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
KO_LT_HSC_ATAC-Seq
transplant status
none
cell type
LSK/CD150+ HSCs
genotype/variation
Ebffl/fl PrxCre

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Total RNA was prepared using RNeasy Micro Kit (Qiagen) according to manufacturer's instructions. mRNA was enriched by using oligo dT magnetic beads for library preparation. Assays for Transposase-Accessible Chromatin with high-throughput sequencing (ATAC-seq) were performed as described before (Buenrostro et al., 2015). To prepare nuclei, 10.000 cells were resuspended in 50 µL of cold lysis buffer (10 mM Tris•Cl at pH 7.4, 10 mM NaCl, 3 mM MgCl2, 0.1% [v/v] Igepal CA-630) and incubated for 15 min on ice. The supernatant was discarded after centrifugation, and the nuclei were used for transposition reaction immediately. The RNA-seq libraries were prepared by using SMART-Seq v4 ultra-low input RNA library preparation protocol according to the manufacturer's instructions. The ATAC-seq libraries were prepared using the NEB Nextera DNA sample preparation kit according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 3000

mm10

Number of total reads
59297390
Reads aligned (%)
73.8
Duplicates removed (%)
63.1
Number of peaks
741 (qval < 1E-05)

mm9

Number of total reads
59297390
Reads aligned (%)
73.7
Duplicates removed (%)
63.2
Number of peaks
703 (qval < 1E-05)

Base call quality data from DBCLS SRA