Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KDM1A

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
tumor type
Merkel cell carcinoma
cell type
MCC tumor derived cell line
cell line
MKL-1
chip antibody
LSD1 (abcam; rabbit; ab17721)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
The ChIP method was modified from protocols described in Schmidt et al.(Schmidt et al., 2009). MKL-1 cells were cross-linked using dual cross-linking with disuccinimidyl glutarate (DSG) and formaldehyde. After cross-linking, cells were lysed using SimpleChIP buffer A and B (Cell signaling) and DNA was processed with the Micrococcal nuclease (New England Biolabs Inc.) for 30 minutes at 37°C followed by sonicating for 20s pulses 5 times at 4°C. 30 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). Amplified libraries were cleaned up using AMPure XP beads (Beckman Coulter) and checked on a Bioanalyzer (Agilent) to confirm a narrow distribution with a peak size around 275 bp. Diluted libraries were used for 50 cycles single-end sequencing on NextSeq 550 systems (Illumina) at the Molecular Biology Core Facilities (MBCF) at Dana-Farber Cancer Institute following the manufacturer's protocol.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
44418207
Reads aligned (%)
89.0
Duplicates removed (%)
7.2
Number of peaks
1936 (qval < 1E-05)

hg38

Number of total reads
44418207
Reads aligned (%)
89.6
Duplicates removed (%)
6.8
Number of peaks
2088 (qval < 1E-05)

Base call quality data from DBCLS SRA