Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
Ctcf

Cell type

Cell type Class
Liver
Cell type
Liver
MeSH Description
A large lobed glandular organ in the abdomen of vertebrates that is responsible for detoxification, metabolism, synthesis and storage of various substances.

Attributes by original data submitter

Sample

source_name
Liver
tissue
Liver
strain
Crl:CD1(ICR) (Charles River, strain code #022)
chip antibody
Millipore anti CTCF (cat# 07-779)
Sex
male
age
8 weeks

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei were isolated by ultracentrifugation in a high sucrose buffer then crosslinked with 0.8% formaldehyde for 9 minutes. Samples were sonicated with a Bioruptor Twin (Diagenode, UCD-400) until the majority of DNA fragments were between 100-400bp (60-70 cycles total, 30 sec ON 30 sec OFF). Chromatin was quantified and 70 ug of chromatinized DNA was incubated with the indicated ChIP antibody. Samples were prepared for sequencing with NEBNext Ultra II DNA Library Prep Kit for Illumina according to the manufacturer's directions for low input samples (New England Biolabs, #E7645). All samples were subjected to double-sided SPRI size selection prior to PCR amplification (Agencourt AMPure XP; Beckman Coulter: A63882). Samples were barcoded using New England Biolabs NEBNext Multiplex Oligos for Illumina (#E7335) with 8 rounds of PCR per the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

mm10

Number of total reads
19943125
Reads aligned (%)
96.4
Duplicates removed (%)
26.6
Number of peaks
36691 (qval < 1E-05)

mm9

Number of total reads
19943125
Reads aligned (%)
96.0
Duplicates removed (%)
26.7
Number of peaks
36672 (qval < 1E-05)

Base call quality data from DBCLS SRA