Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
EPAS1

Cell type

Cell type Class
Epidermis
Cell type
501A
Primary Tissue
Skin
Tissue Diagnosis
Melanoma

Attributes by original data submitter

Sample

source_name
501mel_HIF2_ChIP-seq
cell line
501mel
cell type
melanoma cell line
treated with
1% O2 level for 16hrs
chip antibody
Rabbit Polyclonal in whole antiserum (antigen: HIF2a)
chip antibody vendor
home-made

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP-seq: 3x-15cm dishes of 501mel cells were fixed in 0.4% PFA then cheared with a Covaris S220 for 15 minutes (160 W peak incident power, 5% duty cycle and 200 cycles per burst). The sonicated chromatin were precleared and ChIP was performed using 80ug of the indicated antivodies. Purification of the ChIP-DNA was done using QIAGEN PCR clean-up column RNA-seq: RNA-samples were extracted using QIAGEN RNeasy kit ChIP-seq: Libraries were prepared using recommended Illumina protocols RNA-seq: Library prep using QuantSeq Forward kit (LEXOGEN #015.96), using 500 ng starting material

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
27863101
Reads aligned (%)
88.3
Duplicates removed (%)
7.4
Number of peaks
1442 (qval < 1E-05)

hg38

Number of total reads
27863101
Reads aligned (%)
90.1
Duplicates removed (%)
6.2
Number of peaks
1613 (qval < 1E-05)

Base call quality data from DBCLS SRA