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| Status |
Public on Mar 13, 2018 |
| Title |
Mammalian low cell number and in vivo DamID-seq for transcription factor binding analyses |
| Organism |
Mus musculus |
| Experiment type |
Genome binding/occupancy profiling by high throughput sequencing
Third-party reanalysis
|
| Summary |
Mammalian low cell number and in vivo DamID-seq for transcription factor binding analyses
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| Overall design |
DamID-seq peaks were called for Oct4 from mouse embryonic stem cells (mESC), late streak, early bud mouse embryos (LSEB) and DamID-seq peaks were called for Sox2 from ES-derived neural stem cells (NSC)
DNase-seq hyper-sensitivity data was downloaded from GEO with the BioSample accession number GSM1014154 and compared with DamID-seq signal for E14 mouse embryonic stem cells. This data is linked below as DNase-seq_GSM1014154.tar.
ChIP-Seq raw data was downloaded from GEO (GSE11724, GSE44286, GSE56098) and ERA (ERR216111, ERR414096, ERR414097). Peaks called from Oct4 ChIP-seq were compared to Oct4 DamID-seq peaks for E14 mouse embryonic stem cells. This data is linked below as ChIP-Seq_reanalysis.tar.
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| Contributor(s) |
Tosti L, Ashmore J, Tan NB, Carbone B, Mistri TK, Wilson V, Tomlinson SR, Kaji K |
| Citation(s) |
29572359 |
| Submission date |
Apr 24, 2017 |
| Last update date |
Jul 25, 2021 |
| Contact name |
Keisuke Kaji |
| E-mail(s) |
kkaji@exseed.ed.ac.uk
|
| Organization name |
University of Edinburgh
|
| Department |
MRC Centre for Reproductive Health
|
| Street address |
47 Little France Crescent
|
| City |
Edinburgh |
| State/province |
Midlothian |
| ZIP/Postal code |
EH16 4TJ |
| Country |
United Kingdom |
| |
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| Platforms (2) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
| GPL21103 |
Illumina HiSeq 4000 (Mus musculus) |
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| Samples (58)
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| Relations |
| BioProject |
PRJNA383993 |
| SRA |
SRP105058 |
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