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Sample GSM7103938 Query DataSets for GSM7103938
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.
 
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.
 
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

Supplementary file Size Download File type/resource
GSM7103938_EBF1_dC_rep1.bw 14.2 Mb (ftp)(http) BW
GSM7103938_EBF1_dC_rep1.narrowPeak.gz 319.1 Kb (ftp)(http) NARROWPEAK
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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