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Install and launch IGV before selecting data to visualize
For hg38
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
For hg19
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
Error connecting to IGV?
Analyze
For hg38
Colocalization
Target Genes (TSS ± 1kb)
Target Genes (TSS ± 5kb)
Target Genes (TSS ± 10kb)
For hg19
Colocalization
Target Genes (TSS ± 1kb)
Target Genes (TSS ± 5kb)
Target Genes (TSS ± 10kb)
Download
For hg38
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
For hg19
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
Link Out
Sequence Read Archive
DBCLS SRA
NCBI SRA
ENA
Antigen: ATAC-Seq
wikigenes
PDBj
CellType: LNCAP
ATCC
MeSH
RIKEN BRC
Variation
TogoVar
SRX8746241
GSM4674818: LNCaP95 rep1; Homo sapiens; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Prostate
Cell type
LNCAP
Primary Tissue
Prostate
Tissue Diagnosis
Carcinoma
Attributes by original data submitter
Sample
source_name
Prostate cancer
cell line
LNCaP95
subtype
Castration-resistant adenocarcinoma
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
DNA was extracted from 50,000 cells per cell line after washing, permeabilization, and transposition using the Qiagen MinElute Kit Libraries were constructed based on a published Omni-ATAC protocol (Corces MR, et al. Nature Protocols, 2017)
Sequencing Platform
instrument_model
Illumina HiSeq 2500
Where can I get the processing logs?
Read processing pipeline
log
hg38
Number of total reads
29073795
Reads aligned (%)
95.2
Duplicates removed (%)
10.5
Number of peaks
80243 (qval < 1E-05)
hg19
Number of total reads
29073795
Reads aligned (%)
94.9
Duplicates removed (%)
10.7
Number of peaks
79970 (qval < 1E-05)
Base call quality data from
DBCLS SRA