ojziff / als_genome_instability

Meta-analysis of ipsc-derived motor neurons in ALS

Integrated transcriptome landscape of ALS identifies genome instability linked to TDP-43 pathology

Oliver Ziff 2023

This page contains scripts to analyse the data and reproduce the figures from the manuscript.

Manuscript link

Launch Shiny app

Workbooks

RNA-seq QC and motor neuron identities

ALS iPSN differential expression

ALS genetic subgroup expression

ALS postmortem differential expression

ALS differential splicing

Somatic mutations and gene fusions

Rmarkdown scripts for each of these workbooks can be accessed here

Data availability

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.