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Series GSE29791 Query DataSets for GSE29791
Status Public on Dec 01, 2011
Title Identification of putative targets of Nkx2-5 in Xenopus laevis using gene expression analysis and cross-species annotation
Organism Xenopus laevis
Experiment type Expression profiling by array
Summary While the heart is the first organ to form during development, the earliest molecular mechanisms surrounding specification and differentiation are not clear. In vertebrates, the first marker of cardiac specification is the expression of the homeobox transcription factor Nkx2-5 and its paralogs. While some downstream targets of Nkx2-5 have been discovered, they alone are not sufficient to completely rescue Nkx2-5 knock-downs, suggesting that other targets of Nkx2-5 regulation remain unknown. In order to identify early targets of Nkx2-5, Xenopus laevis embryos were injected with synthetic Nkx2-5 mRNA and changes in gene expression measured using Affymetrix GeneChips. To interpret the data, X. laevis genomic annotation was augmented using cross-species information from the CrossGene database followed by gene ontology enrichment, network analysis, spatial expression, and Nkx2-5 binding site predictions. This allowed us to compile a list of 99 UniGene clusters representing likely early targets of Nkx2-5.
Overall design Nkx2-5+GFP or GFP mRNA was injected into 8 cell Xenopus embryos. Total RNA was collected at St. 11.5.

comparison of gene expression profiles for treated vs, control
Contributor(s) Breese MR, Grow MW, Edenberg HJ
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Submission date Jun 07, 2011
Last update date May 10, 2017
Contact name Marcus Breese
Organization name UCSF
Street address 1550 Fourth St, 382
City San Francisco
State/province CA
ZIP/Postal code 94158
Country USA
Platforms (1)
GPL1318 [Xenopus_laevis] Affymetrix Xenopus laevis Genome Array
Samples (12)
GSM738291 Embryo-control-EXP1-rep1
GSM738292 Embryo-control-EXP1-rep2
GSM738293 Embryo-control-EXP1-rep3
This SubSeries is part of SuperSeries:
GSE29816 Identification of putative targets of Nkx2-5 in Xenopus laevis using gene expression analysis and cross-species.
BioProject PRJNA155215

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
GSE29791_RAW.tar 28.8 Mb (http)(custom) TAR (of CEL, CHP)
Processed data included within Sample table
Processed data provided as supplementary file

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