Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Histone
Antigen
H3K4me1

Cell type

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

Attributes by original data submitter

Sample

source_name
KO2-Late G1
cell line
Fucci human embryonic stem cell
antibody
H3K4me1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-seq, lysates were isolated from sonicated nuclei and histone-DNA complexes were purified with antibody. For 4C, lysates were purified from restriction digested nuclei. ChIP-seq libraries were prepared by HudsonAlpha by first performing end-repair and adapter ligation of Chip'd DNA fragments, followed by size selection and PCR amplifcation to generate the library for sequencing. Library was prepared using the Illumina DNA Library Construction Kit. DNA barcodes were introduced to permit multiple samples per flowcell lane. 4C-libaries were prepared by first digesting nuclei with HindIII, followed by ligation and crosslink reversal. Chromatin was re-digested with NlaIII and re-ligated to generate DNA libraries by PCR using the Expand Long Template Polymerase Kit from Roche.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
24680044
Reads aligned (%)
84.2
Duplicates removed (%)
1.7
Number of peaks
137 (qval < 1E-05)

hg19

Number of total reads
24680044
Reads aligned (%)
84.0
Duplicates removed (%)
1.9
Number of peaks
172 (qval < 1E-05)

Base call quality data from DBCLS SRA