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Series GSE19074 Query DataSets for GSE19074
Status Public on Dec 31, 2009
Title Integration between Notch- and hypoxia-induced transcriptomes
Organism Mus musculus
Experiment type Expression profiling by array
Summary Background: Interaction between key signaling mechanisms is important to generate the diversity in signaling output required for proper control of cellular differentiation and function, although the molecular manifestations of such cross-talk are only partially understood. Notch signaling and the cellular response to hypoxia intersect at different points in the signaling cascades, and in this report we analyze the consequences of this cross-talk at the transcriptome level. Results: Mouse ES cells were subjected to various combinations of hypoxia and/or activated Notch signaling, and the transcriptome changes could be grouped into different categories, reflecting various modes of hypoxia and Notch signaling integration. Two principal categories of novel Notch- and hypoxia-induced genes were identified: i) a larger set of genes induced by one pathway and not significantly affected by the activity status of the other pathway; and ii) a smaller set of genes co-regulated by Notch and hypoxia. In the latter category, we identified genes that were induced by hypoxia and the expression of which was enhanced by active Notch signaling. In addition, a number of genes were induced by Notch and hypoxia independently, and a final category of genes required simultaneous activation of Notch and hypoxia to be significantly induced. Several of the hypoxia- and Notch-induced genes were found to be upregulated in various forms of cancer. Conclusions: We identify novel Notch and hypoxia downstream genes and genes co-regulated by the two pathways, providing a molecular platform to better understand the intersection between the two signaling cascades in normal development and cancer.
Overall design Total RNA was extracted from 7 treatments in 4 biological replicates of mouse embryonic stem (ES) cells. The 7 treatments consist of 1) ES cell medium for 6 hrs (ESC), 2) N2B27 medium for 6 hrs which is the control condition (N2B27), 3) N2B27 medium supplemented with doxycyline (Dox), 4) Pretreatment with DAPT in ES cell medium for 4 hours followed by switch to N2B27 medium for 6 hours (DAPT), 5) N2B27 under 1% oxygen hypoxic conditions (1% O2), 6) N2B27 supplemented with doxycycline under 1% oxygen hypoxic conditions (1% O2+Dox), 7) Pretreatment with DAPT in ES cell medium for 4 hours followed by switch to N2B27 medium for 6 hours (DAPT) under 1% oxygen hypoxic conditions (1% O2+DAPT).
Contributor(s) Main H, Lee KL, Yang H, Haapa-Paananen S, Edgren H, Jin S, Sahlgren C, Kallioniemi O, Poellinger L, Lim B, Lendahl U
Citation(s) 20034489
Submission date Nov 18, 2009
Last update date Jan 18, 2013
Contact name Kian Leong LEE
Phone +(65) 6601 3685
Organization name National University of Singapore (NUS)
Department Duke-NUS Medical School
Lab Cancer & Stem Cell Biology Program (CSCB)
Street address #07-21, 8 College Road
City Singapore
State/province Singapore
ZIP/Postal code 169857
Country Singapore
Platforms (1)
GPL6103 Illumina mouseRef-8 v1.1 expression beadchip
Samples (30)
GSM472204 ES Cells+ESC medium 6 hrs 1
GSM472205 ES Cells+ESC medium 6 hrs 2
GSM472206 ES Cells+ESC medium 6 hrs 3
BioProject PRJNA120477

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
GSE19074_RAW.tar 3.4 Mb (http)(custom) TAR
GSE19074_non-normalized_data.txt.gz 1.6 Mb (ftp)(http) TXT
Raw data are available on Series record
Processed data included within Sample table

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