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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: Input control
wikigenes
PDBj
CellType: MCF-7
ATCC
MeSH
RIKEN BRC
Variation
TogoVar
SRX5457347
GSM3635529: ChIP-seq from MCF-7 (ENCLB099ALY); Homo sapiens; ChIP-Seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
Input control
Antigen
Input control
Cell type
Cell type Class
Breast
Cell type
MCF-7
Primary Tissue
Breast
Site of Extraction
Pleura
Tissue Diagnosis
Adenocarcinoma
Attributes by original data submitter
Sample
sample type
cell line
cell line
MCF-7
sex
female
health state
breast cancer (adenocarcinoma)
dev_stage
adult
age
69 year
donor ID
ENCDO000AAE
lab
Richard Myers, HAIB
passage number
6
Sequenced DNA Library
library_strategy
ChIP-Seq
library_source
GENOMIC
library_selection
ChIP
library_construction_protocol
general protocol: https://www.encodeproject.org/documents/6ecd8240-a351-479b-9de6-f09ca3702ac3/@@download/attachment/ChIP-seq_Protocol_v011014.pdf
Sequencing Platform
instrument_model
Illumina HiSeq 2000
Where can I get the processing logs?
Read processing pipeline
log
hg38
Number of total reads
51134593
Reads aligned (%)
86.7
Duplicates removed (%)
4.0
Number of peaks
1629 (qval < 1E-05)
hg19
Number of total reads
51134593
Reads aligned (%)
86.1
Duplicates removed (%)
5.3
Number of peaks
1603 (qval < 1E-05)
Base call quality data from
DBCLS SRA