Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
SMAD1

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
phsopho-SMAD1/5/8
stable knockdown
GDF6

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

hg19

Number of total reads
63346547
Reads aligned (%)
67.2
Duplicates removed (%)
31.0
Number of peaks
842 (qval < 1E-05)

hg38

Number of total reads
63346547
Reads aligned (%)
69.3
Duplicates removed (%)
29.4
Number of peaks
867 (qval < 1E-05)

Base call quality data from DBCLS SRA