Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
KDM1A

Cell type

Cell type Class
Prostate
Cell type
LNCAP
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma

Attributes by original data submitter

Sample

source_name
LNCaP cells
cell line
LNCaP prostate cancer cells
protocol
G9A knockdown
passages
10
treatment
DHT
chip antibody
LSD1_K114me2 (Schüle Lab)

Sequenced DNA Library

library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
Metzger, E., et al. Phosphorylation of histone H3 at threonine 11 establishes a novel chromatin mark for transcriptional regulation. Nat Cell Biol 10, 53-60 (2008). Libraries were prepared from immunoprecipitated DNA according to standard methods. ChIP-seq libraries were sequenced using a HiSeq 2000 (Illumina) and mapped to the hg19 reference genome using bowtie 2 Langmead, B., Trapnell, C., Pop, M. & Salzberg, S.L. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol 10, R25 (2009).

Sequencing Platform

instrument_model
Illumina HiSeq 2000

hg38

Number of total reads
31424472
Reads aligned (%)
96.5
Duplicates removed (%)
34.5
Number of peaks
1045 (qval < 1E-05)

hg19

Number of total reads
31424472
Reads aligned (%)
95.7
Duplicates removed (%)
36.2
Number of peaks
1086 (qval < 1E-05)

Base call quality data from DBCLS SRA