The G1E Transcriptome Project

Weiss Laboratory, Children's Hospital of Philadelphia

Transcriptome analysis was performed during differentiation of G1E cells, a murine cell line which recapitulates erythropoiesis from the late CFU-E through the basophilic erythroblast stage (Weiss et al., 1997). G1E cells were derived by targeted gene deletion of the single copy of GATA-1 on the X chromosome . GATA-1 is a "master regulator" zinc finger transcription factor which directs erythropoiesis ( Weiss and Orkin, 1995 ). It is found in the promoter of almost all genes which contribute to the erythroid phenotype, and mutations of GATA-1 result in anemia and thrombocytopenia . The analysis was performed using Affymetrix GeneChips, and the microarray data have been deposited with the NIH GEO database, accession GSE628. The results are summarized in Welch et al., 2003. and compiled in the G1EDb database.


Background Information

  • Experimental Description
  • How to use the G1EDb
  • Protocols
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    Downloadable Datasets (Zipped)

  • G1EDb, an MS-Access Database (8.3 Mb)
  • Raw Data in Excel (8.9 Mb) or text (2.9 Mb) format, and legend
  • Summarized Data in Excel (2.2 Mb) or text (4.7Mb) format, and legend
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    Additional Analysis

  • Self-Organizing Map Analysis
  • Hierarchical Clustering
  • Statistical vs. Empiric Algorithm
  • Relationship between p-value, SLR and threshold
  • Most induced/repressed transcripts at 3, 7, 14, 21, and 30 hours
  • Concordance with Dolzig et al. data set
  • Concordance with Gubin et al data set
  • The Most Abundant Transcripts
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    Selected Functional Categories

  • Antioxidants
  • Cytokine Receptor-Like
  • Endosomal
  • Heme Pathway
  • Inorganic Metals
  • Red Cell Membrane
  • Viral/Retro-elements
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    Please direct all comments to: John Welch, M.D., Ph.D.
    Last modification: May 21, 2004