Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Neural
Cell type
Neural progenitor cells
NA
NA

Attributes by original data submitter

Sample

source_name
neural progenitor cells
treatment
induced from hIPS
chip antibody
CTCF (Abcam, ab70303)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For Hi-C, nuclei were extraced after fixing using a cell lysis buffer. For ChIP-seq, nuclei were extracted and chromatins were fragmented by sonication. The TF/histone-DNA complexes were isolated by antibody. All Hi-C libraries were constructed following illumina insctructions accompanying Truseq sample preparation kit. Random indexes were introduced for eHi-C libraries to remove PCR duplication. Generally, PCR amplification was done with 7-9 cycles. All ChIP-seq libraries were generated following a ChIPmentation protocol with Nextera adapters.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
19274609
Reads aligned (%)
31.4
Duplicates removed (%)
66.4
Number of peaks
13768 (qval < 1E-05)

hg38

Number of total reads
19274609
Reads aligned (%)
32.6
Duplicates removed (%)
65.3
Number of peaks
13817 (qval < 1E-05)

Base call quality data from DBCLS SRA