Sample overview

Sample ID: Sample_0003
Biosample name: primed UCLA1 hESCs
Biosample type: Stem Cell
Tissue type: Embryo
Cancer type: Normal
Region number: 94678
Length: 60703.425 kb
GEO/SRA ID: SRR7942724
Mean insert size: 218.196
Standard deviation: 185.502
TSS enrichment score: 35.16620
FRiP: 0.30290
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


Accessible chromatin region of primed UCLA1 hESCs

Use these accessible chromatin regions to analyze or download

TF footprint of primed UCLA1 hESCs


Peak annotation visualization of primed UCLA1 hESCs

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