RNA-seq read files (fastq files) were checked for quality by FastQC
(Babraham Bioinformatics,FastQC/">https://www.bioinformatics.babraham.ac.uk/projects/FastQC/ )
and read trimming was done based on the Phred score and per-base sequence
content (base pairs 13 through 72 were retained). Trimmed Reads were then
mapped against the reference genome and transcriptome (Gencode vM16 and
GRCm38.p5 for mouse, Gencode v27 and GRCh38.p10 for human [22 (link)]) using STAR v2.2.1 [18 (link)]. Relative abundances in Transcripts Per
Million (TPM) for every gene of every sample was quantified by stringtie
v1.3.5 [48 ]. Downstream analyses were
restricted to protein coding genes to make human (total RNA) and mouse
(polyA+ RNA) libraries comparable, hence TPMs of only genes annotated as
coding genes in the Gencode database were renormalized to sum to a million.
Sequencing and mapping statistics reported by STAR are presented inTable 2 .
(Babraham Bioinformatics,
and read trimming was done based on the Phred score and per-base sequence
content (base pairs 13 through 72 were retained). Trimmed Reads were then
mapped against the reference genome and transcriptome (Gencode vM16 and
GRCm38.p5 for mouse, Gencode v27 and GRCh38.p10 for human [22 (link)]) using STAR v2.2.1 [18 (link)]. Relative abundances in Transcripts Per
Million (TPM) for every gene of every sample was quantified by stringtie
v1.3.5 [48 ]. Downstream analyses were
restricted to protein coding genes to make human (total RNA) and mouse
(polyA+ RNA) libraries comparable, hence TPMs of only genes annotated as
coding genes in the Gencode database were renormalized to sum to a million.
Sequencing and mapping statistics reported by STAR are presented in
