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ALS_Pathways

Cell types associated to ALS

snRNA/scRNA-seq datasets used in our paper

Saez-Atienzar et al. Genetic analysis of amyotrophic lateral sclerosis identifies contributing pathways and cell types. Sci Adv. 2021 Jan 15;7(3):eabd9036. doi: 10.1126/sciadv.abd9036.

  1. Human frontal Cortex snRNA-seq dataset. It was generated by Rebekah L. Langston and Mark R. Cookson and deposited by them under GEO accession number GSE163323. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE163323

  2. Human Motor Cortex snRNA-seq. The gene expression matrix was downloaded from the Human M1 10× dataset from Allen Brain Map (http://portal.brain-map.org/atlases-and-data/rnaseq/human-m1-10x).

  3. Human frontal cortex and hippocampus snRNA-seq. The specificity matrix was directly downloaded from https://github.com/RHReynolds/MarkerGenes/tree/master/specificity_matrices. Original ref (1).

  4. Mouse lumbar spinal cord snRNA-seq. Raw data were downloaded from GEO accession number GSE103892. https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE103892. Original ref (2).

  5. Mouse brain scRNA-seq superset. The specificity matrix was downloaded directly from the original paper. Original ref (3)

(1) Habib N, Avraham-Davidi I, Basu A, Burks T, Shekhar K, Hofree M, Choudhury SR, Aguet F, Gelfand E, Ardlie K, Weitz DA, Rozenblatt-Rosen O, Zhang F, Regev A. Massively parallel single-nucleus RNA-seq with DroNc-seq. Nat Methods. 2017 Oct;14(10):955-958. doi: 10.1038/nmeth.4407. Epub 2017 Aug 28. PMID: 28846088; PMCID: PMC5623139.

(2) Sathyamurthy A, Johnson KR, Matson KJE, Dobrott CI, Li L, Ryba AR, Bergman TB, Kelly MC, Kelley MW, Levine AJ. Massively Parallel Single Nucleus Transcriptional Profiling Defines Spinal Cord Neurons and Their Activity during Behavior. Cell Rep. 2018 Feb 20;22(8):2216-2225. doi: 10.1016/j.celrep.2018.02.003. PMID: 29466745; PMCID: PMC5849084.

(3) Skene NG, Bryois J, Bakken TE, Breen G, Crowley JJ, Gaspar HA, Giusti-Rodriguez P, Hodge RD, Miller JA, Muñoz-Manchado AB, O'Donovan MC, Owen MJ, Pardiñas AF, Ryge J, Walters JTR, Linnarsson S, Lein ES; Major Depressive Disorder Working Group of the Psychiatric Genomics Consortium, Sullivan PF, Hjerling-Leffler J. Genetic identification of brain cell types underlying schizophrenia. Nat Genet. 2018 Jun;50(6):825-833. doi: 10.1038/s41588-018-0129-5. Epub 2018 May 21. PMID: 29785013; PMCID: PMC6477180.