Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Blood
Cell type
GM04604
NA
NA

Attributes by original data submitter

Sample

source_name
GM04604 (UN-B)
biomaterial_provider
GM04604
cell type
Lymphoblastoid Cell Line
disease
Unaffected
chip antibody
Diagenode, C15410210

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Chromatin immunoprecipitation was performed according to the Diagenode AutoiDeal ChIP-qPCR kit (Diagenode) standard protocol. Samples of 6 x 106 cells were sonicated using the Diagenode Bioruptor Pico (Diagenode), with 10 cycles of 30 sec “on” and 30 sec “off”. Correct DNA fragmentation was verified by agarose gel electrophoresis. Immunoprecipitation was performed with 4 x 10^6 cells using a CTCF antibody (Diagenode). CTCF ChIP-seq libraries were prepared in triplicate using the Illumina TruSeq ChIP Sample Preparation kit. We performed 1 x 50 bp single-end sequencing with Illumina Hiseq 4000.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg19

Number of total reads
58884075
Reads aligned (%)
87.4
Duplicates removed (%)
10.6
Number of peaks
1458 (qval < 1E-05)

hg38

Number of total reads
58884075
Reads aligned (%)
89.7
Duplicates removed (%)
9.3
Number of peaks
1226 (qval < 1E-05)

Base call quality data from DBCLS SRA