GSE215251
GSE GEOTranscriptome Regulation by PARP13 in Basal and Antiviral States in Human Cells
Organism:
Homo sapiens
Platform:
GPL16791
Samples:
16
Experiment Types:
Expression profiling by high throughput sequencing
Other
Submitted:
Oct 11 2022
Last Updated:
Oct 10 2025
Status:
Public on Sep 11 2023
Contact:
Gene,,Yeo (UCSD)
Relations
SuperSeries of: GSE215249
SuperSeries of: GSE215250
BioProject: https://www.ncbi.nlm.nih.gov/bioproject/PRJNA889426
Summary
This SuperSeries is composed of the SubSeries listed below.
Overall Design
Refer to individual Series
Analysis (5 steps)
View Data Processing
Processing steps for GSE215251
- Reads were first trimmed of adapters and low-complexity sequences with cutadapt 1.14 (-O 5 -f fastq --match-read-wildcards --times 2 -e 0.0 --quality-cutoff 6 -m 18 -b TCGTATGCCGTCTTCTGCTTG -b ATCTCGTATGCCGTCTTCTGCTTG -b CGACAGGTTCAGAGTTCTACAGTCCGACGATC -b GATCGGAAGAGCACACGTCTGAACTCCAGTCAC -b AAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA -b TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT)
- Trimmed reads were then sorted with fastq-tools (fastq-sort)
- Trimmed reads were mapped against RepBase with STAR v2.4.0j to remove reads mapping to repetitive sequences (--outFilterMultimapNmax 10 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
- Remaining reads were mapped to the appropriate genome build (hg19) using STAR aligner (--outFilterMultimapNmax 10 --alignEndsType EndToEnd --outFilterMultimapScoreRange 1 --outSAMmode Full --outFilterType BySJout --outSAMtype BAM Unsorted --outFilterScoreMin 10 --outReadsUnmapped Fastx --outSAMattributes All)
- featureCounts was used to count reads according to gencode v19 annotations (-s 2 -M)
Supplementary Files (1)
GSE215251_RAW.tar
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