Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KDM1A

Cell type

Cell type Class
Breast
Cell type
MDA-MB-231
Primary Tissue
Breast
Site of Extraction
Effusion, Pleural
Tissue Diagnosis
Adenocarcinoma

Attributes by original data submitter

Sample

source_name
MDA-MB-231 cell line
treatment
none
cell line
MDA-MB-231
antibody
LSD1

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Briefly, 5 x 10^6 cells were cross-linked with formaldehyde (1%, 10 min) then quenched with glycine (125mM). Fixed cells were lysed in SDS lysis buffer and chromatin-bound DNA sheared by sonication with a Misonix Sonicator S-4000. ChIP samples were incubated overnight at 4°C with Protein A Magnetic Beads (Millipore) and 10 μg of anti-LSD1 (ab17721; Abcam) antibodies. Protein-DNA cross-links were reversed by incubating overnight at 65°C and purified with the Zymo-SpinTM I kit (Zymo Research). TruSeqLT paired end

Sequencing Platform

instrument_model
NextSeq 500

hg19

Number of total reads
44573423
Reads aligned (%)
71.9
Duplicates removed (%)
55.5
Number of peaks
517 (qval < 1E-05)

hg38

Number of total reads
44573423
Reads aligned (%)
74.0
Duplicates removed (%)
54.6
Number of peaks
978 (qval < 1E-05)

Base call quality data from DBCLS SRA