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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 IDa Sample description Reads sequencedb Reads mappedc Genes expressedd
Leaves YL Fully expanded 2nd 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 2nd trifoliate stage 27,696,970 22,718,724 20,299
  ST Shoot tip, including the apical meristem, collected at the 2nd 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 2nd trifoliate stage of development 24,536,948 21,680,391 18,514
  YR Whole roots, including root tips, collected at the 2nd 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
  1. 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.