An RNA-Seq based gene expression atlas of the common bean

O’Rourke, Jamie A; Iniguez, Luis P; Fu, Fengli; Bucciarelli, Bruna; Miller, Susan S; Jackson, Scott A; McClean, Philip E; Li, Jun; Dai, Xinbin; Zhao, Patrick X; Hernandez, Georgina; Vance, Carroll P

doi:10.1186/1471-2164-15-866

BMC Genomics

Table 1 Tissue samples isolated from Phaseolus vulgaris cv. Negro jamapa for RNA-Seq analysis

From: An RNA-Seq based gene expression atlas of the common bean

Organ	Sample ID^a	Sample description	Reads sequenced^b	Reads mapped^c	Genes expressed^d
Leaves	YL	Fully expanded 2^nd trifoliate leaf tissue from plants provided with fertilizer	24,118,479	21,395,546	19,466
	L5	Leaf tissue collected 5 DAI with effective rhizobium	25,297,092	19,762,749	18,966
	LF	Leaf tissue from fertilized plants collected at the same time of LE and LI	22,692,275	17,581,928	16,103
	LE	Leaf tissue collected 21 DAI with effective rhizobium	23,366,279	17,714,097	16,081
	LI	Leaf tissue collected 21 DAI with ineffective rhizobium	23,257,968	18,820,812	18,523
Stem	YS	All stem internodes above the cotyledon collected at the 2^nd trifoliate stage	27,696,970	22,718,724	20,299
	ST	Shoot tip, including the apical meristem, collected at the 2^nd trifoliate stage	25,826,838	22,358,410	21,142
Flower	FY	Young flowers, collected prior to floral emergence	23,334,037	16,503,930	20,055
Pods	PY	Young pods, collected 1 to 4 days after floral senescence. Samples contain developing embryos at globular stage	26,234,498	17,381,695	12,115
	PH	Pods approximately 9 cm long, associated with seeds at heart stage (pod only)	24,986,174	19,130,051	19,065
	P1	Pods between 10 and 11 cm long, associated with stage 1 seeds (pod only)	24,349,622	16,400,591	15,831
	P2	Pods between 12 and 13 cm long associated with stage 2 seeds (pod only)	21,647,774	18,018,224	18,311
Seeds	SH	Heart stage seeds, between 3 and 4 mm across and ~7 mg	28,222,798	22,972,385	18,668
	S1	Stage 1 seeds, between 6 and 7 mm across and ~50 mg	21,395,296	17,004,466	16,949
	S2	Stage 2 seeds, between 8 and 10 mm across and 140–150 mg	24,696,630	19,949,204	15,363
Roots	RT	Root tips, 0.5 cm of tissue, collected from fertilized plants at 2^nd trifoliate stage of development	24,536,948	21,680,391	18,514
	YR	Whole roots, including root tips, collected at the 2^nd trifoliate stage of development	25,140,904	20,962,342	19,170
	R5	Whole roots separated from 5 day old pre-fixing nodules	27,423,246	23,034,248	19,865
	RF	Whole roots from fertilized plants collected at the same time as RE and RI	25,121,968	21,858951	20,305
	RE	Whole roots separated from fix + nodules collected 21 DAI	24,449,104	21,325,105	20,450
	RI	Whole roots separated from fix- nodules collected 21 DAI	27,834,770	24,188,904	20,697
Nodules	N5	Pre-fixing (fix+) nodules collected 5 DAI	23,909,973	20,774,095	19,102
	NE	Fix + nodules collected 21 DAI	26,350,845	23,035,381	17,011
	NI	Fix- nodules collected 21 DAI	24,875,317	21,877,973	19,278

^aA two-letter ID assigned to each sample. ^bNumber of single end 36 bp reads generated for each sample. ^cNumber of RNA-Seq reads mapping to the genome using Bowtie. ^dNumber of predicted genes expressed with an RPKM ≥ 3 in each sample.

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ISSN: 1471-2164

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