Sample overview

Sample ID: Sample_0642
Biosample name: V6.5 mESCs cultured in 2i+LIF conditions
Biosample type: Stem Cell
Tissue type: Embryo
Cancer type: Normal
Region number: 2178
Length: 691.747 kb
GEO/SRA ID: SRR5815118
Mean insert size: 95.562
Standard deviation: 73.214
TSS enrichment score: 5.46555
FRiP: 0.16253
Diasgnostic plot
The percentages of read pairs in FR, RF, and TANDEM orientations.


Accessible chromatin region of V6.5 mESCs cultured in 2i+LIF conditions

Use these accessible chromatin regions to analyze or download

TF footprint of V6.5 mESCs cultured in 2i+LIF conditions


Peak annotation visualization of V6.5 mESCs cultured in 2i+LIF conditions

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