Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
PTEN

Cell type

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

Attributes by original data submitter

Sample

source_name
cell culture
cell type
HeLa
chip antibody
PTEN 6H2.1 (Millipore, 04-035) and PTEN 138G6 (Cell Signaling, 9559)
growth protocol
grown in DMEM supplemented with 10% FBS, penicillin and streptomycin
genotype/variation
CRISPR-PTEN KO

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Lysates were clarified from sonicated nuclei and prtein-DNA complexes were isolated with antibody RNA-seq: RNA was extracted from cell pellets using Qiagen RNeasy Kit. ChIP-seq: 2-10 ng of DNA were subject to end-repair, A-tailing, and ligation with Illumina Truseq adapters using NEB enzymes (NEB), followed by size-selection of 300-400 bp and amplification for 10-15 cycles using the KAPA HiFi Library Amplification Kit (Kapa Biosystems). RNA-seq: Illumina TruSeq RNALibrary Prep Kit v2 (RS 122-2001) was used with 1 ug of total RNA for the construction of sequencing libraries

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
182877614
Reads aligned (%)
7.3
Duplicates removed (%)
91.7
Number of peaks
1979 (qval < 1E-05)

hg38

Number of total reads
182877614
Reads aligned (%)
8.8
Duplicates removed (%)
90.1
Number of peaks
3036 (qval < 1E-05)

Base call quality data from DBCLS SRA