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Series GSE193238 Query DataSets for GSE193238
Status Public on Jan 28, 2022
Title A primed immune transcriptional programme is activated in oligodendroglia in multiple sclerosis [ATAC-Seq and RNA-Seq]
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Genome binding/occupancy profiling by high throughput sequencing
Summary Multiple sclerosis (MS) is characterized by a targeted attack on oligodendroglia (OLG) and myelin by immune cells, which are thought to be the main drivers of MS susceptibility. We found that immune genes exhibit a primed chromatin state in single mouse and human OLG in a non-disease context, compatible with transitions to immune-competent states in MS. We identified transcription factors as BACH1 and STAT1 involved in immune gene regulation in oligodendrocyte precursor cells (OPCs). A subset of immune genes present bivalency of H3K4me3/H3K27me3 in OPCs, with Polycomb inhibition leading to their increased activation upon interferon-gamma (IFN) treatment. Some MS susceptibility single-nucleotide polymorphisms (SNPs) overlap with these regulatory regions in mouse and human OLG. Treatment of mouse OPCs with IFN leads to chromatin architecture remodeling at these loci and altered expression of interacting genes. Thus, susceptibility for MS may involve OLG, which therefore constitute novel targets for immunological-based therapies for MS.
Overall design Two 10X Genomics single cell multiomics samples one from Multiple Sclerosis mouse model, EAE (at the peak of the disease) and a control sample. From Sox10GFP+ sorted cells from adult mice spinal cords.
Contributor(s) Meijer M, Agirre E, Kabbe M, van Tuijin C, Heskol A, Mendanha Falcao A, Chen X, Chang H, Castelo-Branco G
Citation(s) 35093191
Submission date Jan 07, 2022
Last update date Jan 31, 2022
Contact name Eneritz Agirre
Organization name Karolinska Institutet
Department MBB
Lab Castelo-Branco, Molecular Neurobiology
Street address Solnavägen 9
City Stockholm
ZIP/Postal code 17165
Country Sweden
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (4)
GSM5777132 Ctr_RNA
GSM5777133 EAE_Peak_RNA
GSM5777134 Ctr_ATAC
This SubSeries is part of SuperSeries:
GSE166179 A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis
BioProject PRJNA795472

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SOFT formatted family file(s) SOFTHelp
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Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE193238_EAE_CtrlPeak_multiomics_GEO.rds.gz 951.8 Mb (ftp)(http) RDS
GSE193238_P21208_1004_MOL2_Ctr_RND2_peaks.wig.gz 14.7 Mb (ftp)(http) WIG
GSE193238_P21208_1004_MOL3_Ctr_RND2_peaks.wig.gz 13.9 Mb (ftp)(http) WIG
GSE193238_P21208_1004_MOL56_Ctr_RND1_peaks.wig.gz 16.6 Mb (ftp)(http) WIG
GSE193238_P21208_1004_MOL56_Ctr_RND2_peaks.wig.gz 15.3 Mb (ftp)(http) WIG
GSE193238_P21208_1004_MOL56_Ctr_RND3_peaks.wig.gz 15.6 Mb (ftp)(http) WIG
GSE193238_P21208_1004_OPC_Ctr_RND1_peaks.wig.gz 14.2 Mb (ftp)(http) WIG
GSE193238_P21208_1004_atac_fragments.tsv.gz 631.4 Mb (ftp)(http) TSV
GSE193238_P21208_1004_atac_fragments.tsv.gz.tbi.gz 622.3 Kb (ftp)(http) TBI
GSE193238_P21208_1004_filtered_feature_bc_matrix.h5 51.2 Mb (ftp)(http) H5
GSE193238_P21208_1004_gex_molecule_info.h5 89.7 Mb (ftp)(http) H5
GSE193238_P21208_1005_MOL12_EAE_RND1_peaks.wig.gz 24.9 Mb (ftp)(http) WIG
GSE193238_P21208_1005_MOL12_EAE_RND2_peaks.wig.gz 23.1 Mb (ftp)(http) WIG
GSE193238_P21208_1005_MOL12_EAE_RND3_peaks.wig.gz 23.7 Mb (ftp)(http) WIG
GSE193238_P21208_1005_MOL3_EAE_RND1_peaks.wig.gz 17.1 Mb (ftp)(http) WIG
GSE193238_P21208_1005_MOL3_EAE_RND2_peaks.wig.gz 19.9 Mb (ftp)(http) WIG
GSE193238_P21208_1005_MOL3_EAE_RND3_peaks.wig.gz 18.6 Mb (ftp)(http) WIG
GSE193238_P21208_1005_MOL56_EAE_RND1_peaks.wig.gz 18.5 Mb (ftp)(http) WIG
GSE193238_P21208_1005_MOL56_EAE_RND2_peaks.wig.gz 19.8 Mb (ftp)(http) WIG
GSE193238_P21208_1005_MOL56_EAE_RND3_peaks.wig.gz 19.4 Mb (ftp)(http) WIG
GSE193238_P21208_1005_MiGl_EAE_RND1_peaks.wig.gz 26.2 Mb (ftp)(http) WIG
GSE193238_P21208_1005_MiGl_EAE_RND2_peaks.wig.gz 25.5 Mb (ftp)(http) WIG
GSE193238_P21208_1005_MiGl_EAE_RND3_peaks.wig.gz 24.5 Mb (ftp)(http) WIG
GSE193238_P21208_1005_OPC_EAE_RND2_peaks.wig.gz 11.5 Mb (ftp)(http) WIG
GSE193238_P21208_1005_atac_fragments.tsv.gz 441.4 Mb (ftp)(http) TSV
GSE193238_P21208_1005_atac_fragments.tsv.gz.tbi.gz 567.4 Kb (ftp)(http) TBI
GSE193238_P21208_1005_filtered_feature_bc_matrix.h5 33.8 Mb (ftp)(http) H5
GSE193238_P21208_1005_gex_molecule_info.h5 79.8 Mb (ftp)(http) H5
GSE193238_atac_fragments.tsv.gz 972.5 Mb (ftp)(http) TSV
GSE193238_filtered_feature_bc_matrix.h5 78.6 Mb (ftp)(http) H5
GSE193238_peak2GeneLinks_ALL_EAECtr_multiomics.bedpe.gz 1.0 Mb (ftp)(http) BEDPE
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