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
Bone marrow
cell type
Pro-B cells (c-Kit+ CD19+)
strain
C57BL6/129Ola
age
54-60 days
Sex
female
genotype
Mbd3_Del/Del
cell number
500

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Bone marrow cells were collected from the femurs and tibiae of 7 week old mice. Cells were stained with antibodies and cells belonging to each population sorted using a FACS Influx5 (BD Biosciences) 500 cells were sorted directly into individual wells of a PCR tube containing PBS. Assay for transposase-accessible chromatin using sequencing (ATAC-seq) was performed as previously described (Buenrostro et al (2013) Nat. Methods 10:1213). Pooled libraries were run on an Illumina HiSeq 2500 sequencer. RNA libraries were prepared for sequencing using Illumina Nextera DNA preparation kit

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
27423383
Reads aligned (%)
43.2
Duplicates removed (%)
68.9
Number of peaks
1224 (qval < 1E-05)

mm9

Number of total reads
27423383
Reads aligned (%)
43.1
Duplicates removed (%)
68.8
Number of peaks
1204 (qval < 1E-05)

Base call quality data from DBCLS SRA