Sample overview

Sample ID: Sample_0072
Biosample name: Forebrain neurons
Biosample type: Induced pluripotent stem cell line
Tissue type: Forebrain
Cancer type: Normal
Region number: 19405
Length: 10967.276 kb
GEO/SRA ID: SRR5417036
Mean insert size: 210.347
Standard deviation: 200.393
TSS enrichment score: 7.01608
FRiP: 0.07831
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


Accessible chromatin region of Forebrain neurons

Use these accessible chromatin regions to analyze or download

TF footprint of Forebrain neurons


Peak annotation visualization of Forebrain neurons

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