Sample information curated by ChIP-Atlas

Antigen

Antigen Class
Input control
Antigen
Input control

Cell type

Cell type Class
Epidermis
Cell type
A-375
Primary Tissue
Skin
Tissue Diagnosis
Melanoma

Attributes by original data submitter

Sample

source_name
A375 melanoma cell line
cell type
A375 melanoma cells
antibody
none
stable knockdown
EGFP control

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
ChIP was performed using the Simple ChIP Plus Enzymatic Chromatin IP kit as per manufacturer’s instructions (Cell Signaling#9001) with the phospho-SMAD1/5/8 antibody (Cell Signaling#11971; 1:100). ChIP-ed DNA fragments were added with 'A' base to the 3' end and adapters were ligated. This was followed by PCR amplfication and size selection (100-300bp). After QC, these were used for cluster preparation and HiSeq sequencing.

Sequencing Platform

instrument_model
Illumina HiSeq 4000

hg38

Number of total reads
59581070
Reads aligned (%)
98.8
Duplicates removed (%)
21.2
Number of peaks
772 (qval < 1E-05)

hg19

Number of total reads
59581070
Reads aligned (%)
98.1
Duplicates removed (%)
22.5
Number of peaks
773 (qval < 1E-05)

Base call quality data from DBCLS SRA