|
| Status |
Public on Nov 22, 2022 |
| Title |
EBF1-dTAG_C, 0h, rep2 |
| Sample type |
SRA |
| |
|
| Source name |
A-MuLV transformed pro-B cells
|
| Organism |
Mus musculus |
| Characteristics |
cell type: A-MuLV transformed pro-B cells
genotype: EBF1-dTAG_C
treatment: DMSO 6h
|
| Treatment protocol |
Cells were treated with dTAG-13 (final concentration 0.5 uM) or DMSO for 6 hours.
|
| Growth protocol |
Production of A-MuLV transformed cells with the replacement of endogenous EBF1 by exogenous modified genes was described in Boller et al. 2016. A-MuLV transformed cells were cultured in the RPMI 1640 medium with 10% FCS; 1x Penicillin-Streptomycin-Glutamine; 0.06 mM β-mercaptoethanol.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
ATAC-seq was performed using loaded Tagmentase (Tn5 transposase) Diagenode according to the manufacturer protocol. 50000 cells were incubated with 2.5 μl loaded Tagmentase with the addition of 0.01% Digitonin and 0.1% Tween20 for 30 min at 37°C. Libraries were purified using Zymo DNA Clean and Concentration Kit.
Libraries were amplified using Nextera XT Index Kit v2, 9-10 cycles.
|
| |
|
| Library strategy |
ATAC-seq |
| Library source |
genomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
EBF1-dTAG_C_ATAC-seq_edgeR.csv
|
| Data processing |
Quality control and read mapping was done using snakePipes (v2.5.1), an automatic pipeline for analysis of deep sequencing data.
Reads were mapped to the mouse genome (GRCm38 – mm10) using bowtie2 (v2.3.5.1).
Reads were sorted and indexed using samtools (v1.10) and duplicates were removed by sambamba_markdup.
Coverage bigwig files were created using bamCoverage from deeptools (v3.3.2) with normalization on sequencing depth (CPM).
Peak calling and differential accessibility analysis were performed using the ATACofthesnake pipeline (https://github.com/maxplanck-ie/ATACofthesnake).
Peak calling was performed using MACS2 (v2.2.7.1).
Differential accessibility for the union of all peaks was analyzed with edgeR (3.32.0) for EBF1-dTAG_N and _C samples independently.
Differential motif analysis was performed using MEME (v5.0.2).
Assembly: mm10
Supplementary files format and content: Two tables (.csv) with edgeR results for EBF1-dTAG_N and _C.
Supplementary files format and content: One .narrowPeak file containing the MACS2 output for each ATAC sample.
Supplementary files format and content: One bigwig file (.bw) for each sample.
|
| |
|
| Submission date |
Apr 20, 2022 |
| Last update date |
Nov 22, 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 |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
|
| Relations |
| BioSample |
SAMN27671578 |
| SRA |
SRX14935367 |
