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| Status |
Public on Nov 22, 2022 |
| Title |
Changes in gene expression after EBF1 degradation |
| Organism |
Mus musculus |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
We used the dTAG protein degradation system to rapidly deplete transcription factor EBF1 in the B cell culture. After treatment with dTAG-13 for 6 hours, we performed ChIP-seq, ATAC-seq, and RNA-seq. After the treatment, EBF1 is completely absent from the chromatin. This leads to the closure of EBF1 binding sites and changes in the target gene expression. This approach allowed us to identify direct targets of EBF1 and show the importance of EBF1 for open chromatin maintenance.
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| Overall design |
Stranded RNA-seq of total RNA in EBF1-dTAG_N proB cells before and after 6 hours of treatment with dTAG-13. There are 4 biological replicates for each condition. Reads were counted for exons and genes to obtain intronic counts.
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| |
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| Contributor(s) |
Zolotarev NA |
| Citation(s) |
36409886 |
| |
| Submission date |
Apr 20, 2022 |
| Last update date |
Nov 24, 2022 |
| Contact name |
Nikolay Zolotarev |
| E-mail(s) |
zolotarev@ie-freiburg.mpg.de
|
| Organization name |
Max Planck Institute of Immunobiology and Epigenetics
|
| Department |
Cellular and Molecular Immunology
|
| Lab |
Laboratory Rudolf Grosschedl
|
| Street address |
Stübeweg, 51
|
| City |
Freiburg |
| ZIP/Postal code |
79108 |
| Country |
Germany |
| |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
|
| Samples (8)
|
| GSM6051636 |
EBF1-dTAG_N, 0h, rep4 |
| GSM6051637 |
EBF1-dTAG_N, 6h, rep1 |
| GSM6051638 |
EBF1-dTAG_N, 6h, rep2 |
| GSM6051639 |
EBF1-dTAG_N, 6h, rep3 |
| GSM6051640 |
EBF1-dTAG_N, 6h, rep4 |
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| This SubSeries is part of SuperSeries: |
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| Relations |
| BioProject |
PRJNA828550 |
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