Sample overview

Sample ID: Sample_1262
Biosample name: CD4+ T cell
Biosample type: Primary Cell
Tissue type: Blood
Cancer type: Normal
Region number: 9778
Length: 3522.325 kb
GEO/SRA ID: SRR1556341
Mean insert size: 160.399
Standard deviation: 121.023
TSS enrichment score: 5.17794
FRiP: 0.05431
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


Accessible chromatin region of CD4+ T cell

Use these accessible chromatin regions to analyze or download

TF footprint of CD4+ T cell


Peak annotation visualization of CD4+ T 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