Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CTCF

Cell type

Cell type Class
Blood
Cell type
GM12878
Tissue
blood
Lineage
mesoderm
Description
B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus

Attributes by original data submitter

Sample

source_name
GM12878
biomaterial_provider
GM12878
datatype
ChipSeq
datatype description
Chromatin IP Sequencing
cell description
B-lymphocyte, lymphoblastoid, International HapMap Project - CEPH/Utah - European Caucasion, Epstein-Barr Virus
treatment
None
treatment description
No special treatment or protocol applies
antibody antibodydescription
Rabbit polyclonal. Antibody Target: CTCF
antibody targetdescription
CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
antibody vendorname
Millipore
antibody vendorid
07-729
controlid
wgEncodeEH000528
labversion
baseAlignCounts.pl v 1,fseq v 1.84, iff_GM12878,p-value cutoff: 0.05,1% ENCODE array platform validation tests
replicate
1,3,2
antibody targetdescription
CTCF zinc finger transcription factor. A sequence specific DNA binding protein that functions as an insulator, blocking enhancer activity. It has also been suggested to block the spreading of chromatin structure in certain instances.
antibody vendorname
Millipore
antibody vendorid
07-729
controlid
GM12878/Input
labversion
align_on_cluster_bwa.pl v 1
replicate
1
replicate description
tier 1

Sequenced DNA Library

library_name
GSM822312: UT-A_ChipSeq_GM12878_CTCF
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP

Sequencing Platform

instrument_model
Illumina Genome Analyzer

hg19

Number of total reads
46021263
Reads aligned (%)
52.4
Duplicates removed (%)
20.4
Number of peaks
53038 (qval < 1E-05)

hg38

Number of total reads
46021263
Reads aligned (%)
53.2
Duplicates removed (%)
19.8
Number of peaks
51157 (qval < 1E-05)

Base call quality data from DBCLS SRA