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
Lin- BM progenitors (HSPCs)
cell type
Lin- BM progenitors (HSPCs)
genotype
UTX_WT, Cas9
strain
C57BL/6

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
HSPCs was extracted from bone marrow using the Lineage Cell Depletion Kit (Miltenyi Biotec, cat. no. 130-090-858). The ATAC-seq method was used based on the protocol from Buenrostro et al, 2013 with modifications as described in Kumasaka et al, 2016. Samples were processed with Nextera® Index Kit (Illumina, #FC-121-1011) and Nextera® DNA Sample Preparation Kit (Illumina, # FC-121-1030) ATAC-Seq libraries were prepared for sequencing using standard Illumina protocols

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
21180047
Reads aligned (%)
77.7
Duplicates removed (%)
16.4
Number of peaks
29665 (qval < 1E-05)

mm9

Number of total reads
21180047
Reads aligned (%)
77.7
Duplicates removed (%)
16.5
Number of peaks
29644 (qval < 1E-05)

Base call quality data from DBCLS SRA