Sample overview

Sample ID: Sample_0007
Biosample name: iMeLCs induced from primed UCLA1 hESCs
Biosample type: Stem Cell
Tissue type: Embryo
Cancer type: Normal
Region number: 31268
Length: 17829.782 kb
GEO/SRA ID: SRR7942728
Mean insert size: 196.086
Standard deviation: 155.340
TSS enrichment score: 12.36990
FRiP: 0.06833
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


Accessible chromatin region of iMeLCs induced from primed UCLA1 hESCs

Use these accessible chromatin regions to analyze or download

TF footprint of iMeLCs induced from primed UCLA1 hESCs


Peak annotation visualization of iMeLCs induced from 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