Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Sox2

Cell type

Cell type Class
Placenta
Cell type
Trophoblast stem cells
NA
NA

Attributes by original data submitter

Sample

source_name
EGFP-TS3.5 TS cells
strain
ICR
antibody
Sox2 raised by ourselves

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin was sheared into fragments with an average size of 300-500 bp using a Covaris S220. Sequencing libraries were prepared from ChIP DNA using KAPA Library Amplification Kit (KAPA Biosystem). Briefly, ChIP DNA was end-repaired, A-tailed, ligated to the adapters, size selected to 200-500 bp and amplified by PCR. Libraries were sequenced on the HiSeq 1500 (Illumina) as single-end 50-bp reads.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

mm10

Number of total reads
23543747
Reads aligned (%)
96.6
Duplicates removed (%)
14.1
Number of peaks
5768 (qval < 1E-05)

mm9

Number of total reads
23543747
Reads aligned (%)
96.4
Duplicates removed (%)
14.2
Number of peaks
6036 (qval < 1E-05)

Base call quality data from DBCLS SRA