Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

Cell type Class
Blood
Cell type
Hematopoietic Stem Cells
MeSH Description
Progenitor cells from which all blood cells derived. They are found primarily in the bone marrow and also in small numbers in the peripheral blood.

Attributes by original data submitter

Sample

source_name
hematopoietic stem/progenitor cells
strain
C57BL/6
cell type
hematopoietic stem/progenitor cells
developmental stage
adult

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
For ATAC-seq analysis using the Illumina NextSeq500, ~50,000 cells were processed for tagmentation followed by DNA isolation and library generation. Raw reads that aligned to exactly one location in the reference mouse genome (mm9) were retained for downstream data analysis. Following protocols established by Buenrostro et al. (Curr Protoc Mol Biol. 2015 Jan 5;109:21.29.1-9)

Sequencing Platform

instrument_model
NextSeq 500

mm10

Number of total reads
42356749
Reads aligned (%)
56.3
Duplicates removed (%)
58.5
Number of peaks
22222 (qval < 1E-05)

mm9

Number of total reads
42356749
Reads aligned (%)
56.3
Duplicates removed (%)
58.6
Number of peaks
22180 (qval < 1E-05)

Base call quality data from DBCLS SRA