Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPSC derived cardiac cells
NA
NA

Attributes by original data submitter

Sample

source_name
iPSC-derived cardiomyocytes
cell type
iPSC-derived cardiomyocytes
passages
20-30
iPSc source
individual ID: YRI-NA18852
antibody
Millipore cat#07-436 lot#2684917

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Histone-DNA or PolII-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions provided with the TrueSeq ChIP Sample Preparation Kit (Catalog #: IP-202-1012). 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 ~250-450 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 on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
31576081
Reads aligned (%)
98.2
Duplicates removed (%)
36.4
Number of peaks
733 (qval < 1E-05)

hg19

Number of total reads
31576081
Reads aligned (%)
97.3
Duplicates removed (%)
37.5
Number of peaks
834 (qval < 1E-05)

Base call quality data from DBCLS SRA