Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MITF

Cell type

Cell type Class
Digestive tract
Cell type
COLO 829
Primary Tissue
Skin
Tissue Diagnosis
Melanoma

Attributes by original data submitter

Sample

source_name
COLO829 human melanoma cell line treated with DMSO
cell line
COLO829 melanoma cell line
treatment
DMSO (control)
braf signaling status
ON
chip antibody
anti-MITF (Sigma, HPA003259, lot# A08324)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
20-50 million cells were used. Cells were trypsinized, washed, and cross-linked as described previously(Sen et al. 2008). Lysis with a modified RIPA buffer (1% NP40/Igepal, 0.5% Sodium Deoxycholate, 0.1% SDS, 100uM EDTA in PBS), nuclei were isolated and DNA was sonicated to ~150bp and overnight pulldown was performed with an antibody to MITF (Sigma HPA003259) ChIP-sequencing libraries were prepared with a modified version of NEBNext ChIP-seq library prep kit (NEB) using Ampure beads (Agencourt) for purification. Barcodes were introduced and these libraries were sequenced with 1x50bp reads on the Illumina HiSeq platform.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
18494363
Reads aligned (%)
15.4
Duplicates removed (%)
80.8
Number of peaks
1198 (qval < 1E-05)

hg38

Number of total reads
18494363
Reads aligned (%)
16.6
Duplicates removed (%)
79.5
Number of peaks
1241 (qval < 1E-05)

Base call quality data from DBCLS SRA