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 type
cell line
chip antibody
cell signaling cat. 2729S

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Nuclei were extracted from HeLa cells and sonicated using the Covaris instrument. The resulting chromatin was isolated from clarified from sonicated nuclei. The histone-DNA complexes were immunoprecipitated with antibody. Libraries were prepared according to Illumina's instructions accompanying the truseq chip-seq kit from illumina (IP-202-1012). Briefly the ends of DNA are repaired using a combination of T4 DNA polymerase and Klenow DNA polymerase. An 'A' base is then added to the blunt and phosphorylated ends using the Klenow fragment (3' to 5' exo minus), this prepares the fragments for ligation of the adapters which have a 'T' overhang in their 3' end. The illumina specific adapters are then ligated to the DNA fragments and the library is amplified by PCR. The resulting, size selected libraries were sequenced in the Illumina Hiseq 2000.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
38054602
Reads aligned (%)
97.4
Duplicates removed (%)
55.4
Number of peaks
1107 (qval < 1E-05)

hg19

Number of total reads
38054602
Reads aligned (%)
96.5
Duplicates removed (%)
57.1
Number of peaks
1020 (qval < 1E-05)

Base call quality data from DBCLS SRA