Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

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

ENA first public
2012-12-13
ENA last update
2018-03-08
External Id
SAMEA1570921
INSDC center alias
Cancer Research UK
INSDC center name
Cancer Research UK
INSDC first public
2012-12-13T17:01:35Z
INSDC last update
2018-03-08T15:45:58Z
INSDC status
public
Submitter Id
E-MTAB-1104:hsa1294
age
NA year
broker name
ArrayExpress
common name
human
developmental stage
adult
genotype
wild type
individual
hsa1294
organism part
liver
sample name
E-MTAB-1104:hsa1294
sex
male

Sequenced DNA Library

library_name
hsa1294
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
doi:10.1016/j.ymeth.2009.03.001; Crosslinked animal livers were dounce homogenized into a single cell suspension and rinsed with ice cold PBS. Each pellet of cross-linked material was resuspended in 10 ml of LB1 (50 mM Hepes-KOH, pH 7.5; 140 mM NaCl; 1mM EDTA; 10% Glycerol; 0.5% NP-40 or Igepal CA-630; 0.25% Triton X-100) and pelleted again by centrifugation at 2,000 x rcf for 4 minutes at 4 C. Pellets were then rinsed in 10 ml of LB2 (10 mM Tris-HCL, pH8.0; 200 mM NaCl; 1 mM EDTA; 0.5 mM EGTA) and pelleted again by centrifugation at 2,000 x rcf for 4 minutes at 4 C. The nuclei preparation was resuspended in 3 ml LB3 (10 mM Tris-HCl, pH 8; 100 mM NaCl; 1 mM EDTA; 0.5 mM EGTA; 0.1% Na-Deoxycholate; 0.5% N-lauroylsarcosine). Chromatin in the nuclei fraction was fragmented to an average length of 300 bp by sonication. After sonication 300 ul of 10% Triton X-100 was added to the 3 ml of sonicated lysate and debris was removed by centrifugation at 20,000 x rcf for 10 minutes at 4 C.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg38

Number of total reads
15902430
Reads aligned (%)
73.2
Duplicates removed (%)
68.5
Number of peaks
19393 (qval < 1E-05)

hg19

Number of total reads
15902430
Reads aligned (%)
73.0
Duplicates removed (%)
68.8
Number of peaks
19270 (qval < 1E-05)

Base call quality data from DBCLS SRA