|
Status |
Public on Jan 18, 2024 |
Title |
EBF1_dC_rep1 |
Sample type |
SRA |
|
|
Source name |
pro-B cells
|
Organism |
Mus musculus |
Characteristics |
cell type: pro-B cells genotype: EBF1 dC
|
Growth protocol |
Ebf1-/- fetal liver cells were transduced with EBF1 wt, dC, or YmA. Cells were incubated for 8 days, 50000 CD19+ cells were FACS sorted.
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Cell pellets were resuspended in 50 ul Tagmentation Mix (10 mM HEPES pH 7.0; 25 mM NaCl; 5 mM MgCl2; 0.01% Digitonin; 0.1% Tween-20; 300 ng loaded Tagmentase) and incubated in the thermoshaker for 30 min, 700 rpm, 37°C. DNA was purified using Zymo DNA Clean and Concentration Kit. Libraries were amplified using Nextera XT Index Kit v2, 15-17 cycles.
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|
|
Library strategy |
ATAC-seq |
Library source |
genomic |
Library selection |
other |
Instrument model |
Illumina NovaSeq 6000 |
|
|
Data processing |
Quality control and read mapping was done using snakePipes, an automatic pipeline for analysis of deep sequencing data. Reads were mapped to the mouse genome (GRCm38 – mm10) using bowtie2. Reads were sorted and indexed using samtools and duplicates were removed by sambamba_markdup. Peak calling was performed using MACS2. Coverage bigwig files were created using bamCoverage from deeptools. Assembly: mm10 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.
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|
|
Submission date |
Mar 17, 2023 |
Last update date |
Jan 18, 2024 |
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) |
GSE227613 |
ATAC-seq of pro-B cells to test the role of phase separation in EBF1 pioneering function |
GSE227617 |
The role of phase separation in EBF1 pioneering function |
|
Relations |
BioSample |
SAMN33799524 |
SRA |
SRX19712241 |