Sample overview

Sample ID: Sample_0041
Biosample name: prefrontal cortex
Biosample type: Tissue
Tissue type: Brain
Cancer type: Normal
Region number: 66056
Length: 37364.129 kb
GEO/SRA ID: SRR5343858
Mean insert size: 168.210
Standard deviation: 134.320
TSS enrichment score: 31.47940
FRiP: 0.07185
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


Accessible chromatin region of prefrontal cortex

Use these accessible chromatin regions to analyze or download

TF footprint of prefrontal cortex


Peak annotation visualization of prefrontal cortex

Plot A

Plot B

Plot A: a pie chart of annotated genomic features.
Note A: the proportion of annotating genomic region (Promoter, 5'UTR, 3'UTR, Exon, Intron, Downstream and Intergenic).
Plot B: a heatmap of peaks binding to TSS region.
Note B: the profile of ATAC peaks binding to TSS region (+/- 1kb).

Software and parameters used

Read mapping: bowtie2(v2.2.5) -p 10 -X 2000 -x -S
Duplicates Removing: picard MarkDuplicates REMOVE_DUPLICATES=true ASSUME_SORTED=true
Peak calling: macs2(2.1.2) --broad--SPMR --nomodel --extsize 200 -q 0.01
Trimming the adapter: trim_galore --phred33 --stringency 3 --length 20