Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Pluripotent stem cell
Cell type
iPSC derived neural crests
NA
NA

Attributes by original data submitter

Sample

source_name
neural crest stem cells
disease
Control
chip antibody
Diagenode C15410210-50

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Between 10-20 millions cells were cross-linked with 1% formaldehyde in fixation solution directly in culture dishes and incubated for 5 minutes at RT and then 40 minutes at 4°C. Cross linking reaction was stopped by addition of 0.125M Glycine. For ChIP-seq, we used the iDeal ChIP-seq kit for Transcription Factors and iDeal ChIP-seq kit for Histones (Diagenode). Chromatin extraction, immunoprecipitations and DNA purifications is performed as recommended by the manufacturer ChIP samples were purified using Agencourt AMPure XP beads (Beckman Coulter) and quantified with the Qubit (Invitrogen). ChIP-seq libraries were prepared from 10 ng of double-stranded purified DNA using the MicroPlex Library Preparation kit v2 (C05010014, Diagenode s.a., Seraing, Belgium), according to manufacturer's instructions. In the first step, the DNA was repaired and yielded molecules with blunt ends. In the next step, stem-loop adaptors with blocked 5 prime ends were ligated to the 5 prime end of the genomic DNA, leaving a nick at the 3 prime end. The adaptors cannot ligate to each other and do not have single-strand tails, avoiding non-specific background. In the final step, the 3 prime ends of the genomic DNA were extended to complete library synthesis and Illumina compatible indexes were added through a PCR amplification (7 cycles). Amplified libraries were purified and size-selected using Agencourt AMPure XP beads (Beckman Coulter) to remove unincorporated primers and other reagents.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
29113677
Reads aligned (%)
97.5
Duplicates removed (%)
11.3
Number of peaks
22086 (qval < 1E-05)

hg19

Number of total reads
29113677
Reads aligned (%)
96.5
Duplicates removed (%)
12.4
Number of peaks
22249 (qval < 1E-05)

Base call quality data from DBCLS SRA