Sample overview

Sample ID: Sample_0649
Biosample name: Control transfected (twice) V6.5 mESCs cultured for eight passages in 2i+LIF media
Biosample type: Stem Cell
Tissue type: Embryo
Cancer type: Normal
Region number: 412
Length: 139.036 kb
GEO/SRA ID: SRR5815127
Mean insert size: --
Standard deviation: --
TSS enrichment score: 3.69802
FRiP: 0.22928
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.

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Accessible chromatin region of Control transfected (twice) V6.5 mESCs cultured for eight passages in 2i+LIF media

Use these accessible chromatin regions to analyze or download

TF footprint of Control transfected (twice) V6.5 mESCs cultured for eight passages in 2i+LIF media


Peak annotation visualization of Control transfected (twice) V6.5 mESCs cultured for eight passages in 2i+LIF media

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