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
Embryonic day 14.5 fetal liver hematopoietic stem cells
strain
B6129SF1
tissue
Fetal liver
age
Embryonic day 14.5

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
E14.5 fetal liver and adult bone marrow were dissected and HSCs were purified using cell surface marker: Lin-Sca1+cKit+CD135-. 50,000 FACS-sorted cells were lyzed and treated with Nextera Tn5 transposase. Libraries were amplified using 1x NEBNext PCR master mix and custom Nextera PCR primers. Libraries were size-selected at 100-700 bp by gel extraction. Libraries were quantified with KAPA qPCR and bioanalyzer prior to pair-end sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
23796233
Reads aligned (%)
51.1
Duplicates removed (%)
28.4
Number of peaks
15317 (qval < 1E-05)

mm9

Number of total reads
23796233
Reads aligned (%)
51.1
Duplicates removed (%)
28.5
Number of peaks
15222 (qval < 1E-05)

Base call quality data from DBCLS SRA