Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Unclassified
Antigen
Unclassified

Cell type

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

Attributes by original data submitter

Sample

source_name
501mel_Negative control for MITF
cell line
501mel
cell type
melanoma cell line
treated with
1% O2 level for 16hrs

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

hg38

Number of total reads
72500302
Reads aligned (%)
58.4
Duplicates removed (%)
17.2
Number of peaks
3266 (qval < 1E-05)

hg19

Number of total reads
72500302
Reads aligned (%)
57.9
Duplicates removed (%)
18.8
Number of peaks
3486 (qval < 1E-05)

Base call quality data from DBCLS SRA