Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
MAX

Cell type

Cell type Class
Epidermis
Cell type
MKL-1
Primary Tissue
Skin
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
Merkel cell carcinoma cell line
cell line
MKL-1
cell type
Merkel cell carcinoma
merkel cell polyomavirus
positive
chip antibody
Max (Santa Cruz, SC-197)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Lysates were clarified from sonicated nuclei as described in 'ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions. 2009 Methods 48, no. 3: 240-248.' 10 ng of DNA from ChIP experiments or input DNA were prepared for sequencing with NEBNext ChIP-seq Library Prep Reagent Set for Illumina (New England Biolabs). Diluted libraries were used for 50 cycles single-end sequencing on HiSeq2000 system (Illumina) at the Center for Cancer Computational Biology (CCCB) at Dana-Farber Cancer Institute following the manufacturer’s protocol.

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg19

Number of total reads
44924658
Reads aligned (%)
35.1
Duplicates removed (%)
64.1
Number of peaks
41676 (qval < 1E-05)

hg38

Number of total reads
44924658
Reads aligned (%)
36.3
Duplicates removed (%)
63.2
Number of peaks
41861 (qval < 1E-05)

Base call quality data from DBCLS SRA