Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Blood
Cell type
81.3
Primary Tissue
Blood
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

ENA first public
2013-04-22
ENA last update
2018-03-08
External Id
SAMEA1877861
INSDC center alias
EFPL
INSDC center name
EFPL
INSDC first public
2013-04-22T17:03:04Z
INSDC last update
2018-03-08T16:17:57Z
INSDC status
public
Submitter Id
E-MTAB-1511:Human lymphoblastoid 1
broker name
ArrayExpress
cell line
81.3
cell type
lymphoblastoid
common name
human
sample name
E-MTAB-1511:Human lymphoblastoid 1

Sequenced DNA Library

library_name
Hsa-LCL-813-ChIP1
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lymphoblast cell lines were obtained for seven primate species. All cell lines were transformed by the Epstein Barr virus except for the macaque cell lines that were transformed by a herpesvirus. Cells were grown in suspension at a confluency of 200 000-1 x106 cells/ml in RPMI1640 media supplemented with 10% Fetal Bovine Serum and 2 mM L-glutamine. C57BL/6J mice were housed in the Biological Resources Unit under UK Home Office licensing. Tissue was obtained from at least two independent males and cross-linked as described in (Schmidt, Methods,2009). Male and female human tissue samples were obtained from biopsied tissue collected at Addenbrooke's Hospital, Cambridge, and were provided by the Biobank under human tissue license 08/H0308/117. Liver tissue was also obtained from the Liver Tissue Distribution Program (NIDDK contract number N01-DK-9-2310) at the University of Pittsburgh. 1x10^8 cells were cross-linked with 1% formaldehyde as previously described (Schmidt, Methods,2009). ChIP-seq assays were performed as previously described (Schmidt, 2009). Protein-bound DNA was immunoprecipitated with antibodies against CTCF (Millipore, 07-729), or YY1 (Santa Cruz, sc-281).

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg38

Number of total reads
23303348
Reads aligned (%)
90.9
Duplicates removed (%)
9.7
Number of peaks
25470 (qval < 1E-05)

hg19

Number of total reads
23303348
Reads aligned (%)
90.0
Duplicates removed (%)
10.8
Number of peaks
26554 (qval < 1E-05)

Base call quality data from DBCLS SRA