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Series GSE21529 Query DataSets for GSE21529
Status Public on Mar 02, 2011
Title Cardiac transcription factors in HL-1 cells: gene expression and genome binding profiling
Organism Mus musculus
Experiment type Expression profiling by array
Genome binding/occupancy profiling by high throughput sequencing
Summary [1] Gene expression profiling in Gata4, Mef2a knockdown in HL-1 cells.
HL-1 cells infected with adenovirus expressing either control siRNA or Gata4, and Gata4 & Mef2a siRNA.

[2] Genome-wide maps of cardiac transcription factors binding region in HL-1 cells.
We performed bio-ChIP-seq using streptavidin beads immunoprecipitation of biotinylated 5 cardiac transcription factors (fbio) and P300 antibody ChIP-seq.
We used a dox-inducible dual adenovirus system to express biotinylated Core Cardiac TFs in HL1. One adenovirus expressed the dox-activated reverse tet activator protein (rtTA) and the E. coli biotinylating enzyme BirA from the cardiac specific rat troponin T promoter. The second virus expressed a Core Cardiac TF fused to a C-terminal flag-bio epitope tag, where bio is the 15 amino acid substrate for BirA. This in vivo biotinylation approach permits pulldown of different factors to be performed under identical, stringent conditions, and circumvents limitations posed by available antibodies. We titrated adenovirus and dox doses to express GATA4flbio and MEF2Aflbio at near endogenous levels. The same conditions were then used to express SRFflbio, TBX5flbio, and NKX2-5flbio.
Reference:
12. de Boer E, Rodriguez P, Bonte E, Krijgsveld J, Katsantoni E et al. (2003) Efficient biotinylation and single-step purification of tagged transcription factors in mammalian cells and transgenic mice. Proc Natl Acad Sci U S A 100: 7480-7485.
 
Overall design [1] Gene expression profiling: Identify differentially expressed genes after siRNA Gata4 or Gata4_Mef2a double knockdown in HL-1 cells

[2] Genome occupancy profiling: Identify cardiac active enhancers by identified 5 cardiac transcription factors and P300 peaks.
 
Contributor(s) Kong S, He A, Pu WT
Citation(s) 21415370
Submission date Apr 27, 2010
Last update date Mar 08, 2019
Contact name Sek Won Kong
E-mail swkong@enders.tch.harvard.edu
Phone 617-919-2689
Organization name Boston Children's Hospital
Department Informatics Program
Lab EN137
Street address 300 Longwood Avenue
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platforms (2)
GPL6246 [MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version]
GPL9185 Illumina Genome Analyzer (Mus musculus)
Samples (17)
GSM537748 Gata4 Mef2a kd rep1 [genex]
GSM537749 Gata4 Mef2a kd rep2 [genex]
GSM537750 Gata4 Mef2a kd rep3 [genex]
Relations
SRA SRP002689
BioProject PRJNA125947

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
GSE21529_AnalysisSummary.txt.gz 110 b (ftp)(http) TXT
GSE21529_RAW.tar 38.4 Mb (http)(custom) TAR (of CEL, GFF)
GSE21529_README_GFFfiles.txt 1.1 Kb (ftp)(http) TXT
Raw data are available in SRA
Processed data included within Sample table
Processed data provided as supplementary file

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