Sample information curated by ChIP-Atlas

Antigen

Antigen Class
ATAC-Seq
Antigen
ATAC-Seq

Cell type

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

Attributes by original data submitter

Sample

source_name
MKL-1 MCC Cells
cell type
MCC tumor derived cell line
cell line
MKL-1

Sequenced DNA Library

library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
Cells were washed with PBS twice to achieve >85% viable cells in pellets. ATAC-seq protocol was modified from Corces et al. The transpose reaction was performed using TDE1 Tn5 transposase (15027865; Illumina) and TD buffer (15027866; Illumina). The reactions were cleaned up using MinElute PCR Purification Kit (28004; Qiagen) and amplified using NEBNext High-Fidelity 2X PCR Master Mix (M0541S; New England Biolabs Inc.) with a total of 7 cycles. The libraries were cleaned up using MinElute PCR Purification Kit and additionally with AMPure XP beads (Beckman Coulter) to remove primer dimers and large fragments.

Sequencing Platform

instrument_model
NextSeq 500

hg38

Number of total reads
58086725
Reads aligned (%)
98.6
Duplicates removed (%)
30.3
Number of peaks
66928 (qval < 1E-05)

hg19

Number of total reads
58086725
Reads aligned (%)
98.3
Duplicates removed (%)
30.4
Number of peaks
66672 (qval < 1E-05)

Base call quality data from DBCLS SRA