Accessibility Summary



Overview

This ATAC-seq dataset contains accessibility profiles for 8 samples. The table below contains an overview of the provided sample annotation.

sampleId tissue time replicate bamFile .bamPath
kidney_14_5_REP1 kidney_14_5_REP1 kidney 14.5 1 /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/kidney_14_5_REP1.mLb.clN.sorted.bam /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/kidney_14_5_REP1.mLb.clN.sorted.bam
kidney_14_5_REP2 kidney_14_5_REP2 kidney 14.5 2 /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/kidney_14_5_REP2.mLb.clN.sorted.bam /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/kidney_14_5_REP2.mLb.clN.sorted.bam
kidney_15_5_REP1 kidney_15_5_REP1 kidney 15.5 1 /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/kidney_15_5_REP1.mLb.clN.sorted.bam /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/kidney_15_5_REP1.mLb.clN.sorted.bam
kidney_15_5_REP2 kidney_15_5_REP2 kidney 15.5 2 /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/kidney_15_5_REP2.mLb.clN.sorted.bam /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/kidney_15_5_REP2.mLb.clN.sorted.bam
liver_14_5_REP1 liver_14_5_REP1 liver 14.5 1 /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/liver_14_5_REP1.mLb.clN.sorted.bam /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/liver_14_5_REP1.mLb.clN.sorted.bam
liver_14_5_REP2 liver_14_5_REP2 liver 14.5 2 /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/liver_14_5_REP2.mLb.clN.sorted.bam /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/liver_14_5_REP2.mLb.clN.sorted.bam
liver_15_5_REP1 liver_15_5_REP1 liver 15.5 1 /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/liver_15_5_REP1.mLb.clN.sorted.bam /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/liver_15_5_REP1.mLb.clN.sorted.bam
liver_15_5_REP2 liver_15_5_REP2 liver 15.5 2 /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/liver_15_5_REP2.mLb.clN.sorted.bam /vol/COMPEPIWS/groups/atacseq1/tasks/nextflow_run/results/bwa/merged_library/liver_15_5_REP2.mLb.clN.sorted.bam

Sample annotation table as TSV file

Signal has been summarized for the following region sets:

#regions transformations
tiling 280370
promoter 1216
consensusPeaks 6259

Fragment data IS available.

Sample QC

This section contains per-sample quality control plots and data. The table below contains fragment counts for each sample.

#fragments
kidney_14_5_REP1 1526264
kidney_14_5_REP2 1765791
kidney_15_5_REP1 1731145
kidney_15_5_REP2 1946286
liver_14_5_REP1 886943
liver_14_5_REP2 2211394
liver_15_5_REP1 1416303
liver_15_5_REP2 856264
Figure 1

Open PDF Figure 1

Number of fragments per sample

Fragment size distribution

The following plot illustrates the fragment size distribution for each sample. Periodicity indicating nucleosome-bound DNA is generally an indicator of good data quality.

Sample

Figure 2

Open PDF Figure 2

Fragment size distribution

TSS profile

The following plot illustrates genome-wide enrichment of ATAC signal around transcription start sites (TSS). It is indicative of the signal-to-noise ratio in the dataset. High enrichment of signal in at TSSs compared to background indicates good sample quality. Ideally, there is a dip in the TSS profile corresponding the +1 nucleosome.

Sample

Figure 3

Open PDF Figure 3

TSS profile. Genome-wide aggregate of TSS +/- 2kb. Signal was normalized to the mean signal in the 100-bp-wide windows in the tails of the plot. A smoothing window of width 25bp has been applied to draw the profile curve.

Figure 4

Open PDF Figure 4

Scatterplot of QC metrics