Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SOX2

Cell type

Cell type Class
Neural
Cell type
ReN-VM
NA
NA

Attributes by original data submitter

Sample

source_name
differentiating neural culture
cell line
ReN-VM
treatment
non-targeting siRNA
chip antibody
Santa Cruz SOX2 (sc-17320)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei and SOX2-DNA complexes were isolated with antibody. Libraries were prepared according to Illumina's instructions accompanying the DNA Sample Kit (Part# 0801-0303). Briefly, DNA was end-repaired using a combination of T4 DNA polymerase, E. coli DNA Pol I large fragment (Klenow polymerase) and T4 polynucleotide kinase. The blunt, phosphorylated ends were treated with Klenow fragment (32 to 52 exo minus) and dATP to yield a protruding 3- 'A' base for ligation of Illumina's adapters which have a single 'T' base overhang at the 3’ end. After adapter ligation DNA was PCR amplified with Illumina primers for 15 cycles and library fragments of ~250 bp (insert plus adaptor and PCR primer sequences) were band isolated from an agarose gel. The purified DNA was captured on an Illumina flow cell for cluster generation. Libraries were sequenced on the Genome Analyzer following the manufacturer's protocols.

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
136402240
Reads aligned (%)
67.6
Duplicates removed (%)
27.5
Number of peaks
4708 (qval < 1E-05)

hg38

Number of total reads
136402240
Reads aligned (%)
69.4
Duplicates removed (%)
26.4
Number of peaks
5602 (qval < 1E-05)

Base call quality data from DBCLS SRA