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Series GSE201141 Query DataSets for GSE201141
Status Public on Nov 22, 2022
Title ATAC-seq after EBF1 degradation
Organism Mus musculus
Experiment type Genome binding/occupancy 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.
 
Overall design ATAC-seq in EBF1-dTAG_N and _C proB cells before and after 6 hours of treatment with dTAG-13. There are 2 biological replicates for each condition.
 
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
 
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (8)
GSM6051621 EBF1-dTAG_C, 0h, rep1
GSM6051622 EBF1-dTAG_C, 0h, rep2
GSM6051623 EBF1-dTAG_C, 6h, rep1
This SubSeries is part of SuperSeries:
GSE201144 EBF1 degradation in B Cells
Relations
BioProject PRJNA828540

Download family Format
SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE201141_EBF1-dTAG_C_ATAC-seq_edgeR.csv.gz 2.8 Mb (ftp)(http) CSV
GSE201141_EBF1-dTAG_N_ATAC-seq_edgeR.csv.gz 2.9 Mb (ftp)(http) CSV
GSE201141_RAW.tar 321.5 Mb (http)(custom) TAR (of BW, NARROWPEAK)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file
Processed data are available on Series record

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