Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SOD1

Cell type

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

Attributes by original data submitter

Sample

source_name
Cervix
cell line
HeLa cervical adenocarcinoma cell line
treatment
treated with hydrogen peroxide
chip antibody
anti-human SOD1 primary antibody (Abcam; ab16831)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Briefly, the cells were incubated with 1% formaldehyde for 10 min, and then incubated with 0.125 M glycine (final concentration) for 5 min. The nuclei of each sample was incubated with 0.6 μL micrococcal nuclease in MNase digestion buffer working solution for 5 min. The input DNA was prepared by treating aliquots of chromatin with NaCl, proteinase K and heat for de-crosslinking. The supernatants of experimental groups were incubated with 8 μL immunoprecipitation grade anti-human SOD1 primary antibody (Abcam; ab16831) overnight at 4 °C on a rocking platform. Following capturing the immune complex using Protein A/G Plus Agarose, the immune complexes were treated with NaCl, proteinase K and heated for de-crosslinking. Finally, DNAs were purified using Agencourt AMPure XP (Beckman Coulter; 15770600). Illumina sequencing libraries were prepared from ChIP and Input DNAs by the standard consecutive enzymatic steps of end-polishing, dA-addition, and adaptor ligation. After amplification by PCR, the resulting DNA libraries were quantified and sequenced on the Illumina HiSeq platform according to the manufacturer's instructions.

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
17739338
Reads aligned (%)
94.5
Duplicates removed (%)
2.5
Number of peaks
331 (qval < 1E-05)

hg38

Number of total reads
17739338
Reads aligned (%)
96.1
Duplicates removed (%)
1.6
Number of peaks
265 (qval < 1E-05)

Base call quality data from DBCLS SRA