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 and progenitor cells (Lin-, cKit+ bone marrow cells)
strain
C57B6/129 hybrid
tissue
Bone marrow
genotype/variation
wildtype

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
60.000 cells were washed once with 100µl PBS and resuspended in 50µl lysis buffer (10mM Tris-HCl pH 7.4, 10mM NaCl, 3mM MgCl2, 0.2% IGEPAL CA-630). The suspension of nuclei was then centrifuged for 10min at 500g at 4°C, followed by the addition of 50µl transposition reaction mix (25µl TD buffer, 2.5µl Tn5 Transposase and 22.5µl Nuclease Free H2O) and incubation at 37°C for 30min. DNA was isolated using MinElute Kit (Qiagen). Libraries were amplified by PCR (13 cycles). After the PCR reaction, the library was selected for fragments between 100 and 1000bp with AmpureXP beads (Beckman Coulter). Libraries were purified with Qiaquick PCR (Qiagen) and integrity checked on a Bioanalyzer before sequencing. Libraries were amplified by PCR (13 cycles). After the PCR reaction, the library was selected for fragments between 100 and 1000bp with AmpureXP beads (Beckman Coulter). Libraries were purified with Qiaquick PCR (Qiagen) and integrity checked on a Bioanalyzer before sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

mm10

Number of total reads
57024714
Reads aligned (%)
96.8
Duplicates removed (%)
20.3
Number of peaks
77040 (qval < 1E-05)

mm9

Number of total reads
57024714
Reads aligned (%)
96.6
Duplicates removed (%)
20.4
Number of peaks
76994 (qval < 1E-05)

Base call quality data from DBCLS SRA