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| 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
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| 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.
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| 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.
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| Contributor(s) |
Kong S, He A, Pu WT |
| Citation(s) |
21415370 |
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| Submission date |
Apr 27, 2010 |
| Last update date |
May 15, 2019 |
| Contact name |
Sek Won Kong |
| E-mail(s) |
[email protected]
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| Phone |
617-919-2689
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| Organization name |
Boston Children's Hospital
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| Department |
Informatics Program
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| Lab |
EN137
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| Street address |
300 Longwood Avenue
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| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
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| Platforms (2) |
| GPL6246 |
[MoGene-1_0-st] Affymetrix Mouse Gene 1.0 ST Array [transcript (gene) version] |
| GPL9185 |
Illumina Genome Analyzer (Mus musculus) |
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| Samples (17)
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| Relations |
| SRA |
SRP002689 |
| BioProject |
PRJNA125947 |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data included within Sample table |
| Processed data provided as supplementary file |
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