Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
B-cell-biased lymphoid progenitors
NA
NA

Attributes by original data submitter

Sample

source_name
Bone marrow
cell type
B-biased lymphoid progenitor (BLP, Lin- Sca-1+ c-Kit+ Flt3hi IL-7Ra+ Ly6D+ B220-)
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
31200009
Reads aligned (%)
18.3
Duplicates removed (%)
54.7
Number of peaks
87 (qval < 1E-05)

mm9

Number of total reads
31200009
Reads aligned (%)
18.3
Duplicates removed (%)
54.6
Number of peaks
81 (qval < 1E-05)

Base call quality data from DBCLS SRA