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Install and launch IGV before selecting data to visualize
For mm10
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
For mm9
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
Error connecting to IGV?
Analyze
For mm10
Colocalization
Target Genes (TSS ± 1kb)
Target Genes (TSS ± 5kb)
Target Genes (TSS ± 10kb)
For mm9
Colocalization
Target Genes (TSS ± 1kb)
Target Genes (TSS ± 5kb)
Target Genes (TSS ± 10kb)
Download
For mm10
BigWig
Peak-call (q < 1E-05)
Peak-call (q < 1E-10)
Peak-call (q < 1E-20)
For mm9
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: MEF
ATCC
MeSH
RIKEN BRC
SRX4826330
GSM3425931: WV2 ATAC; Mus musculus; ATAC-seq
Sample information curated by ChIP-Atlas
Antigen
Antigen Class
ATAC-Seq
Antigen
ATAC-Seq
Cell type
Cell type Class
Embryonic fibroblast
Cell type
MEF
Tissue
Embryonic Fibroblast
Lineage
primaryCells
Description
Mouse Embryonic Fibroblast
Attributes by original data submitter
Sample
source_name
mouse embryonic fibroblasts
cell type
mouse embryonic fibroblasts
genotype/variation
Wild Type
starved/stimulated
Starved
Sequenced DNA Library
library_strategy
ATAC-seq
library_source
GENOMIC
library_selection
other
library_construction_protocol
ATAC-seq was performed using the Omni-ATAC protocol (Corces et al., 2017).
Sequencing Platform
instrument_model
Illumina HiSeq 2000
Where can I get the processing logs?
Read processing pipeline
log
mm10
Number of total reads
16482757
Reads aligned (%)
90.7
Duplicates removed (%)
11.0
Number of peaks
11290 (qval < 1E-05)
mm9
Number of total reads
16482757
Reads aligned (%)
90.6
Duplicates removed (%)
11.0
Number of peaks
11207 (qval < 1E-05)
Base call quality data from
DBCLS SRA