Sample overview

Sample ID: Sample_0141
Biosample name: Glioblastoma stem cell
Biosample type: Stem Cell
Tissue type: Brain
Cancer type: Glioblastoma
Region number: 38396
Length: 25974.33 kb
GEO/SRA ID: SRR7642285
Mean insert size: 181.622
Standard deviation: 146.358
TSS enrichment score: 129.88200
FRiP: 0.43804
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


Accessible chromatin region of Glioblastoma stem cell

Use these accessible chromatin regions to analyze or download

TF footprint of Glioblastoma stem cell


Peak annotation visualization of Glioblastoma stem cell

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