Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EPAS1

Cell type

Cell type Class
Kidney
Cell type
786-O
Primary Tissue
Kidney
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
Renal Cancer Cell Line
cell line
786-O
transfection
HIF-2a (pRRL-HIF-2a)
chip antibody
HIF-2alpha Antibody (PM9)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: Cells were fixed with 1% formaldehyde and quenched with glycine (125mM). After washing, cells were lysed (1%SDS, 10mM EDTA, 50mM Tris-HCl pH 8.1) and sonicated (Diagenode Biorupter, Belgium). Chromatin was immunoprecipitated using rabbit polyclonal antisera to HIF-1? (PM14), HIF-2? (PM9), HIF-1? (NB-100-110, Novus Biologicals, UK) or pre-immune serum as control. Eluted chromatin was heated to reverse cross-linking, treated with proteinase-K and purified with phenol:chloroform:isoamyl alcohol and ethanol precipitation RNA-seq: Total RNA was prepared using the mirVana miRNA Isolation Kit (Ambion; Life Technologies Ltd, Paisley, UK) and treated with DNaseI (TURBO DNA‐free™, Ambion). Directional PolyA+ RNA libraries were then prepared using the ScriptSeq™ v2 RNA‐Seq kit (Epicentre, Madison, WI, USA). Standard Illumina protocol

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
56005259
Reads aligned (%)
30.6
Duplicates removed (%)
83.8
Number of peaks
3188 (qval < 1E-05)

hg38

Number of total reads
56005259
Reads aligned (%)
32.3
Duplicates removed (%)
83.0
Number of peaks
3380 (qval < 1E-05)

Base call quality data from DBCLS SRA