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| 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
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| 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).
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| 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.
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| 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 |
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| Submission date |
Nov 01, 2019 |
| Last update date |
Apr 21, 2020 |
| Contact name |
Jeffrey D. Steimle |
| E-mail(s) |
jeffrey.steimle@bcm.edu, jsteimle@uchicago.edu, jsteimle@alumni.nd.edu
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| Phone |
7137985917
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| Organization name |
Baylor College of Medicine
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| Department |
Molecular Physiology and Biophysics
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| Lab |
Room 504E, Mail Stop BCM335
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| Street address |
1 Baylor Plaza
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| City |
Houston |
| State/province |
TX |
| ZIP/Postal code |
77030 |
| Country |
USA |
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| Platforms (1) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (3) |
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| Relations |
| BioProject |
PRJNA587057 |
| SRA |
SRP227916 |
