Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
TFAM

Cell type

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

Attributes by original data submitter

Sample

source_name
Hela_TFAM_20F8A9
cell line
HeLa
chip antibody
custom antibody, 20F8A9

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were fixed for 10min at RT in 1% formaldehyde, harvested using a cell scraper, washed once in ice-cold PBS, and resuspended in RIPA buffer with protease inhibitor. The sample was then sonicated using an 3.2mm microtip (QSonica Sonicator 4000) at 30s on 30s off intervals and 40% amplitude for 180min while in a -30C 3:1 isopropanol and water bath containing dry ice. Subsequent steps were performed as per the standard protocol. DNA was size-selected during library building to an average fragment size of 200bp. Libraries were sequenced using Illumina HiSeq 2000. Libraries were generated following Illumina's DNA Sample Prep Kit protocol

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
64920099
Reads aligned (%)
68.7
Duplicates removed (%)
6.2
Number of peaks
1282 (qval < 1E-05)

hg38

Number of total reads
64920099
Reads aligned (%)
70.9
Duplicates removed (%)
4.3
Number of peaks
1294 (qval < 1E-05)

Base call quality data from DBCLS SRA