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 cells
cell line
HeLa
passage
10
genotype
control
chip antibody
none

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
After cross-linking, crude nuclear extracts were isolated and subjected to sonication. After immunoprecipitation with the anti-acetyl H3 antibody , the histone-DNA immunocomplexes were purified by co-precipitation with protein A-Sepharose (GE Healthcare, UK). Ovation Ultralow Library System v2' kits (NuGEN, San Carlos, CA, USA) were used for the library preparation, according to the manufacturer instructions. The input and immunoprecipitated samples, as well as the final libraries were quantified by using a fluorometer (Qubit 2.0; Invitrogen, Carlsbad, CA, USA) and quality tested using an Agilent 2100 Bioanalyser RNA nanoassay (Agilent Technologies, Santa Clara, CA, USA) and real-time Stratagen Mx3000P (Agilent Technologies, Santa Clara, CA, USA). The libraries were then processed with Illumina cBot for cluster generation on a flowcell, according to the manufacturer instructions and sequenced on single-end mode at the multiplexing level requested on HiSeq2500 (Illumina, San Diego, CA, USA).

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg38

Number of total reads
23297685
Reads aligned (%)
97.0
Duplicates removed (%)
4.8
Number of peaks
579 (qval < 1E-05)

hg19

Number of total reads
23297685
Reads aligned (%)
96.6
Duplicates removed (%)
5.7
Number of peaks
665 (qval < 1E-05)

Base call quality data from DBCLS SRA