Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMC3

Cell type

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

Attributes by original data submitter

Sample

source_name
Embryonic stem cell
tissue
Embryonic stem cell
differentiation time
day00
genotype
H9 MLC2v:H2B
matched input
day00.Input.Batch3.Rep1
chip antibody
SMC3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The ChIP-seq has been carried out as previously described (Jolma et al., 2013; Tuupanen et al., 2012; Yan et al., 2013). Briefly, 2 million cells were crosslinked with 1% formadehyde for 15 min at RT. The reaction was quenched by adding 125 mM of Glycine and incubating for 5 min at RT. Cells were lysed in RIPA buffer (10 mM TrisHCl pH 8.0, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% SDS, 0.1% sodium deoxycholate) supplemented with protease inhibitor (Roche). And chromatin was sonicated into short fragments (300-700 bp). The fragmented chromatin was incubated with antibodies to pull down the specific DNA bound TFs or histones. After intensive wash, DNA was purified and prepared as sequencing library using illumina Truseq LT kit. Several samples with different indexes were pooled together for 50 or 100 cycles of single read sequencing with illumina Hiseq 2500.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
35315750
Reads aligned (%)
85.8
Duplicates removed (%)
6.6
Number of peaks
8327 (qval < 1E-05)

hg38

Number of total reads
35315750
Reads aligned (%)
87.7
Duplicates removed (%)
5.4
Number of peaks
8297 (qval < 1E-05)

Base call quality data from DBCLS SRA