Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Others
Cell type
Mesenchymal stem cells
NA
NA

Attributes by original data submitter

Sample

ENA first public
2013-09-01
ENA last update
2018-03-08
ENA-CHECKLIST
ERC000011
External Id
SAMEA2171844
INSDC center alias
Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital HF
INSDC center name
Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital HF
INSDC first public
2013-09-01T17:01:55Z
INSDC last update
2018-03-08T16:41:23Z
INSDC status
public
Submitter Id
E-MTAB-1828:iMSC3
broker name
ArrayExpress
cell line
iMSC3
cell type
immortalized mesenchymal stem cell
common name
human
developmental stage
28-day differentiated
developmental stage
day-0 undifferentiated
sample name
E-MTAB-1828:iMSC3
specimen with known storage state
fresh specimen

Sequenced DNA Library

library_name
extract4
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Minimum essential medium alpha with glutamax (Invitrogen), 10% fetal calf serum Growth medium (column N) supplemented with 67 uM ascorbic acid 2-phosphate (Sigma-Aldrich), 3.5 mM beta-glycerol phosphate (Sigma-Aldrich) and 10 nM dexamethasone (Sigma-Aldrich) Chromatin immunoprecipitation followed by phenol:chloroform:isoamylalcohol extraction of DNA Library prep TRUSeq, ChIP-Seq library prep Illumina.

Sequencing Platform

instrument_model
Illumina Genome Analyzer II

hg38

Number of total reads
34960120
Reads aligned (%)
98.6
Duplicates removed (%)
2.0
Number of peaks
1144 (qval < 1E-05)

hg19

Number of total reads
34960120
Reads aligned (%)
97.9
Duplicates removed (%)
3.3
Number of peaks
1324 (qval < 1E-05)

Base call quality data from DBCLS SRA