Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me3

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPS cells
NA
NA

Attributes by original data submitter

Sample

source_name
AS iPS H3K4me3
biomaterial_provider
Coriell Cell repositories; http://ccr.coriell.org/
biomaterial_provider
GM20409
source cell type
B-lymphocyte
cell type
iPSC derived from Angelman syndrome patient

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Fixed cells were sonicated using Bioruptor to achieve 200–700 bp size chromatin fragments. Solubilized chromatin was immunoprecipiated with antibody against H3K4me3 (Abcam 8580). Antibody–chromatin complexes were pulled down using Dynabeads protein A (Invitrogen), washed and then eluted. After cross-linking reversal, RNase and proteinase K treatment, immunoprecipiated DNA was purified using AMPure beads (Beckman Coulter). ChIP DNA were end-repaired and 5′ phosphorylated using T4 DNA Polymerase, Klenow and T4 Polynucleotide Kinase (Enzymatics). A single adenine was added to 3′ ends by Klenow (3→5′ exo-), and double-stranded Bioo Illumina Adapters (Bioo Scientific) were ligated to the ends of the ChIP fragments. Adaptor-ligated ChIP DNA fragments were subjected to 15 cycles of PCR amplification using Q5 polymerase (NEB). AMPure beads were used to purify DNA after each step (Beckman Coulter). Pooled libraries were sequenced on the HiSeq2500 (V4 Chemistry) for single-end 50 bp according to the manufacturer’s instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
22251617
Reads aligned (%)
98.9
Duplicates removed (%)
6.4
Number of peaks
23557 (qval < 1E-05)

hg19

Number of total reads
22251617
Reads aligned (%)
98.6
Duplicates removed (%)
6.8
Number of peaks
23505 (qval < 1E-05)

Base call quality data from DBCLS SRA