Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
Pro-B cells
NA
NA

Attributes by original data submitter

Sample

source_name
ATAC_6hrs
cell type source
Ebf1-deficient B cell progenitors
stage post dox treatment
6 hrs

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
ATAC-seq library was prepared using Nextera DNA Library Prep Kit (Illumina). Briefly, 100,000 cells were resuspended in 50µl of cold lysis buffer (10mM Tris·Cl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.1% (v/v) Igepal CA-630) and incubated on ice for 15 min. Immediately after lysis, nuclei were collected and re-suspended in the transposase reaction mix (25 μL 2× TD buffer, 2.5 μL transposase (TDE1) and 22.5 μL nuclease-free water). The transposition reaction was carried out for 30 minutes at 37 °C and immediately put on ice. Then the sample was purified using MinElute PCR Purification Kit (Qiagen). Following purification, the library was amplified using indexed Nextera PCR primers and NEBNext High-Fidelity 2× PCR Master Mix. Finally the library was purified using MinElute PCR Purification Kit. Libraries were prepared via the Nextera® DNA Sample Preparation library preparation protocol according to manufacturer's instructions

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
50669345
Reads aligned (%)
79.3
Duplicates removed (%)
21.3
Number of peaks
5197 (qval < 1E-05)

mm9

Number of total reads
50669345
Reads aligned (%)
79.2
Duplicates removed (%)
21.4
Number of peaks
5211 (qval < 1E-05)

Base call quality data from DBCLS SRA