Sample information curated by ChIP-Atlas

Antigen

Antigen Class
No description
Antigen
NA

Cell type

Cell type Class
Lung
Cell type
A549
Primary Tissue
Lung
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

ENA first public
2016-06-01
ENA last update
2018-03-09
ENA-CHECKLIST
ERC000011
External Id
SAMEA3661574
INSDC center alias
Shanghai Center for Systems Biomedicine, School of Biomedical Engineering and Bio-ID Center, Shanghai Jiao Tong University
INSDC center name
Shanghai Center for Systems Biomedicine, School of Biomedical Engineering and Bio-ID Center, Shanghai Jiao Tong University
INSDC first public
2016-06-01T17:01:04Z
INSDC last update
2018-03-09T09:24:50Z
INSDC status
public
Submitter Id
E-MTAB-3992:A549 H3K4Me3 ChIP-seq
broker name
ArrayExpress
cell line
A549
cell type
lung cancer cell
common name
human
disease
non-small cell lung carcinoma
sample name
E-MTAB-3992:A549 H3K4Me3 ChIP-seq

Sequenced DNA Library

library_name
A549 H3K4Me3 ChIP-seq
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
90% RPMI1640 + 10% FBS For library, 40~50ng immunoprecipitated DNA were end-repaired and ligated adapters to the DNA fragments using NEBNext Ultra End-Repair/dA-Tailing Module and NEBNext Ultra Ligation Module (NEB, USA), respectively. DNA size selection was performed using 2% Agarose Gel, then 200~500bp DNA fragments were excised and purified using Qiagen Gel Extraction Kit (Qiagen, Germany). Each sample was amplified 14 cycles in a DNA thermal cycler using Q5 High-Fidelity DNA Polymerase (NEB, USA) and corresponding PCR Master Mix.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
41079846
Reads aligned (%)
98.9
Duplicates removed (%)
39.4
Number of peaks
35131 (qval < 1E-05)

hg19

Number of total reads
41079846
Reads aligned (%)
98.5
Duplicates removed (%)
40.1
Number of peaks
35220 (qval < 1E-05)

Base call quality data from DBCLS SRA