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
C-FA-iPSC#1
antibody
Anti-trimethyl-histoneH3(lys4) Polyclonal Antibody Cat. #07-473 Millipore
cell type
Induced pluripotent stem cells from human fibroblasts from patients with FA disease
genotype correction status
corrected

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Immunocomplexes were incubated with 1:1 mix of protein A and G Dynabeads (Invitrogen, Carlsbad, CA) for 2 hours at 4°C, with rotation. Beads were immobilised on magnetic racks and the supernatants discarded, after which the beads were washed with low salt buffer, high salt buffer and LiCl buffer. All washes were carried out for 5 minutes at 4°C on a rotating wheel in the presence of protease inhibitors. Beads were then resuspended in 100 μl of elution buffer and DNA complexes were decrosslinked at 65 °C for 3 hour with shaking. DNA was then eluted in 50 μl of water using the PCR purification kit (QIAGEN). Libraries were prepared using the NEBNext® ChIP-Seq Library Prep Reagent Set for Illumina® kit (ref. E6200S) according to the manufacturer's protocol. Briefly, 10 ng of input and ChIP enriched DNA were subjected to end repair, addition of “A” bases to 3′ ends and ligation of PE adapters. All purification steps were performed using Qiagen PCR purification columns (refs. 50928106 and 50928006). Library size selection was done with 2% low-range agarose gels and DNA was extracted using QIAquick Gel extraction kit (ref. 50928706, Qiagen) and eluted in 36 µl EB. Library amplification was performed by PCR on the size selected fragments. Final libraries were analyzed using Agilent DNA 1000 chip to estimate the quantity and check size distribution, and were then quantified by qPCR using the KAPA Library Quantification Kit (ref. KK4835, KapaBiosystems) prior to amplification with Illumina’s cBot. Sequencing was done on the HiSeq2000, Single Reads, 50nts.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
59327477
Reads aligned (%)
98.9
Duplicates removed (%)
28.3
Number of peaks
39332 (qval < 1E-05)

hg19

Number of total reads
59327477
Reads aligned (%)
98.6
Duplicates removed (%)
28.8
Number of peaks
39539 (qval < 1E-05)

Base call quality data from DBCLS SRA