Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
GATA2

Cell type

Cell type Class
Cardiovascular
Cell type
HMVEC
Primary Tissue
Blood Vessel
Tissue Diagnosis
Normal

Attributes by original data submitter

Sample

Alias
1
Description
LEC1 GATA2 ChIPseq
ENA checklist
ERC000011
INSDC center name
CENTRE FOR CANCER BIOLOGY
INSDC first public
2015-05-22T17:38:31Z
INSDC last update
2015-05-22T07:39:38Z
INSDC status
public
SRA accession
ERS738983
Sample Name
ERS738983
Title
LEC1 GATA2 ChIPseq
cell_line
Adult human dermal lymphatic microvascular endothelial cells HMVEC-dLyAd (hLEC)
cell_type
Endothelial
culture_collection
Hematology department, Centre For Cancer Biology
geographic location (country and/or sea)
Australia
tissue_lib
Lonza

Sequenced DNA Library

library_name
Illumina TruSeq
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-Seq library preparation and sequencing was carried out at the ACRF Cancer Genomics Facility, Centre for Cancer Biology, Adelaide. ChIP-Seq libraries were prepared according to Illumina’s TruSeq Sample Prep Guide Revision A with some minor modifications.  Briefly, DNA was end-repaired, followed by adenylation of the 3’ ends.  Next, Illumina indexing adapters were ligated to the DNA. 18 cycles of PCR was performed to enrich for successfully adapter ligated molecules. Ligation products were purified with a 2% Pippin Prep gel (Sage Science), selecting a size range of 250 – 300 base pairs.  The size distribution and yield of the purified libraries were determined using an Agilent Bioanalyzer High Sensitivity chip and Qubit dsDNA HS assay (Invitrogen), respectively.  Libraries were pooled in equimolar ratios and sequenced in one lane of a HiSeq 2500 short read flowcell (1 x 50bp).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
35946092
Reads aligned (%)
26.6
Duplicates removed (%)
72.5
Number of peaks
8671 (qval < 1E-05)

hg38

Number of total reads
35946092
Reads aligned (%)
28.4
Duplicates removed (%)
71.0
Number of peaks
8674 (qval < 1E-05)

Base call quality data from DBCLS SRA