Oliver Ziff 2023
This page contains scripts to analyse the data and reproduce the figures from the manuscript.
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RNA-seq QC and motor neuron identities
ALS iPSN differential expression
ALS genetic subgroup expression
ALS postmortem differential expression
Somatic mutations and gene fusions
Rmarkdown scripts for each of these workbooks can be accessed here
Raw RNA sequencing fastq files were accessed for each of the iPS motor-neuron datasets in this table:
| Reference | Accession # | Mutation | ALS n | Control n | Library type | Paper URL |
|---|---|---|---|---|---|---|
| Sareen et al, 2013 | GSE52202 | C9orf72 | 4 | 4 | polyA | https://www.ncbi.nlm.nih.gov/pubmed/24154603 |
| Kiskinis et al, 2014 | GSE54409 | SOD1 | 2 | 3 | polyA | https://www.ncbi.nlm.nih.gov/pubmed/24704492 |
| Kapeli et al, 2016 | GSE77702 | FUS | 3 | 2 | polyA | https://www.ncbi.nlm.nih.gov/pubmed/27378374 |
| Wang et al, 2017 | GSE95089 | SOD1 | 2 | 2 | polyA | https://pubmed.ncbi.nlm.nih.gov/28401346/ |
| De Santis et al, 2017 | GSE94888 | FUS | 3 | 3 | Ribo-zero | https://www.ncbi.nlm.nih.gov/pubmed/28988989 |
| Bhinge et al, 2017 | PRJNA361408 | SOD1 | 2 | 2 | Ribo-zero | https://pubmed.ncbi.nlm.nih.gov/28366453/ |
| Luisier et al, 2018 | GSE98290 | VCP | 3 | 3 | polyA | https://pubmed.ncbi.nlm.nih.gov/29789581/ |
| Abo-Rady et al, 2020 | GSE143743 | C9orf72 | 3 | 3 | polyA | https://pubmed.ncbi.nlm.nih.gov/32084385/ |
| Dafinca et al. 2020 | GSE139144 | C9orf72 | 4 | 8 | polyA | https://pubmed.ncbi.nlm.nih.gov/32330447/ |
| GSE147544 | TARDBP | 6 | 4 | |||
| Catanese et al., 2021 | GSE168831 | C9orf72 | 6 | 6 | polyA | https://pubmed.ncbi.nlm.nih.gov/34125498/ |
| FUS | 6 | |||||
| Smith et al, 2021 | PRJEB47567 | TARDBP | 3 | 2 | polyA | https://pubmed.ncbi.nlm.nih.gov/34660586/ |
| Hawkins et al, 2022 | GSE203168 | FUS | 2 | 2 | Ribo-zero | https://pubmed.ncbi.nlm.nih.gov/35750046/ |
| Sommer et al, 2022 | GSE201407 | C9orf72 | 6 | 6 | polyA | https://pubmed.ncbi.nlm.nih.gov/35774867/ |
| NeuroLINCS, 2022 | phs001231.v2.p1 | sporadic | 8 | 14 | Ribo-zero | https://pubmed.ncbi.nlm.nih.gov/34746695/ |
| SOD1 | 6 | |||||
| C9orf72 | 16 | |||||
| Answer ALS, 2022 | AnswerALS data portal | sporadic | 200 | 42 | Ribo-zero | https://pubmed.ncbi.nlm.nih.gov/35115730/ |
| C9orf72 | 21 | |||||
| SOD1 | 8 | |||||
| 6 other ALS mutations | 9 |
Post-mortem raw sequencing data is accessible at GSE137810 and https://collaborators.nygenome.org/.
Raw fastq files were downloaded with nf-core/fetchngs v1.9 and processed with nf-core/rnaseq v3.9 utilising alignment with STAR and read quantification with salmon.
Differential gene expression was performed using DESeq2 contrasting ALS versus control, adjusting for dataset and sex batch effects.
Differential splicing was analysed with MAJIQ v2.4 contrasting ALS versus control, adjusting for dataset and sex batch effects.
Variant analysis was performed using nf-core/rnavar v1.0.0, which is based on GATK v4.2.6 short variant discovery workflow. Adjustment for read coverage and age were performed.
RNA fusion analysis was performed on paired-end datasets using nf-core/rnafusion v2.0.0, utilising the STAR-Fusion workflow. Adjustment was made for dataset, read coverage and age.
Schematics were created using BioRender.