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
non-specific IgG antibody

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
HeLa cells transiently expressing 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 (F1804, Sigma, USA) or anti-mouse IgG antibody (sc-2025. Santa cruz, USA). Input was taken from starting material before immunoprecipitation. ChIP DNA for Zaa biological replicates and control DNA (IgG ChIP and input) were used for sequencing library construction. Sequencing libraries were prepared using Aceel-NGS DNA library kits according to the manufacturer's instructions. PCR products were purified with HiAccuBead (AccuGene, Korea). Purified PCR products are eluted in low-EDTA TE buffer.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
23605902
Reads aligned (%)
95.7
Duplicates removed (%)
2.4
Number of peaks
769 (qval < 1E-05)

hg19

Number of total reads
23605902
Reads aligned (%)
95.0
Duplicates removed (%)
2.5
Number of peaks
402 (qval < 1E-05)

Base call quality data from DBCLS SRA