GSE281960

Investigational eIF2B activator DNL343 modulates the Integrated Stress Response in Preclinical Models of TDP-43 Pathology.

1. Sequencing adapters were trimmed from the raw reads with skewer.
2. Reads were aligned to the human genome version GRCh38_p126.
3. A STAR index (version 2.7.1a) was built with the –sjdbOverhang=50 argument.
4. Splice junctions from Gencode gene models (release M28) were provided via the –sjdbGTFfile argument.
5. STAR alignments were generated with the following parameters: –outFilterType BySJout, –quantMode TranscriptomeSAM, –outFilterIntronMotifs RemoveNoncanonicalUnannotated, –outSAMstrandField intronMotif, –outSAMattributes NH HI AS nM MD XS and –outSAMunmapped Within.
6. Alignments were obtained with the following parameters: –readFilesCommand zcat –outFilterType BySJout –outFilterMultimapNmax 20 –alignSJoverhangMin 8 –alignSJDBoverhangMin 1 –outFilterMismatchNmax 999 –outFilterMismatchNoverLmax 0.6 –alignIntronMin 20 –alignIntronMax 1000000 –alignMatesGapMax 1000000 –quantMode GeneCounts –outSAMunmapped Within –outSAMattributes NH HI AS nM MD XS –outSAMstrandField intronMotif –outSAMtype BAM SortedByCoordinate –outBAMcompression 6.
7. Alignments sharing the same UMI and genomic coordinate were deduplicated using the collapse_UMI_bam tool (Lexogen).
8. The raw gene expression matrix was constructed from the 'forward' column of STAR's ReadsPerGene.out.tab output files using R.

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