Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Uterus
Cell type
HeLa
Primary Tissue
Cervix
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
HeLa cell line
cell line
HeLa
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
HeLa cells transiently expressing Flag-Za or Flag-Zaa were cross-linked with 1% formaldehyde for 10 minutes at room temperature and cross-linking was quenched with 137 mM glycine. After nucleus extraction, isolated nucleus pellets were resuspended in Sonication buffer (50mM HEPES [pH7.9], 140mM NaCl, 1mM EDTA, 1% triton X-100, 0.1% Na-deoxycholate, 0.1% SDS, 1X protease inhibitor). The chromatin was sonicated to the range of 100-300 bp, and then immunoprecipitated overnight using an anti-Flag antibody (Sigma, USA). Sequencing libraries were manually generated for high-throughput sequencing. Either end of DNA strands was filled using the Epicentre DNA END-Repair kit (Epicentre Biotechnologies, Madison, WI). Adenine was added at 3' ends by Taq DNA polymerase (New England Biolabs, Beverly, MA) under dATP conditions. Illumina's adaptor oligomers was ligated at both ends using Quick Ligation kit (Qiagen, Germantown, MD). After purified twice, DNA libraries are amplified using Solexa primers (Illumina, San Diego, CA) and Phusion PCR master mix (Thermo Scientific, Hudson, NH).

Sequencing Platform

instrument_model
Illumina Genome Analyzer IIx

hg38

Number of total reads
29278503
Reads aligned (%)
97.8
Duplicates removed (%)
57.3
Number of peaks
546 (qval < 1E-05)

hg19

Number of total reads
29278503
Reads aligned (%)
97.0
Duplicates removed (%)
59.0
Number of peaks
531 (qval < 1E-05)

Base call quality data from DBCLS SRA