OligoInternode

Single Cell Transcriptomics and Epigenomics

Single-cell RNA-Seq and ATAC-Seq of human forebrain (PCW 7-11)

Dataset: Single-cell RNA-Seq and ATAC-Seq of human forebrain (PCW 7-11)

This dataset accompanies the manuscript below. This dataset features single-cell RNA-Seq of ATAC-Seq data of  the human forebrain at post conceptual weeks (PCW) 8 to 10 and single-cell ATAC-Seq of the human forebrain PCW 8.5-11.

Developmental landscape of human forebrain at a single-cell level unveils early waves of oligodendrogenesis
David van Bruggen, Fabio Pohl, Christoffer Mattsson Langseth, Petra Kukanja, HowerLee, Mukund Kabbe, Mandy Meijer, Markus M. Hilscher, Mats Nilsson, Erik Sundström, Gonçalo Castelo-Branco

Single-cell ATAC-Seq and scRNA/ATAC multiome of oligodendroglia in a mouse model of multiple sclerosis and in human grey matter

Datasets via ShinyApps:

• Dataset scATAC-Seq oligodendroglia mouse EAE
• Dataset scATAC-seq multiome oligodendroglia mouse EAE
• Dataset scRNA-seq multiome oligodendroglia mouse EAE
• Dataset scATAC-seq multiome human grey matter
• Dataset scRNA-seq multiome human grey matter

All datasets via UCSC Cell Browser

IGV sessions and code.

Data via GEO and EGA accession EGAS00001005911

These datasets accompany the manuscript below. These datasets feature single-cell ATAC-Seq and scRNA/ATAC multiome data of the oligodendrocyte lineage from the spinal cord of mice induced with experimental autoimmune encephalomyelitis (EAE), which mimics several aspects of MS. It also includes scRNA/ATAC multiome data of human grey matter.

­Epigenomic priming of immune genes implicates oligodendroglia in multiple sclerosis susceptibility
Mandy Meijer*, Eneritz Agirre*, Mukund Kabbe, Cassandra A. van Tuijn, Abeer Heskol, Chao Zheng, Ana Mendanha Falcão, Marek Bartosovic, Leslie Kirby, Daniela Calini, Michael R. Johnson, M. Ryan Corces, Thomas J. Montine, Xingqi Chen, Howard Y. Chang, Dheeraj Malhotra, and Gonçalo Castelo-Branco
Neuron 2022 doi: 10.1016/j.neuron.2021.12.034

Single-cell RNA-Seq of oligodendrocyte lineage in zebrafish

Dataset "Oligodendrocyte lineage in zebrafish"

This dataset accompanies the manuscript below, and features single-cell RNA-Seq from fluorescence activated cell sorting of Tg(olig1:memEYFP) zebrafish at 5 days post fertilisation, performed in collaboration between our lab and Tim Czopka’s lab.

Functionally distinct subgroups of oligodendrocyte precursor cells integrate neural activity and execute myelin formation.
Marisca R, Hoche T, Agirre E, Hoodless LJ, Barkey W, Auer F, Castelo-Branco G, Czopka T
Nat Neurosci 2020 Mar;23(3):363-374

Single nuclei RNA- sequencing from the white matter of individuals with progressive MS and non-neurological controls

Dataset "Single nuclei RNA- sequencing from the white matter of individuals with progressive MS and non-neurological controls"

• via Shinyapp
• via UCSC Cell Browser

This dataset accompanies the manuscript below, and features the CCA alignment clustering of white matter tissue from 4 progressive Multiple sclerosis patients different lesions and 5 non neurological controls from the manuscript (Jäkel & Agirre et. al., Altered human oligodendrocyte heterogeneity in multiple sclerosis)

Altered human oligodendrocyte heterogeneity in multiple sclerosis.
Jäkel S, Agirre E, Mendanha Falcão A, van Bruggen D, Lee KW, Knuesel I, Malhotra D, Ffrench-Constant C, Williams A, Castelo-Branco G
Nature 2019 Feb;566(7745):543-547

Single-cell RNA-Seq of oligodendrocyte lineage in a mouse model of multiple sclerosis

Dataset "Oligodendrocyte lineage in a mouse model of multiple sclerosis"

• via Shinyapp 
• via UCSC Cell Browser 

This dataset accompanies the manuscript below, published in Nature Medicine 2018. This dataset features single-cell transcriptomics data (SmartSeq2) of the oligodendrocyte lineage from the spinal cord of mice induced with experimental autoimmune encephalomyelitis (EAE), which mimics several aspects of MS.

Disease-specific oligodendrocyte lineage cells arise in multiple sclerosis.
Falcão AM, van Bruggen D, Marques S, Meijer M, Jäkel S, Agirre E, Samudyata , Floriddia EM, Vanichkina DP, Ffrench-Constant C, Williams A, Guerreiro-Cacais AO, Castelo-Branco G
Nat Med 2018 Dec;24(12):1837-1844

Single-cell RNA-Seq of OPCs throughout mouse development

Dataset "OPCs throughout mouse development"
via Shinyapp
via UCSC Cell Browser 

This dataset accompanies the manuscript below, deposited in BioRxiv and published in Developmental Cell in 2018. This dataset features bulk-RNA-seq data and single-cell transcriptomics data of time points E13.5, P7, and juvenile and adult mice, using STRT-Seq.

Transcriptional Convergence of Oligodendrocyte Lineage Progenitors during Development.
Marques S, van Bruggen D, Vanichkina DP, Floriddia EM, Munguba H, Väremo L, Giacomello S, Falcão AM, Meijer M, Björklund ÅK, Hjerling-Leffler J, Taft RJ, Castelo-Branco G
Dev Cell 2018 Aug;46(4):504-517.e7

Single-cell RNA-Seq of oligodendrocyte lineage in the juvenile and adult mouse CNS

Dataset "Oligodendrocyte lineage"
via Linnarsson’s lab interface 
via UCSC Cell Browser

This dataset accompanies the manuscript below, published in Science 2016. This dataset features single-cell transcriptomics data of juvenile and adult central nervous system, covering 10 different regions and approximately 5 thousands cells of the oligodendrocyte lineage, using STRT-Seq. The data and web resource was produced in collaboration with Sten Linnarsson’s lab.

Oligodendrocyte heterogeneity in the mouse juvenile and adult central nervous system.
Marques S, Zeisel A, Codeluppi S, van Bruggen D, Mendanha Falcão A, Xiao L, et al
Science 2016 Jun;352(6291):1326-1329

We also recommend the following resources from Sten Linnarsson’s lab, which provide extraordinary insights of cells lineages in the CNS at a single cell level, including oligodendrocyte lineage:

• Molecular architecture of the mouse nervous system
• Single-cell analysis of mouse cortex

And the pioneering resource from Ben Barres’s lab with bulk RNA-Seq.