GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE62040 Query DataSets for GSE62040
Status Public on Oct 31, 2016
Title Rb1+/+ versus Rb1ΔS/ΔS RNA Seq
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Upon G1-S transition, cyclin-dependent kinases (CDKs) phosphorylate the retinoblastoma tumor suppressor protein (pRB) to release E2F transcription factors, which activate transcriptional programs, required for S-phase entry. Beyond the G1-S transition, pRB activity remains poorly understood. Our lab has discovered that hyperphosphorylated pRB (ppRB), found beyond G1, retains exclusive binding to E2F1 through an alternate E2F1-‘specific’ binding site at the pRB c-terminus. We have developed a gene-targeted mouse model that is defective for the E2F1-‘specific’ interaction. We are exploring the function of this complex through genome-wide expression profiling. Overall, this work suggests an alternate pRB-E2F1 complex persists beyond the G1-S transition to establish regions of constitutive heterochromatin.
Overall design 1. Total RNA from passage 4 quiescent MEFs isolated using TRIzol RNA extraction protocol
2. rRNA was depleted from total RNA using the RiboMinus Euk System V2 protocol according to manufacturer’s procotol
3. rRNA-depleted RNA samples were submitted for picoanalyzer analysis to determine concentration, purity, and rRNA content
4. Three wild-type and three mutant RNA samples with <10% rRNA remaining were submitted for library construction
5. Library was used for Illumina HiSeq 2500 paired end sequencing.
Contributor(s) Dick FA, Ishak CA, Marshall AE, Ferwati S
Citation(s) 27889452
Submission date Oct 03, 2014
Last update date May 15, 2019
Contact name Fred Dick
Organization name Western University
Street address Cancer Research Labs 790 Commissioners Road East
City London
State/province ON
ZIP/Postal code N6A 4L6
Country Canada
Platforms (1)
GPL17021 Illumina HiSeq 2500 (Mus musculus)
Samples (6)
GSM1518795 Rb1+/+ - 1 - rRNA-depleted RNA
GSM1518796 Rb1+/+ - 3 - rRNA-depleted RNA
GSM1518797 Rb1+/+ - 4 - rRNA-depleted RNA
This SubSeries is part of SuperSeries:
GSE85640 A commonly inactivated tumor suppressor silences endogenous retroelements in somatic cells
BioProject PRJNA263014
SRA SRP048623

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE62040_gene_exp.diff.gz 849.8 Kb (ftp)(http) DIFF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap