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| Status |
Public on Jan 01, 2019 |
| Title |
Genome-wide maps of Trim33, Ctcf and H3K27ac binding in embryoid bodies |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
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| Summary |
We report high throughput profiling and co-occupancy of Trim33, Ctcf and H3K27ac in differentiating embryoid bodies derived from mouse embryonic stem cells. An average of ~37 million reads were generated for each of the described samples and input sample generating 4,426, 52,446, 30,047 peaks respectively for Trim33, CTCF and H3K27ac. Motif enrichment analyses for Trim33 ChiP-Seq data returned CTCF and BORIS (CTCF analog) motifs as best matches. Of the merged peaks, 723 were shared by Trim33, CTCF as well as H3K27ac. In addition, 1299 peaks were shared by Trim33 and CTCF, 1131 were shared by Trim33 and H3K27ac and 3321 were shared by CTCF and H3K27ac.
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| Overall design |
Examination of genome-wide binding of Trim33, Ctcf and H3K27ac in differentiating embryoid bodies at day 6 in culture in vitro.
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| Contributor(s) |
Rajderkar SS, Kaartinen VM |
| Citation(s) |
29090280, 30940539 |
| NIH grant(s) |
| Grant ID |
Grant title |
Affiliation |
Name |
| R01 DE013085 |
The Role of TGF-Beta3 in Palatogenesis |
REGENTS OF THE UNIVERSITY OF MICHIGAN - ANN ARBOR |
VESA M KAARTINEN |
| R01 HL074862 |
Activin Receptor-Like Kinase-2 in Cardiac Morphogenesis |
REGENTS OF THE UNIVERSITY OF MICHIGAN - ANN ARBOR |
VESA M KAARTINEN |
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| Submission date |
Sep 12, 2018 |
| Last update date |
Apr 09, 2019 |
| Contact name |
Vesa Matti Kaartinen |
| E-mail(s) |
vesak@umich.edu
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| Phone |
734 615 4726
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| Organization name |
University of Michigan
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| Department |
BMS
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| Lab |
Kaartinen
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| Street address |
1011 N. University
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| City |
Ann Arbor |
| State/province |
MI |
| ZIP/Postal code |
48109 |
| Country |
USA |
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| Platforms (1) |
| GPL19057 |
Illumina NextSeq 500 (Mus musculus) |
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| Samples (4)
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| Relations |
| BioProject |
PRJNA490537 |
| SRA |
SRP161607 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE119874_00GOMichigan_EB-d6_summary.xlsx.gz |
17.7 Kb |
(ftp)(http) |
XLSX |
| GSE119874_RAW.tar |
556.5 Mb |
(http)(custom) |
TAR (of BW, NARROWPEAK) |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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