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Series GSE139803 Query DataSets for GSE139803
Status Public on Apr 21, 2020
Title TBX5 ChIP from the Fetal Heart
Organism Mus musculus
Experiment type Genome binding/occupancy profiling by high throughput sequencing
Summary T-box transcription factors play critical roles in the development and identity of the heart. Tbx5 has been implicated as a regulator of the fast-conducting, ventricular conduction system, while Tbx3 has been implicated as a regulator of the slow-conducting node. We hypothesize TBX5 and TBX3 share common binding sites in cardiomyocytes to positively or negatively regulate transcription, respectively, for cardiac cell identity and conduction. To this end, we performed ChIP-sequencing to identify localization of TBX5 during fetal heart development and have compared it with previously published histone (GEO Series: GSE31039; ENCODE Accessions: ENCSR080GQM, ENCSR000CDL, ENCSR000CDM, ENCSR052CDF, ENCSR345RKE, ENCSR007XTC, ENCSR360ANE, ENCSR000CDK, and ENCSR357OED) and TBX3 ChIP-seq (GSM862695).
Overall design Hearts were dissected from E14.5 CD-1 mouse embryos. Two biological replicates were generated. For immunoprecipitation, the chromatin extract was incubated with 5ug of the anti-TBX5 antibody (Santa Cruz Biotechnology sc-17866; Lot #G1516) at 4°C for >12 hours in a total volume of 200 μL. Libraries from ChIP and input DNA were prepared using NEBNext Ultra DNA Library Prep Kit (E7370S). During library preparation, adaptor-ligated DNA fragments of 200-650 bp in size were selected before PCR amplification using Sera-Mag magnetic beads (GE, 6515-2105-050-250). DNA libraries were sequenced using Illumina Hi-seq instruments (single-end 50 base) by the Genomics Core Facility at the University of Chicago.
Contributor(s) Steimle JD, Ikegami K, Burnicka-Turek O, Moskowitz IP
Citation(s) 32290757
NIH grant(s)
Grant ID Grant title Affiliation Name
R21 AG054770 Mechanisms in Lamin A function in gene regulation UNIVERSITY OF CHICAGO Kohta Ikegami
R33 AG054770 Mechanisms in Lamin A function in gene regulation UNIVERSITY OF CHICAGO Kohta Ikegami
R01 HL114010 Transcriptional Control of Cardiac Conduction System Function by T-box Genes UNIVERSITY OF CHICAGO Ivan Paul Moskowitz
R01 HL126509 Gene Regulatory Networks for Cardiac Morphogenesis UNIVERSITY OF NORTH CAROLINA AT CHAPEL HILL Ivan Paul Moskowitz
Submission date Nov 01, 2019
Last update date Apr 21, 2020
Contact name Jeffrey D. Steimle
Phone 7137985917
Organization name Baylor College of Medicine
Department Molecular Physiology and Biophysics
Lab Room 504E, Mail Stop BCM335
Street address 1 Baylor Plaza
City Houston
State/province TX
ZIP/Postal code 77030
Country USA
Platforms (1)
GPL21103 Illumina HiSeq 4000 (Mus musculus)
Samples (3)
GSM4146599 TBX5_ChIP_1
GSM4146600 TBX5_ChIP_2
GSM4146601 TBX5_Input
BioProject PRJNA587057
SRA SRP227916

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 319.8 Mb (ftp)(http) BW
GSE139803_Pooled_TBX5_peaks.bed.gz 141.0 Kb (ftp)(http) BED
GSE139803_Pooled_TBX5_peaks.narrowPeak.gz 294.7 Kb (ftp)(http) NARROWPEAK
GSE139803_SupplementaryDataset.txt.gz 409.9 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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