OligoInternode

Our group has generated web resources from our single-cell and bulk transcriptomic and epigenomic datasets, where you can enter your gene of interest and investigate its expression pattern in the identified oligodendrocyte lineage populations/states, how your gene of interest is differentially expressed or the chromatin landscape in regulatory regions surrounding your gene of interest.

Artwork from Gonçalo Castelo-Branco’s laboratory. Illustrator: Amagoia Agirre
Illustrator: Amagoia Agirre.

Single Cell Epigenomics

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

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

This dataset accompanies the manuscript below. This dataset features single-cell ATAC-Seq data of the oligodendrocyte lineage from the spinal cord of mice induced with experimental autoimmune encephalomyelitis (EAE), which mimics several aspects of MS.

A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis
Mandy Meijer*, Eneritz Agirre*, Mukund Kabbe, Cassandra A. van Tuijn, Abeer Heskol, Ana Mendanha Falcão, M.Ryan Corces, Thomas J. Montine, Xingqi Chen, Howard Y. Chang, and Gonçalo Castelo-Branco

Single-cell Cut&Tag of histone modifications and transcription factors in the mouse brain

Dataset "Single-cell Cut&Tag of histone modifications and transcription factors in the mouse brain"

This dataset accompanies the manuscript below. This dataset features single-cell Cut&Tag data of H3K4me3, H3K27ac, H3K27me3, H3K36me3, Olig2 and Rad21 in several neural lineages (with a focus on the oligodendrocyte lineage), from the juvenile mouse brain.

Single-cell profiling of histone modifications in the mouse brain
Marek Bartosovic, Mukund Kabbe and Gonçalo Castelo-Branco

Single Cell Transcriptomics

Single-cell RNA-Seq of ventrally and dorsally derived oligodendrocyte lineage in the adult corpus callosum

Datasets "Corpus callosum dataset (Chromium Single Cell A Chip kit v2)"

This dataset accompanies the manuscript below, deposit in BioRxiv, and features single-cell RNA-Seq (10x Genomics 3’ libraries) of ventrally (eGFP+) and dorsally (TdTom+) derived OL lineage cells from the P60 corpus callosum of Emx1::Cre-Sox10::GFP-TdTom mice.

Single-cell RNA-Seq of oligodendrocyte lineage following traumatic spinal cord injury

Dataset "Spinal cord injury dataset (Chromium Single Cell A Chip kit v3)"

This dataset accompanies the manuscript below, deposit in BioRxiv, and features single-cell RNA-Seq (10x Genomics 3’ libraries) of OL lineage from Sox10::Cre-GFP mice following traumatic spinal cord injury (dorsal funiculi transection). GFP sorted cell from the injury site, regions of Wallerian degeneration rostral and caudal to injury and thoracic spinal cord segments from laminectomy control were analysed.

Distinct oligodendrocyte populations have spatial preference and injury-specific responses
Elisa M. Floriddia, Shupei Zhang, David van Bruggen, João P. Gonçalves dos Santos, Müge Altinkök, Enric Llorens-Bobadilla, Jonas Frisén, Gonçalo Castelo-Branco

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
Roberta Marisca1,3,#, Tobias Hoche1,#, Eneritz Agirre4, Laura Jane Hoodless1, Wenke Barkey1, Franziska Auer1,3, Gonçalo Castelo-Branco4,5, Tim Czopka1,2,3,*, Nature Neuroscience 2020

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"

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
Sarah Jäkel†, Eneritz Agirre†, Ana Mendanha Falcão, David van Bruggen, Ka Wai Lee, Irene Knuesel, Dheeraj Malhotra, Charles ffrench-Constant*, Anna Williams*, Gonçalo Castelo-Branco*
Nature, online 23 januari 2019

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

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

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
Ana Mendanha Falcão* David van Bruggen*, Sueli Marques, Eneritz Agirre, Mandy Meijer, Sarah Jäkel, André Ortlieb Guerreiro-Cacais, Darya Vanichkina, Elisa M. Floriddia, Charles ffrench-Constant, Anna Williams, Gonçalo Castelo-Branco
Nature Medicine, 2018, in press

Single-cell RNA-Seq of OPCs throughout mouse development

Dataset "OPCs throughout mouse development"

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 the oligodendrocyte lineage progenitors during development
Sueli Marques, David van Bruggen, Darya Vanichkina, Elisa M. Floriddia, Hermany Munguba, Leif Väremo, Stefania Giacomello, Ana Mendanha Falcão, Mandy Meijer, Åsa K. Björklund, Jens Hjerling-Leffler, Ryan J. Taft, Gonçalo Castelo-Branco

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

Dataset "Oligodendrocyte lineage"

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:

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