Sample overview

Sample ID: Sample_0006
Biosample name: primed UCLA2 hESCs
Biosample type: Stem Cell
Tissue type: Embryo
Cancer type: Normal
Region number: 127089
Length: 61745.097 kb
GEO/SRA ID: SRR7942727
Mean insert size: 166.678
Standard deviation: 122.663
TSS enrichment score: 47.88180
FRiP: 0.40153
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


Accessible chromatin region of primed UCLA2 hESCs

Use these accessible chromatin regions to analyze or download

TF footprint of primed UCLA2 hESCs


Peak annotation visualization of primed UCLA2 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