initiation, young globular embryo tissue, embryogenic, regeneratable, non-transformable	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220392	SRR5220373	single-end	embryo	6 weeks	6 wk globular rep2,40 mg/l of 2,4 D medium, Embryo Initiation, young globular embryo tissue, embryogenic, regeneratable, non-transformable	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220393	SRR5220374	single-end	embryo	6 weeks	6 wk globular rep3,20 mg/l of 2,4 D medium, Embryo Maintenance, young globular embryo tissue, embryogenic, can regenerate, non-transformable	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220394	SRR5220375	single-end	embryo	6 weeks	6 wk diff rep1,20 mg/l of 2,4 D medium, Embryo Maintenance, differentiated embryo, non-embryogenic	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220395	SRR5220376	single-end	embryo	6 weeks	6 wk diff rep2,20 mg/l of 2,4 D medium, Embryo Maintenance, differentiated embryo, non-embryogenic	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220396	SRR5220377	single-end	embryo	6 weeks	6 wk diff rep3,20 mg/l of 2,4 D medium, Embryo Maintenance, differentiated embryo, non-embryogenic	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220397	SRR5220378	single-end	embryo	10 weeks + 4 days	4-day subculture rep1,20 mg/l of 2,4 D medium, Embryo Maintenance, globular embryo,embryogenic, regeneratable, transformable	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220398	SRR5220379	single-end	embryo	10 weeks + 4 days	4-day subculture rep2,20 mg/l of 2,4 D medium, Embryo Maintenance, globular embryo,embryogenic, regeneratable, transformable	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220399	SRR5220380	single-end	embryo	10 weeks + 4 days	4-day subculture rep3,20 mg/l of 2,4 D medium, Embryo Maintenance	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220400	SRR5220381	single-end	embryo	6 months	6 mo globular rep1,20 mg/l of 2,4 D medium, Embryo Maintenance, globular embryo,embryogenic, regeneratable, transformable	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220401	SRR5220382	single-end	embryo	6 months	6 mo globular rep2,20 mg/l of 2,4 D medium, Embryo Maintenance, globular embryo,embryogenic, regeneratable, transformable	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220402	SRR5220383	single-end	embryo	6 months	6 mo globular rep3,20 mg/l of 2,4 D medium, Embryo Maintenance, globular embryo,embryogenic, regeneratable, transformable	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220403	SRR5220384	single-end	embryo	12 months	12 mo globular,20 mg/l of 2,4 D medium, Embryo Maintenance, old globular embryo, embryogenic, non-regeneratble, non-transformable	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220404	SRR5220385	single-end	embryo	12 months	12 mo dif,20 mg/l of 2,4 D medium, Embryo Maintenance, old differentiated embryo, non-embryogenic, non-regeneratable, non-transformable	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR5220405	SRR5220386	single-end	embryo	8 year	8 yr globular,20 mg/l of 2,4 D medium, Embryo Maintenance, old globular embryo, embryogenic, non-regeneratable, non-transformable	Jack	Illumina HiSeq 2500	Five samples throughout specific stages of tissue culture were analyzed in tripiicate for changes in DNA methylation, RNA expression and smalL RNA abundance					
SRR955302	SRR955406	single-end	embryonic_axis	Early maturation-stage	Early maturation-stage embryonic axis	Williams 82	Illumina HiSeq 2000	Soybean plants (Williams 82) were grown under standard greenhouse conditions (Le et al., PNAS 2010). Whole seeds containing early-maturation (EM) stage embryos were collected. The embryo was dissected out of the seed coat and the axis was manually separated from the cotyledons of the EM-stage embryo					
SRR394314	SRR394318	single-end	leaf	14 days after germination	profiling of leaves	cultivar Heinong44	Illumina Genome Analyzer IIx	Soybean seeds of Glycine max cultivar Heinong44 were respectively planted in the experimental station and growth chambers in Beijing on May. Soybean cotyledons were dissected from seeds of 20 days after flowering (DAF). Roots, stems, and leaves were harvested from the plants cultivated for 14 days in growth chambers.					
SRR7124309	SRR7124207	single-end	leaf	None	gmax FC33243 Anderson	FC33243 Anderson	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124310	SRR7124208	single-end	leaf	None	gmax PI548360 Korean	PI548360 Korean	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124311	SRR7124209	single-end	leaf	None	gmax PI548362 Lincoln	PI548362 Lincoln	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124312	SRR7124210	single-end	leaf	None	gmax PI548379 Mandarin	PI548379 Mandarin	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124313	SRR7124211	single-end	leaf	None	gmax PI548391 Mukden	PI548391 Mukden	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124314	SRR7124212	single-end	leaf	None	gmax PI548406 Richland	PI548406 Richland	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124315	SRR7124213	single-end	leaf	None	gmax PI548456 Haberlandt	PI548456 Haberlandt	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124316	SRR7124214	single-end	leaf	None	gmax PI548477 Ogden	PI548477 Ogden	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124317	SRR7124215	single-end	leaf	None	gmax PI548484 Ralsoy	PI548484 Ralsoy	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124318	SRR7124216	single-end	leaf	None	gmax PI548485 Roanoke	PI548485 Roanoke	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124319	SRR7124217	single-end	leaf	None	gmax PI548488 S-100	PI548488 S-100	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124320	SRR7124218	single-end	leaf	None	gmax PI508266 Young	PI508266 Young	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124321	SRR7124219	single-end	leaf	None	gmax PI548493 Tokyo	PI548493 Tokyo	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124322	SRR7124220	single-end	leaf	None	gmax PI548505 Amcor	PI548505 Amcor	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124323	SRR7124221	single-end	leaf	None	gmax PI548510 Beeson	PI548510 Beeson	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124324	SRR7124222	single-end	leaf	None	gmax PI548512 Century	PI548512 Century	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124325	SRR7124223	single-end	leaf	None	gmax PI548516 Blackhawk	PI548516 Blackhawk	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124326	SRR7124224	single-end	leaf	None	gmax PI548517 Bonus	PI548517 Bonus	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124327	SRR7124225	single-end	leaf	None	gmax PI548523 Pella	PI548523 Pella	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124328	SRR7124226	single-end	leaf	None	gmax PI548527 Calland	PI548527 Calland	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124329	SRR7124227	single-end	leaf	None	gmax PI548530 Chippewa	PI548530 Chippewa	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124330	SRR7124228	single-end	leaf	None	gmax PI548533 Clark	PI548533 Clark	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124331	SRR7124229	single-end	leaf	None	gmax PI518671 Williams82	PI518671 Williams82	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124332	SRR7124230	single-end	leaf	None	gmax PI548540 Corsoy	PI548540 Corsoy	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124333	SRR7124231	single-end	leaf	None	gmax PI548542 Cumberland	PI548542 Cumberland	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124334	SRR7124232	single-end	leaf	None	gmax PI548543 Oakland	PI548543 Oakland	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124335	SRR7124233	single-end	leaf	None	gmax PI548545 Merit	PI548545 Merit	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124336	SRR7124234	single-end	leaf	None	gmax PI548555 Douglas	PI548555 Douglas	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124337	SRR7124235	single-end	leaf	None	gmax PI548562 Ford	PI548562 Ford	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124338	SRR7124236	single-end	leaf	None	gmax PI548570 Harcor	PI548570 Harcor	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124339	SRR7124237	single-end	leaf	None	gmax PI548573 Harosoy	PI548573 Harosoy	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124340	SRR7124238	single-end	leaf	None	gmax PI548574 Shelby	PI548574 Shelby	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124341	SRR7124239	single-end	leaf	None	gmax PI548577 Hawkeye	PI548577 Hawkeye	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124342	SRR7124240	single-end	leaf	None	gmax PI518673 Lawrence	PI518673 Lawrence	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124343	SRR7124241	single-end	leaf	None	gmax PI548586 Kent	PI548586 Kent	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124344	SRR7124242	single-end	leaf	None	gmax PI548603 Perry	PI548603 Perry	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124345	SRR7124243	single-end	leaf	None	gmax PI548628 Wayne	PI548628 Wayne	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124346	SRR7124244	single-end	leaf	None	gmax PI548631 Williams	PI548631 Williams	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124347	SRR7124245	single-end	leaf	None	gmax PI548632 Woodworth	PI548632 Woodworth	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124348	SRR7124246	single-end	leaf	None	gmax PI548634 Zane	PI548634 Zane	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124349	SRR7124247	single-end	leaf	None	gmax PI548654 Hill	PI548654 Hill	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124350	SRR7124248	single-end	leaf	None	gmax PI548657 Jackson	PI548657 Jackson	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124351	SRR7124249	single-end	leaf	None	gmax PI548975 Centennial	PI548975 Centennial	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124352	SRR7124250	single-end	leaf	None	gmax PI548980 Hood	PI548980 Hood	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124353	SRR7124251	single-end	leaf	None	gmax PI548298 A.K.(Harrow)	PI548298 A.K.(Harrow)	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124354	SRR7124252	single-end	leaf	None	gmax PI548983 Tracy	PI548983 Tracy	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124355	SRR7124253	single-end	leaf	None	gmax PI548986 Brim	PI548986 Brim	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124356	SRR7124254	single-end	leaf	None	gmax PI548987 Dare	PI548987 Dare	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124357	SRR7124255	single-end	leaf	None	gmax PI548988 Pickett	PI548988 Pickett	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124358	SRR7124256	single-end	leaf	None	gmax PI548989 Ransom	PI548989 Ransom	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124359	SRR7124257	single-end	leaf	None	gmax PI553039 Davis	PI553039 Davis	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124360	SRR7124258	single-end	leaf	None	gmax PI553046 Gasoy17	PI553046 Gasoy17	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124361	SRR7124259	single-end	leaf	None	gmax PI572239 Holladay	PI572239 Holladay	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124362	SRR7124260	single-end	leaf	None	gmax PI617045 NC-Roy	PI617045 NC-Roy	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124363	SRR7124261	single-end	leaf	None	gmax PI630984 5601T	PI630984 5601T	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124364	SRR7124262	single-end	leaf	None	gmax PI548311 Capital	PI548311 Capital	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124365	SRR7124263	single-end	leaf	None	gmax PI641156 NC-Raleigh	PI641156 NC-Raleigh	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124366	SRR7124264	single-end	leaf	None	gmax PI88788 unnamed	PI88788 unnamed	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124367	SRR7124265	single-end	leaf	None	gmax PI548318 Dunfield	PI548318 Dunfield	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124368	SRR7124266	single-end	leaf	None	gmax PI548348 Illini	PI548348 Illini	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124369	SRR7124267	single-end	leaf	None	gmax PI548356 Kanro	PI548356 Kanro	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124370	SRR7124308	single-end	leaf	None	gmax NAM IA3023	NAM IA3023	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124371	SRR7124268	single-end	leaf	None	gmax NAM02 TN05-3027	NAM02 TN05-3027	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124372	SRR7124269	single-end	leaf	None	gmax NAM03 4J105-3-4	NAM03 4J105-3-4	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124373	SRR7124270	single-end	leaf	None	gmax NAM04 5M20-2-5-2	NAM04 5M20-2-5-2	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124374	SRR7124271	single-end	leaf	None	gmax NAM05 CL0J095-4-6	NAM05 CL0J095-4-6	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124375	SRR7124272	single-end	leaf	None	gmax NAM06 CL0J173-6-8	NAM06 CL0J173-6-8	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124376	SRR7124273	single-end	leaf	None	gmax NAM08 HS6-3976	NAM08 HS6-3976	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124377	SRR7124274	single-end	leaf	None	gmax NAM09 Prohio	NAM09 Prohio	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124378	SRR7124275	single-end	leaf	None	gmax NAM10 LD00-3309	NAM10 LD00-3309	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124379	SRR7124276	single-end	leaf	None	gmax NAM11 LD01-5907	NAM11 LD01-5907	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124380	SRR7124277	single-end	leaf	None	gmax NAM12 LD02-4485	NAM12 LD02-4485	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124381	SRR7124278	single-end	leaf	None	gmax NAM13 LD02-9050	NAM13 LD02-9050	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124382	SRR7124279	single-end	leaf	None	gmax NAM14 Magellan	NAM14 Magellan	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124383	SRR7124280	single-end	leaf	None	gmax NAM15 Maverick	NAM15 Maverick	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124384	SRR7124281	single-end	leaf	None	gmax NAM17 S06-13640	NAM17 S06-13640	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124385	SRR7124282	single-end	leaf	None	gmax NAM18 NE3001	NAM18 NE3001	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124386	SRR7124283	single-end	leaf	None	gmax NAM22 Skylla	NAM22 Skylla	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124387	SRR7124284	single-end	leaf	None	gmax NAM23 U03-100612	NAM23 U03-100612	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124388	SRR7124285	single-end	leaf	None	gmax NAM24 LG03-2979	NAM24 LG03-2979	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124389	SRR7124286	single-end	leaf	None	gmax NAM25 LG03-3191	NAM25 LG03-3191	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124390	SRR7124287	single-end	leaf	None	gmax NAM26 LG04-4717	NAM26 LG04-4717	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124391	SRR7124288	single-end	leaf	None	gmax NAM27 LG05-4292	NAM27 LG05-4292	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124392	SRR7124289	single-end	leaf	None	gmax NAM28 LG05-4317	NAM28 LG05-4317	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124393	SRR7124290	single-end	leaf	None	gmax NAM29 LG05-4464	NAM29 LG05-4464	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124394	SRR7124291	single-end	leaf	None	gmax NAM30 LG05-4832	NAM30 LG05-4832	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124395	SRR7124292	single-end	leaf	None	gmax NAM31 LG90-2550	NAM31 LG90-2550	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124396	SRR7124293	single-end	leaf	None	gmax NAM32 LG92-1255	NAM32 LG92-1255	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124397	SRR7124294	single-end	leaf	None	gmax NAM33 LG94-1128	NAM33 LG94-1128	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124398	SRR7124295	single-end	leaf	None	gmax NAM34 LG94-1906	NAM34 LG94-1906	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124399	SRR7124296	single-end	leaf	None	gmax NAM36 LG97-7012	NAM36 LG97-7012	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124400	SRR7124297	single-end	leaf	None	gmax NAM37 LG98-1605	NAM37 LG98-1605	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124401	SRR7124298	single-end	leaf	None	gmax NAM38 LG00-3377	NAM38 LG00-3377	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124402	SRR7124299	single-end	leaf	None	gmax NAM39 LG04-6000	NAM39 LG04-6000	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124403	SRR7124300	single-end	leaf	None	gmax NAM40 PI398.881	NAM40 PI398.881	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124404	SRR7124301	single-end	leaf	None	gmax NAM41 PI427.136	NAM41 PI427.136	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124405	SRR7124302	single-end	leaf	None	gmax NAM42 PI437.169B	NAM42 PI437.169B	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124406	SRR7124303	single-end	leaf	None	gmax NAM46 PI507.681B	NAM46 PI507.681B	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124407	SRR7124304	single-end	leaf	None	gmax NAM48 PI518.751	NAM48 PI518.751	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124408	SRR7124305	single-end	leaf	None	gmax NAM50 PI561.370	NAM50 PI561.370	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124409	SRR7124306	single-end	leaf	None	gmax NAM54 PI404.188A	NAM54 PI404.188A	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR7124410	SRR7124307	single-end	leaf	None	gmax NAM64 PI574.486	NAM64 PI574.486	Illumina HiSeq 2000	MethylC-seq libraries were prepared as previously described in (Urich et al. 2015). RNA-seq libraries were constructed using Illumina TruSeq Stranded RNA LT Kit (Illumina, San Diego, CA) following the manufacturer’s instructions with limited modifications. The starting quantity of total RNA was adjusted to 1.3 μg, and all volumes were reduced to a third of the described quantity. Small RNA-seq libraries were prepared using the Illumina TruSeq Small RNA Library PrepKit v2 according to the manufacturer's instructions.					
SRR2051074	SRR2051082	single-end	leaf	4 hours 	control	None	Illumina HiSeq 2000	For the stress treatment 200mM of NaCl were added to the nutrient solution of one group of plantlets and nothing was added to the control group. After 4 hours the the leaves from both groups were harvested to RNA isolation.Soybean seeds were germinated in moistened filter paper, 25°C for 2 days. The seedlings were growth in hydroponic system with Hoagland's nutrient solution for 15 days.					
SRR2051075	SRR2051083	single-end	leaf	4 hours 	control	None	Illumina HiSeq 2000	For the stress treatment 200mM of NaCl were added to the nutrient solution of one group of plantlets and nothing was added to the control group. After 4 hours the the leaves from both groups were harvested to RNA isolation.Soybean seeds were germinated in moistened filter paper, 25°C for 2 days. The seedlings were growth in hydroponic system with Hoagland's nutrient solution for 15 days.					
SRR2051078	SRR2051086	single-end	leaf	4 hours 	salt stress	None	Illumina HiSeq 2000	For the stress treatment 200mM of NaCl were added to the nutrient solution of one group of plantlets and nothing was added to the control group. After 4 hours the the leaves from both groups were harvested to RNA isolation.Soybean seeds were germinated in moistened filter paper, 25°C for 2 days. The seedlings were growth in hydroponic system with Hoagland's nutrient solution for 15 days.					
SRR2051079	SRR2051087	single-end	leaf	4 hours 	salt stress	None	Illumina HiSeq 2000	For the stress treatment 200mM of NaCl were added to the nutrient solution of one group of plantlets and nothing was added to the control group. After 4 hours the the leaves from both groups were harvested to RNA isolation.Soybean seeds were germinated in moistened filter paper, 25°C for 2 days. The seedlings were growth in hydroponic system with Hoagland's nutrient solution for 15 days.					
SRR3160566	SRR3160561	single-end	leaf	14 days post-inoculation	Rsv1_Mock	Rsv1-genotype soybean,PI96983	Illumina MiSeq	Leaves were mechanically inoculated by SMV-L, SMV-G7 and Mock (buffer) after germination at 10 days.Soybeans were grown in a growth chamber under a 16 h light at 22°C and 8 h dark at 18°C.					
SRR3160568	SRR3160563	single-end	leaf	14 days post-inoculation	Rsv1_SMV-L	Rsv1-genotype soybean,PI96983	Illumina MiSeq	Leaves were mechanically inoculated by SMV-L, SMV-G7 and Mock (buffer) after germination at 10 days.Soybeans were grown in a growth chamber under a 16 h light at 22°C and 8 h dark at 18°C.					
SRR3160569	SRR3160565	single-end	leaf	14 days post-inoculation	Rsv1_SMV-G7	Rsv1-genotype soybean,PI96983	Illumina MiSeq	Leaves were mechanically inoculated by SMV-L, SMV-G7 and Mock (buffer) after germination at 10 days.Soybeans were grown in a growth chamber under a 16 h light at 22°C and 8 h dark at 18°C.					
SRR3090714	SRR3090710	single-end	leaf	14 days post-inoculation	Williams82_Mock	Williams82,Susceptible	Illumina MiSeq	Leaves were mechanically inoculated by SMV-L, SMV-LRB,SMV-G7 and Mock (buffer) after germination at 10 days.Soybeans were grown in a growth chamber under a 16 h light at 22°C and 8 h dark at 18°C.					
SRR3090715	SRR3090711	single-end	leaf	14 days post-inoculation	Williams82_SMV-L	Williams82,Susceptible	Illumina MiSeq	Leaves were mechanically inoculated by SMV-L, SMV-LRB,SMV-G7 and Mock (buffer) after germination at 10 days.Soybeans were grown in a growth chamber under a 16 h light at 22°C and 8 h dark at 18°C.					
SRR3090716	SRR3090712	single-end	leaf	14 days post-inoculation	Williams82_SMV-LRB	Williams82,Susceptible	Illumina MiSeq	Leaves were mechanically inoculated by SMV-L, SMV-LRB,SMV-G7 and Mock (buffer) after germination at 10 days.Soybeans were grown in a growth chamber under a 16 h light at 22°C and 8 h dark at 18°C.					
SRR3090717	SRR3090713	single-end	leaf	14 days post-inoculation	Williams82_SMV-G7	Williams82,Susceptible	Illumina MiSeq	Leaves were mechanically inoculated by SMV-L, SMV-LRB,SMV-G7 and Mock (buffer) after germination at 10 days.Soybeans were grown in a growth chamber under a 16 h light at 22°C and 8 h dark at 18°C.					
SRR394312	SRR394316	single-end	root	14 days after germination	profiling of roots	cultivar Heinong44	Illumina Genome Analyzer IIx	Soybean seeds of Glycine max cultivar Heinong44 were respectively planted in the experimental station and growth chambers in Beijing on May. Soybean cotyledons were dissected from seeds of 20 days after flowering (DAF). Roots, stems, and leaves were harvested from the plants cultivated for 14 days in growth chambers.					
SRR2051076	SRR2051084	single-end	root	4 hours 	control	None	Illumina HiSeq 2000	For the stress treatment 200mM of NaCl were added to the nutrient solution of one group of plantlets and nothing was added to the control group. After 4 hours the the leaves from both groups were harvested to RNA isolation.Soybean seeds were germinated in moistened filter paper, 25°C for 2 days. The seedlings were growth in hydroponic system with Hoagland's nutrient solution for 15 days.					
SRR2051077	SRR2051085	single-end	root	4 hours 	control	None	Illumina HiSeq 2000	For the stress treatment 200mM of NaCl were added to the nutrient solution of one group of plantlets and nothing was added to the control group. After 4 hours the the leaves from both groups were harvested to RNA isolation.Soybean seeds were germinated in moistened filter paper, 25°C for 2 days. The seedlings were growth in hydroponic system with Hoagland's nutrient solution for 15 days.					
SRR2051080	SRR2051088	single-end	root	4 hours 	salt stress	None	Illumina HiSeq 2000	For the stress treatment 200mM of NaCl were added to the nutrient solution of one group of plantlets and nothing was added to the control group. After 4 hours the the leaves from both groups were harvested to RNA isolation.Soybean seeds were germinated in moistened filter paper, 25°C for 2 days. The seedlings were growth in hydroponic system with Hoagland's nutrient solution for 15 days.					
SRR2051081	SRR2051089	single-end	root	4 hours 	salt stress	None	Illumina HiSeq 2000	For the stress treatment 200mM of NaCl were added to the nutrient solution of one group of plantlets and nothing was added to the control group. After 4 hours the the leaves from both groups were harvested to RNA isolation.Soybean seeds were germinated in moistened filter paper, 25°C for 2 days. The seedlings were growth in hydroponic system with Hoagland's nutrient solution for 15 days.					
SRR394313	SRR394317	single-end	stem	14 days after germination	profiling of stems	cultivar Heinong44	Illumina Genome Analyzer IIx	Soybean seeds of Glycine max cultivar Heinong44 were respectively planted in the experimental station and growth chambers in Beijing on May. Soybean cotyledons were dissected from seeds of 20 days after flowering (DAF). Roots, stems, and leaves were harvested from the plants cultivated for 14 days in growth chambers.