OligoInternode
Our group has generated web resources from our single-cell, bulk and spatial transcriptomic and epigenomic datasets, where one can enter your gene of interest and investigate its expression pattern in the identified populations and cell states, including the oligodendrocyte lineage. One can explore how a gene of interest is differentially expressed or the chromatin landscape in regulatory regions surrounding your gene of interest.
Spatial Transcriptomics and Epigenomics
Dataset: Single cell-resolution in situ sequencing of spinal cords of the EAE mouse model of MS and human MS spinal cord
- All datasets via
These spatial datasets accompany the manuscript below, in collaboration with Prof. Mats Nilsson, Stockholm University. They feature single-cell spatial expression profiling using In situ sequencing characterising the spatio-temporal dynamics of major cellular subtypes in EAE and MS spinal cord archival tissue (in this case using the Xenium in situ sequencing platform from 10X Genomics).
C. M. Langseth*, P. Kukanja*, L. A. Rubio RodrÃguez-Kirby, E. Agirre, A. Raman, C. Yokota, C. Avenel, K. Tiklová, A. O. Guerreiro-Cacais, T. Olsson, M. M. Hilscher, M. Nilsson,* G. Castelo-Branco*
Dataset: Spatial epigenome–transcriptome of mouse embryo E13.5, mouse juvenile brain (P22) and human adult hippocampus
- All datasets via
- All datasets via
These spatial datasets accompanies the manuscript below, in collaboration with , Yale University, US. They feature dBit-Seq, profiling simultaneously RNA and chromatin accessibility (ATAC), or RNA and CUT&Tag (for H3K27me3 (repressive mark), H3K4me3 (active mark) of H3K27ac (active mark), in several complex tissues.
Di Zhang, Yanxiang Deng, Petra Kukanja, Eneritz Agirre, Marek Bartosovic, Mingze Dong, Cong Ma, Sai Ma, Graham Su, Shuozhen Bao, Yang Liu, Yang Xiao, Gorazd B. Rosoklija, Andrew J. Dwork, J. John Mann, Kam W. Leong, Maura Boldrini, Liya Wang, Maximilian Haeussler, Benjamin J. Raphael, Yuval Kluger, Gonçalo Castelo-Branco*, Rong Fan*
Nature 616, 113–122 (2023).
Dataset: Spatial chromatin accessibility of mouse embryo E13.5, mouse juvenile brain and human adult hippocampus
All datasets via
These spatial datasets accompanies the manuscript below, in collaboration with at Yale University. We have implemented ATAC-Seq at a spatial level, probing chromatin accessibility at a spatial level in complex tissue.
Deng Y, Bartosovic M, Ma S, Zhang D, Kukanja P, Xiao Y, Su G, Liu Y, Qin X, Rosoklija GB, Dwork AJ, Mann JJ, Xu ML, Halene S, Craft JE, Leong KW, Boldrini M, Castelo-Branco G, Fan R
Nature 2022 Sep;609(7926):375-383
Dataset: Spatially resolved chromatin modification profiling of mouse embryo E13.5 and mouse juvenile brain
All datasets via
These spatial datasets accompanies the manuscript below, in collaboration with at Yale University. We have implemented CUT&Tag (for H3K27me3 (repressive mark) and H3K4me3 (active mark)) at a spatial level, probing different histone modifications in complex tissues.
Deng Y, Bartosovic M, Kukanja P, Zhang D, Liu Y, Su G, Enninful A, Bai Z, Castelo-Branco G, Fan R
Science 2022 Feb;375(6581):681-686
Single Cell Transcriptomics and Epigenomics
Single-cell RNA-Seq and ATAC-Seq of human forebrain (PCW 7-11)
Dataset:
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.
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:
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All datasets via
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Data via 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.
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 ""
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.
Bartosovic M, Castelo-Branco G
Nat Biotechnol 2022 Dec;():
Single-cell Cut&Tag of histone modifications and transcription factors in the mouse brain
Dataset ""
Dataset via
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.
Bartosovic M, Kabbe M, Castelo-Branco G
Nat Biotechnol 2021 Apr;():
Single Cell Transcriptomics
Single-cell RNA-Seq of ventrally and dorsally derived oligodendrocyte lineage in the adult corpus callosum
Datasets ""
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 ""
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.
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 ""
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 .
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"
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)
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"
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.
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"
This dataset accompanies the manuscript below, and published in 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.
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"
This dataset accompanies the manuscript below, published in . 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 .
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 .