Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Epitope tags

Cell type

Cell type Class
Blood
Cell type
Leukemia stem cell lines
NA
NA

Attributes by original data submitter

Sample

source_name
RH-RAS LSCs
cell line
RH-RAS LSC
chip antibody
myc tag, 9e10

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
29195863
Reads aligned (%)
90.0
Duplicates removed (%)
27.6
Number of peaks
366 (qval < 1E-05)

mm9

Number of total reads
29195863
Reads aligned (%)
89.8
Duplicates removed (%)
27.7
Number of peaks
377 (qval < 1E-05)

Base call quality data from DBCLS SRA