|
| Status |
Public on Feb 27, 2018 |
| Title |
Genome-wide binding reveals intrinsic specificity and regulatory function of lineage-specifying bHLH transcription factors (RNA-Seq). |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Developmental mechanisms of lineage specification are crucial to tissue-specific gene regulation, and crucial lineage-specification factors are associated with developmental and oncogenic diseases. The mechanisms by which these factors regulate their distinct transcriptional profiles remains unclear. Comparison of their binding in a common context reveals that such specificity is intrinsic to these factors, and not simply a consequence of distinction in preference for, or availability of accessible chromatin at their respective binding sites.
|
| |
|
| Overall design |
ChIP-seq performed on murine ESCs as part of bHLH transcription factor binding screen. The antibodies used were directed against bHLH factors ASCL1, ASCL2-FLAG, and MYOD-FLAG to observe TF binding. H3K27ac enrichment was assayed using an antibody recognizing this mark for comparison to TF binding, gene expression, and chromatin accessibility from the same cell lines.
|
| |
|
| Contributor(s) |
Casey BH, Kollipara RK, Johnson JE |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| |
| Submission date |
Apr 12, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Jane E Johnson |
| E-mail(s) |
jane.johnson@utsouthwestern.edu
|
| Organization name |
UT Southwestern Medical Center
|
| Department |
Neuroscience
|
| Street address |
5323 Harry Hines Blvd
|
| City |
Dallas |
| State/province |
TX |
| ZIP/Postal code |
75390-9111 |
| Country |
USA |
| |
|
| Platforms (1) |
| GPL17021 |
Illumina HiSeq 2500 (Mus musculus) |
|
| Samples (18)
|
| GSM2576053 |
RNA-seq replicate 1 from dox+ ctrl uninduced SA-tTA-Ascl1 ESCs |
| GSM2576054 |
RNA-seq replicate 2 from dox+ ctrl uninduced SA-tTA-Ascl1 ESCs |
| GSM2576055 |
RNA-seq replicate 3 from dox+ ctrl uninduced SA-tTA-Ascl1 ESCs |
| GSM2576056 |
RNA-seq replicate 1 from dox- 24h induced SA-tTA-Ascl1 ESCs |
| GSM2576057 |
RNA-seq replicate 2 from dox- 24h induced SA-tTA-Ascl1 ESCs |
| GSM2576058 |
RNA-seq replicate 3 from dox- 24h induced SA-tTA-Ascl1 ESCs |
| GSM2576059 |
RNA-seq replicate 1 from dox+ ctrl uninduced SA-tTA-Ascl2 ESCs |
| GSM2576060 |
RNA-seq replicate 2 from dox+ ctrl uninduced SA-tTA-Ascl2 ESCs |
| GSM2576061 |
RNA-seq replicate 3 from dox+ ctrl uninduced SA-tTA-Ascl2 ESCs |
| GSM2576062 |
RNA-seq replicate 1 from dox- 24h induced SA-tTA-Ascl2 ESCs |
| GSM2576063 |
RNA-seq replicate 2 from dox- 24h induced SA-tTA-Ascl2 ESCs |
| GSM2576064 |
RNA-seq replicate 3 from dox- 24h induced SA-tTA-Ascl2 ESCs |
| GSM2576065 |
RNA-seq replicate 1 from dox+ ctrl uninduced SA-tTA-MyoD ESCs |
| GSM2576066 |
RNA-seq replicate 2 from dox+ ctrl uninduced SA-tTA-MyoD ESCs |
| GSM2576067 |
RNA-seq replicate 3 from dox+ ctrl uninduced SA-tTA-MyoD ESCs |
| GSM2576068 |
RNA-seq replicate 1 from dox- 24h induced SA-tTA-MyoD ESCs |
| GSM2576069 |
RNA-seq replicate 2 from dox- 24h induced SA-tTA-MyoD ESCs |
| GSM2576070 |
RNA-seq replicate 3 from dox- 24h induced SA-tTA-MyoD ESCs |
|
| This SubSeries is part of SuperSeries: |
| GSE97715 |
Genome-wide binding reveals intrinsic specificity and regulatory function of lineage-specifying bHLH transcription factors |
|
| Relations |
| BioProject |
PRJNA382709 |
| SRA |
SRP103844 |
Less...
More...