Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMC3

Cell type

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

Attributes by original data submitter

Sample

source_name
cervical carcinoma
cell type
HeLa Kyoto
RNAi
Pds5SA/B RNAi
genotype
Pds5SA/B depletion
chip antibody
SMC3

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-Seq: Cells were cross-linked and scrapped of the plate. The DNA was fragmented and the protein of interest was immunoprecipitated with indicated antibodies; Adaptors were ligated to the 5' and 3' ends and the library was prepared for Illumina sequencing by a qPCR amplification step. ChIP as well as Hi-C libraries were prepared for sequencing using standard Illumina protocols.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
24106796
Reads aligned (%)
60.6
Duplicates removed (%)
37.4
Number of peaks
28881 (qval < 1E-05)

hg38

Number of total reads
24106796
Reads aligned (%)
61.8
Duplicates removed (%)
36.5
Number of peaks
28892 (qval < 1E-05)

Base call quality data from DBCLS SRA