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.
Single Cell Transcriptomics and Epigenomics
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
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 Epigenomics
Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag
Dataset "Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag"
Dataset via USCS Cell Browser.
This dataset accompanies the manuscript below. This dataset features simultaneous mapping of three epigenomic modalities, H3K27ac, H3K27me3 and ATAC at single-cell resolution using nanobody-Tn5 fusion proteins in several neural lineages (with a focus on the oligodendrocyte lineage), from the juvenile mouse brain.
Multimodal chromatin profiling using nanobody-based single-cell CUT&Tag
Marek Bartosovic & Gonçalo Castelo-Branco
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, mouse ES cells, mouse 3T3 cells and mouse Oli-neu cells.
Single-cell CUT&Tag profiles histone modifications and transcription factors in complex tissues.
Bartosovic M, Kabbe M, Castelo-Branco G
Nat Biotechnol 2021 Apr;():
Access the article via SharedIT
Single Cell Transcriptomics
Single-cell RNA-Seq of ventrally and dorsally derived oligodendrocyte lineage in the adult corpus callosum
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
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 different responses to spinal cord injury.
Floriddia EM, Lourenço T, Zhang S, van Bruggen D, Hilscher MM, Kukanja P, et al
Nat Commun 2020 11;11(1):5860
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
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
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
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
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.