Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Neural
Cell type
Anterior temporal cortex
NA
NA

Attributes by original data submitter

Sample

source_name
Adult anterior temporal cortex
developmental stage
Adult
tissue
brain (anterior temporal cortex)
chip antibody
CTCF (Abcam, ab70303, lot# GR320146-4)

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

hg38

Number of total reads
21754373
Reads aligned (%)
98.0
Duplicates removed (%)
25.8
Number of peaks
5961 (qval < 1E-05)

hg19

Number of total reads
21754373
Reads aligned (%)
97.5
Duplicates removed (%)
26.7
Number of peaks
5952 (qval < 1E-05)

Base call quality data from DBCLS SRA