Please cite: Jamie A O'Rourke, Luis P Iniguez, Fengli Fu, Bruna Bucciarelli, Susan S Miller, Scott A Jackson, Philip E McClean, Jun Li, Xinbin Dai, Patrick X Zhao, Georgina Hernandez and Carroll P Vance. An RNA-Seq based gene expression atlas of the common bean. BMC Genomics 2014, 15:866.
Welcome to PvGEA
A Common Bean Gene Expression Atlas    
 
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Download whole dataset

         Normalized Data (used for analysis) click HERE

         Raw Data (Number of mapped reads per gene per tissue) click HERE

This suite of expression data provides a platform for common bean functional genomics, including:

  • YL- Fully expanded 2nd trifoliate leaf tissue from plants provided with fertilizer
  • L5- Leaf tissue collected 5 days after plants were inoculated with effective rhizoubium
  • LF- Leaf tissue from fertilized plants collected at the same time of LE and LI
  • LE- Leaf tissue collected 21 days after plants were inoculated with effective rhizobium
  • LI- Leaf tissue collected 21 days after plants were inoculated with ineffective rhizobium
  • YS- All stem internodes above the cotyledon collected at the 2nd trifoliate stage
  • ST- Shoot tip, including the apical meristem, collected at the 2nd trifoliate stage
  • FY- Young flowers, collected prior to floral emergence
  • PY- Young pods, collected 1 to 4 days after floral senescence. Samples contain developing embryos at globular stage
  • PH- Pods approximately 9cm long, associated with seeds at heart stage (pod only)
  • P1- Pods between 10 and 11 cm long, associated with stage 1 seeds (pod only)
  • P2- Pods between 12 and 13 cm long associated with stage 2 seeds (pod only)
  • SH- Heart stage seeds, between 3 and 4 mm across and approximately 7 mg
  • S1- Stage 1 seeds, between 6 and 7 mm across and approximately 50 mg
  • S2- Stage 2 seeds, between 8 and 10 mm across and between 140 and 150 mg
  • RT- Root tips, 0.5 cm of tissue, collected from fertilized plants at 2nd trifoliate stage of development.
  • YR- Whole roots, including root tips, collected at the 2nd trifoliate stage of development
  • R5- Whole roots separated from 5 day old pre-fixing nodules
  • RF- Whole roots from fertilized plants collected at the same time as RE and RI
  • RE- Whole roots separated from fix+ nodules collected 21 days after inoculation
  • RI- Whole roots separated from fix- nodules collected 21 days after inoculation
  • N5- Pre-fixing (effective) nodules collected 5 days after inoculation
  • NE- Effectively fixing nodules collected 21 days after inoculation
  • NI- Ineffectively fixing nodules collected 21 days after inoculation



Data & bioinformatic resources were generated by the laboratory of Dr. Carroll P. Vance, USDA-ARS, St. Paul, MN, Dr. Patrick X. Zhao at the Samuel Roberts Noble Foundation, and many international collaborators.