Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Blood
Cell type
GM10847
Tissue
blood
Lineage
mesoderm
Description
lymphoblastoid, International HapMap Project, CEPH/Utah, treatment: Epstein-Barr Virus transformed

Attributes by original data submitter

Sample

source_name
Lymphoblastoid Cell Lines
cell line
10847
antibody
CTCF
replicate
2.2

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
For ChIP-Seq, nuclear lysates were sonicated using a Branson 250 Sonifier (power setting 2, 100% duty cycle for 7 x 30-s intervals). Clarified lysates corresponding to 20 million cells were treated with 1-5ug of antibody (Table S4) coupled to Protein G Dynabeads (Invitrogen #10003D, New York). The protein-DNA complexes were washed with RIPA buffer and eluted in 1% SDS TE at 65°C. An aliquot of clarified lysate was reserved as “input DNA” and handled in parallel with the immunoprecipitated samples following elution from Dynabeads. For RNA-Seq, Total RNA was extracted using Trizol (Lifetechnologies, Grand Island, NY) reagent according to the manufacturer's instructions, then purified using the Qiagen RNeasy kit (Qiagen, Valencia, CA) and treated with RNAse-free DNase (Qiagen). RNA integrity was checked on a Bioanalyzer (Agilent, Santa Clara CA) and only RNA with an RNA integrity number (RIN) of > 9.5was used for subsequent library construction. Purified total RNA was depleted of ribosomal RNA using the Ribo-Zero Magnetic Gold Kit (Human/Mouse/Rat) (Epicentre Biotechnologies, Madison, WI). ChIP DNA sequencing libraries were generated according to Illumina DNA Tru-Seq DNA Sample Preparation Kit Instructions (Illumina Part # FC-121-2001, San Diego, CA). For RNA-Seq, stranded libraries were prepared following a dUTP protocol. Briefly, ~100 ng of rRNA depleted RNA were fragmented with 10 x fragmentation buffer (Lifetechnologies, #AM8740) for 2 min at 70 °C. First-strand cDNA synthesis was primed with random hexamers. Actinomycin D was added to reduce anti-sense artifacts. For second-strand synthesis dTTP was replaced with dUTP. The cDNA was endrepaired, A-tailed and Illumina TruSeq adapters were added. After size-selection on an agarose gel the second strand was eliminated by digestion with AmpErase Uracil Nglycosylase (UNG) (Lifetechnologies, N8080096) and after PCR amplification samples were sequenced on the Illumina Hi-Seq 2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
30773580
Reads aligned (%)
192.0
Duplicates removed (%)
2.6
Number of peaks
37145 (qval < 1E-05)

hg38

Number of total reads
30773580
Reads aligned (%)
193.6
Duplicates removed (%)
2.5
Number of peaks
36168 (qval < 1E-05)

Base call quality data from DBCLS SRA