Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SOX2

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPS derived neural cells
NA
NA

Attributes by original data submitter

Sample

source_name
iPSC-derived human Neural Progenitor Cell, inhibition of the PI3K and MAPK signaling pathways
chip antibody
Sox2
cell type
Neural Progenitor Cell
treatment
No Treatment
cell line
Derived by Pollard et al., 2009 Cell Stem Cell, GNS G179. Deposited by Steve Pollard, Austin Smith, Peter Dirks and Ian Clarke at the biorep S.r.l. Catalog number NS00011*B

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
3*105 cells were fixed using 1% PFA, treated with glycine 0.1M and resuspended in nuclei lysis buffer (SDS 1%, EDTA 100mM, Tris-HCl 50mM pH7.5). Chromatin samples were sonicated with a Branson Digital Sonifier to generate DNA fragments from 200 to 1000 bp, diluted with ChIP RIPA Buffer (Tris-HCl 0.1mM pH7.5, EDTA 1mM, EGTA 0.5mM, Triton X-100 1%, SDS 0.1%, Deoxycolic acid 0.1%, NaCl 140mM) and incubated with Dynabeads Protein A (Invitrogen) coupled to the specific antibody. After overnight incubation, the immunocomplexes were eluted in ChIP elution buffer (Tris-HCl 20mM pH7.5, EDTA 5mM, NaCl 140mM, SDS 1%, proteinase K 40mg/ml) and the crosslinking was reverted overnight at 65ºC. DNA was recovered by phenol/chloroform extraction and quantified by quantitative PCR using SYBR green on an ABI Prism 7300 system. ChIP DNA was prepared into ChIP-Seq libraries using NEBNext Ultra DNA Library Prep Kit for Illumina according to manufacturer's instructions except adapters were purchased from Bioo Scientific. Briefly, ChIP DNA was end-repaired, adenylated and adapter ligated. Adapter-ligated DNA was subjected to 12 cycles of PCR using NEB Q5 PCR mastermix. AMPure beads were used to purify sequencing libraries from reactions (Beckman Coulter). ChIP-Seq libraries were quantified using Invitrogen Qubit, Agilent Tape station and Kapa library quantification qPCR kit. Libraries were pooled and sequenced single-end 50bp on Illumina HiSeq 2500.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
16466179
Reads aligned (%)
84.0
Duplicates removed (%)
7.0
Number of peaks
748 (qval < 1E-05)

hg38

Number of total reads
16466179
Reads aligned (%)
84.8
Duplicates removed (%)
6.6
Number of peaks
749 (qval < 1E-05)

Base call quality data from DBCLS SRA