Sample information curated by ChIP-Atlas

Antigen

Antigen Class
TFs and others
Antigen
CHD1

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
CHD1 knockdown
passages
10
treatment
DHT
chip antibody
anti-CHD1 (Bethyl, catalog# A301-218A, lot# A301-218A-1)

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

hg19

Number of total reads
39543052
Reads aligned (%)
86.7
Duplicates removed (%)
10.5
Number of peaks
1401 (qval < 1E-05)

hg38

Number of total reads
39543052
Reads aligned (%)
89.2
Duplicates removed (%)
8.8
Number of peaks
1413 (qval < 1E-05)

Base call quality data from DBCLS SRA