E-GEOD-6547 - Transcription profiling of C. elegans pocket protein ortholog, lin-35

Status
Submitted on 15 December 2006, released on 14 June 2008, last updated on 27 March 2012
Organism
Caenorhabditis elegans
Samples (18)
Array (1)
Protocols (5)
Description
LIN-35 is the single C. elegans ortholog of the mammalian pocket protein family members, pRb, p107, and p130. To gain insight into the roles of pocket proteins during development, a microarray analysis was performed with lin-35 mutants. Stage-specific regulation patterns were revealed, indicating that LIN-35 plays diverse roles at distinct developmental stages. LIN-35 was found to repress the expression of many genes involved in cell proliferation in larvae, an activity that is carried out in conjunction with E2F. In addition, LIN-35 was found to regulate neuronal genes during embryogenesis and targets of the intestinal-specific GATA transcription factor, ELT-2, at multiple developmental stages. Additional findings suggest that LIN-35 functions in cell cycle regulation in embryos in a manner that is independent of E2F. A comparison of LIN-35-regulated genes with known fly and mammalian pocket-protein targets revealed a high degree of overlap, indicating strong conservation of pocket protein functions in diverse phyla. Based on microarray results and our refinement of the C. elegans E2F consensus sequence, we were able to generate a comprehensive list of putative E2F-regulated genes in C. elegans. These results implicate a large number of genes previously unconnected to cell cycle control as having potential roles in this process. Experiment Overall Design: We compared transcriptom profiles of lin-35 mutants and control N2 worms at 3 developmental stages (embryonic, L1 and L4). Experiment Overall Design: Each comparison was done in triplicate on independently grown and isolated animals.
Experiment types
transcription profiling by array, unknown experiment type
Contact
Citation
Transcriptome profiling of the C. elegans Rb ortholog reveals diverse developmental roles. Natalia V Kirienko, David S Fay. Dev Biol 305(2):674-84 (2007)
MIAME
PlatformsProtocolsVariablesProcessedRaw
Files
Investigation descriptionE-GEOD-6547.idf.txt
Sample and data relationshipE-GEOD-6547.sdrf.txt
Raw data (1)E-GEOD-6547.raw.1.zip
Processed data (1)E-GEOD-6547.processed.1.zip
Array designA-AFFY-60.adf.txt
R ExpressionSetE-GEOD-6547.eSet.r
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