Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Neural
Cell type
Retina
MeSH Description
The ten-layered nervous tissue membrane of the eye. It is continuous with the OPTIC NERVE and receives images of external objects and transmits visual impulses to the brain. Its outer surface is in contact with the CHOROID and the inner surface with the VITREOUS BODY. The outer-most layer is pigmented, whereas the inner nine layers are transparent.

Attributes by original data submitter

Sample

source_name
retina
age
fetal week 23
chip antibody
CTCF (ActiveMotif,61311)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP with iDeal ChIP-seq kit (Diagenode # C01010051), MinElute PCR-purification kit (QIAGEN #28006), quantified using the Quant-iT PicoGreen ds DNA assay (Life Technologies #Q33120) Libraries were prepared from 5-10 ng DNA using the NEBNext ChIP-Seq Library Prep Reagent Set for Illumina with NEBNext High-Fidelity 2x PCR Master Mix according to the manufacturer’s instructions (New England Biolabs, Ipswich, MA) with the following modifications: A 1:1 Ampure cleanup was added after adaptor ligation a total of 2 times.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
36765423
Reads aligned (%)
91.3
Duplicates removed (%)
6.0
Number of peaks
24634 (qval < 1E-05)

hg38

Number of total reads
36765423
Reads aligned (%)
93.4
Duplicates removed (%)
4.6
Number of peaks
24818 (qval < 1E-05)

Base call quality data from DBCLS SRA