Sample overview

Sample ID: Sample_0016
Biosample name: cKIT/TNAP-sorted hPGCs from human embryonic gonad
Biosample type: Stem Cell
Tissue type: Embryo
Cancer type: Normal
Region number: 21508
Length: 9831.39 kb
GEO/SRA ID: SRR7942739
Mean insert size: 145.828
Standard deviation: 115.841
TSS enrichment score: 8.42947
FRiP: 0.06813
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


Accessible chromatin region of cKIT/TNAP-sorted hPGCs from human embryonic gonad

Use these accessible chromatin regions to analyze or download

TF footprint of cKIT/TNAP-sorted hPGCs from human embryonic gonad


Peak annotation visualization of cKIT/TNAP-sorted hPGCs from human embryonic gonad

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