Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

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
Primary HSPC Cells
genotype
DNMT3A WT with NRAS G12D
chip batch
batch 1
chip antibody
none
cell type
Lin- enriched hematopoietic stem/progenitor cells

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and DNMT3A R882H- or histone-DNA complexes were isolated with indicated antibodies. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
19919007
Reads aligned (%)
97.8
Duplicates removed (%)
12.5
Number of peaks
427 (qval < 1E-05)

mm9

Number of total reads
19919007
Reads aligned (%)
97.5
Duplicates removed (%)
12.5
Number of peaks
443 (qval < 1E-05)

Base call quality data from DBCLS SRA