Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMARCA4

Cell type

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

Attributes by original data submitter

Sample

source_name
501Mel
cell line
501Mel
cell type
melanoma
chip antibody
BRG1 : Abcam (clone EPNCIR111A, ab110641)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
BRG1 ChIP experiments were performed on native Mnase-digested chromatin isolated from 501Mel cells (Kasinathan et al., 2014). SOX10 and 3HA-MITF ChIP experiments were performed on 0,4% PFA-fixed chromatin isolated from 501Mel and Cl8 cells respectively according to standard protocols as previously described (Strub et al., 2011). . Up to 60 ug of chromatin was subjected to immunoprecipation with a specific antibody. The libraries were sequenced on the Illumina Hiseq 2500 as single-end 50 base reads following Illumina’s instructions

Sequencing Platform

instrument_model
Illumina HiSeq 2500

hg19

Number of total reads
50190992
Reads aligned (%)
56.2
Duplicates removed (%)
39.6
Number of peaks
17136 (qval < 1E-05)

hg38

Number of total reads
50190992
Reads aligned (%)
57.0
Duplicates removed (%)
38.8
Number of peaks
17283 (qval < 1E-05)

Base call quality data from DBCLS SRA