Skip to main content
. Author manuscript; available in PMC: 2022 Nov 28.
Published in final edited form as: Cell Rep. 2022 Nov 1;41(5):111585. doi: 10.1016/j.celrep.2022.111585

KEY RESOURCES TABLE.

REAGENT or RESOURCE SOURCE IDENTIFIER
Biological samples
See Table S1 for a complete list of all human samples used in the current study N/A N/A
See Table S5 for a complete list of all macaque and mouse samples used in the current study N/A N/A
Deposited data
Raw RNA-seq & WGS data – DLPFC https://www.synapse.org syn21557948
Raw RNA-seq data – Cerebrum & Cerebellum https://www.ebi.ac.uk/arrayexpress/ E-MTAB-6814
Raw RNA-seq data – Cortex and normal aging https://www.synapse.org syn7416949
Raw RNA-seq data – hESC differentiation https://www.ncbi.nlm.nih.gov/geo/ GSE56796
Raw RNA-seq data – hiPSC differentiation https://www.ncbi.nlm.nih.gov/bioproject/ PRJNA596331
Raw RNA-seq data – Rhesus Macaque https://www.ncbi.nlm.nih.gov/bioproject/ PRJNA448973
Raw RNA-seq data – Mouse https://www.ncbi.nlm.nih.gov/sra SRP055008
Processed RNA editing calls – DLPFC, Cerebrum & Cerebellum https://www.synapse.org syn26434508
Software and algorithms
Code used to process data This paper https://doi.org/10.5281/zenodo.7108745
STAR v2.7.3 Dobin etal., 201377 https://github.com/alexdobin/STAR
REDItools v2.0 Flati et al., 202040 https://github.com/BioinfoUNIBA/REDItools2
JACUSA2 Piechotta et al., 202241 https://github.com/dieterich-lab/JACUSA2
SAMtools v1.16 Harvard Medical School, Boston https://github.com/samtools/samtools
Picard v.2.22.3 Broad Institute, Boston https://github.com/broadinstitute/picard/
ANNOVAR (Oct 24 2019) Wang etal., 201078 https://github.com/WGLab/doc-ANNOVAR
Phastcons v.3.15 Hubisz et al., 201179 https://bioconductor.org/packages/release/data/annotation/html/phastCons100way.UCSC.hg38.html
Mice: Multivariate Imputation by Chained Equations v.3.14.0 Buuren etal., 201080 https://cran.r-project.org/web/packages/mice/index.html
RNAEditingIndexer v.1 Roth etal., 201939 https://github.com/a2iEditing/RNAEditingIndexer
bMINDv 0.3.2 Wang etal., 202181 https://github.com/randel/MIND
limma v.3.36.3 N/A https://bioconductor.org/packages/release/bioc/html/limma.html
ToppGene Suite software Chen et al., 200982 https://toppgene.cchmc.org/enrichment.jsp
SynGO Koopmans et al., 201983 https://www.syngoportal.org
GeneOverlap v.1.32.0 Shen et al., 202284 https://bioconductor.org/packages/release/bioc/html/GeneOverlap.html
RNA hyper-editing v.1 Porath et al., 201421 https://github.com/hagitpt/Hyper-editing
miRANDA v.3.3 Betel etal., 201085 https://bioweb.pasteur.fr/packages/pack@miRanda@3.3a
SpliceAI v.1.3.1 Jaganathan et al., 201986 https://github.com/Illumina/SpliceAI
SIRI v.1 Yeom etal., 202187 https://github.com/Xinglab/siri
Viennarna v.2.4.12 (RNAfold) Hofacker et al., 200388 https://github.com/ViennaRNA/ViennaRNA
fastQTL v.2.184 Ongen et al., 201689 https://github.com/francois-a/fastqtl
Coloc v2 Dobbyn etal., 201890 https://github.com/Stahl-Lab-MSSM/coloc2