Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KDM1A

Cell type

Cell type Class
Digestive tract
Cell type
SW 480
Primary Tissue
unresolved
Tissue Diagnosis
unresolved

Attributes by original data submitter

Sample

source_name
SW480 Cells
genotype
wildtype
chip antibody
LSD1 (abcam, ab17721)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Cells were trypsonized prior to histone ChIP-seq (iDeal ChIP-seq Kit for Histones, Diagenode: C01010051) or scraped prior to transcription factor ChIP-seq (iDeal ChIP-seq kit for Transcription Factors, Diagenode: C01010055). Libraries were generated for sequencing using the NEBNext Ultra DNA Library Prep Kit for Illumina (NEB) per manufacturer's protocol.

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
36080555
Reads aligned (%)
182.4
Duplicates removed (%)
7.1
Number of peaks
1008 (qval < 1E-05)

hg38

Number of total reads
36080555
Reads aligned (%)
184.2
Duplicates removed (%)
7.0
Number of peaks
986 (qval < 1E-05)

Base call quality data from DBCLS SRA