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Series GSE193240 Query DataSets for GSE193240
Status Public on Jan 28, 2022
Title A primed immune transcriptional programme is activated in oligodendroglia in multiple sclerosis [ATAC-Seq and RNA-Seq II]
Organism Homo sapiens
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 Grey matter brain control samples one from 2 donors.
Access to raw fastq and bam files through portal, accession ID EGAD00001008457 .
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)
GPL24676 Illumina NovaSeq 6000 (Homo sapiens)
Samples (4)
GSM5777208 PD003 Expression
GSM5777209 PD004 Expression
GSM5777210 PD003 Chromatin accessibility
This SubSeries is part of SuperSeries:
GSE166179 A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis
BioProject PRJNA795471

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

Supplementary file Size Download File type/resource
GSE193240_HS_GM_Ctrl_multiomics_UCSC.rds.gz 893.3 Mb (ftp)(http) RDS
GSE193240_PD003_atac_HS_Ctr_roche_ASTRO_RND.wig.gz 17.7 Mb (ftp)(http) WIG
GSE193240_PD003_atac_HS_Ctr_roche_EXCNEU_RND.wig.gz 74.6 Mb (ftp)(http) WIG
GSE193240_PD003_atac_HS_Ctr_roche_INHNEU_RND.wig.gz 36.5 Mb (ftp)(http) WIG
GSE193240_PD003_atac_HS_Ctr_roche_MIGL_RND.wig.gz 19.9 Mb (ftp)(http) WIG
GSE193240_PD003_atac_HS_Ctr_roche_OLIGO_RND.wig.gz 19.9 Mb (ftp)(http) WIG
GSE193240_PD003_atac_HS_Ctr_roche_OPC_RND.wig.gz 29.8 Mb (ftp)(http) WIG
GSE193240_PD003_atac_fragments.tsv.gz 2.3 Gb (ftp)(http) TSV
GSE193240_PD003_atac_fragments.tsv.gz.tbi.gz 1.1 Mb (ftp)(http) TBI
GSE193240_PD003_filtered_feature_bc_matrix.h5 87.5 Mb (ftp)(http) H5
GSE193240_PD003_gex_molecule_info.h5 487.7 Mb (ftp)(http) H5
GSE193240_PD003_raw_feature_bc_matrix.h5 120.1 Mb (ftp)(http) H5
GSE193240_PD004_atac_HS_Ctr_roche_ASTRO_RND.wig.gz 24.0 Mb (ftp)(http) WIG
GSE193240_PD004_atac_HS_Ctr_roche_EXCNEU_RND.wig.gz 71.8 Mb (ftp)(http) WIG
GSE193240_PD004_atac_HS_Ctr_roche_INHNEU_RND.wig.gz 37.0 Mb (ftp)(http) WIG
GSE193240_PD004_atac_HS_Ctr_roche_MIGL_RND.wig.gz 27.8 Mb (ftp)(http) WIG
GSE193240_PD004_atac_HS_Ctr_roche_OLIGO_RND.wig.gz 17.3 Mb (ftp)(http) WIG
GSE193240_PD004_atac_HS_Ctr_roche_OPC_RND.wig.gz 33.2 Mb (ftp)(http) WIG
GSE193240_PD004_atac_fragments.tsv.gz 2.1 Gb (ftp)(http) TSV
GSE193240_PD004_atac_fragments.tsv.gz.tbi.gz 1.1 Mb (ftp)(http) TBI
GSE193240_PD004_filtered_feature_bc_matrix.h5 84.5 Mb (ftp)(http) H5
GSE193240_PD004_gex_molecule_info.h5 381.5 Mb (ftp)(http) H5
GSE193240_PD004_raw_feature_bc_matrix.h5 112.6 Mb (ftp)(http) H5
GSE193240_atac_HS_Celltypes_GMCtr_fc4.hg38.AnnotatePeaks.bed.gz 2.3 Mb (ftp)(http) BED
GSE193240_atac_HS_Ctr_roche_ASTRO.bam.broad_peaks.broadPeak.bed.gz 268.9 Kb (ftp)(http) BED
GSE193240_atac_HS_Ctr_roche_ASTRO_RND.wig.gz 41.2 Mb (ftp)(http) WIG
GSE193240_atac_HS_Ctr_roche_ENDO.bam.broad_peaks.broadPeak.bed.gz 340.6 Kb (ftp)(http) BED
GSE193240_atac_HS_Ctr_roche_EXCNEU.bam.broad_peaks.broadPeak.bed.gz 323.6 Kb (ftp)(http) BED
GSE193240_atac_HS_Ctr_roche_EXCNEU_RND.wig.gz 144.8 Mb (ftp)(http) WIG
GSE193240_atac_HS_Ctr_roche_INHNEU.bam.broad_peaks.broadPeak.bed.gz 395.7 Kb (ftp)(http) BED
GSE193240_atac_HS_Ctr_roche_INHNEU_RND.wig.gz 72.9 Mb (ftp)(http) WIG
GSE193240_atac_HS_Ctr_roche_MIGL.bam.broad_peaks.broadPeak.bed.gz 517.9 Kb (ftp)(http) BED
GSE193240_atac_HS_Ctr_roche_MIGL_RND.wig.gz 19.9 Mb (ftp)(http) WIG
GSE193240_atac_HS_Ctr_roche_OLIGO.bam.broad_peaks.broadPeak.bed.gz 308.6 Kb (ftp)(http) BED
GSE193240_atac_HS_Ctr_roche_OLIGO_RND.wig.gz 36.2 Mb (ftp)(http) WIG
GSE193240_atac_HS_Ctr_roche_OPC.bam.broad_peaks.broadPeak.bed.gz 457.6 Kb (ftp)(http) BED
GSE193240_atac_HS_Ctr_roche_OPC_RND.wig.gz 61.7 Mb (ftp)(http) WIG
GSE193240_peak2GeneLinks_ALL_GMCTR_roche_CtrMS_multiomics_08.bedpe.gz 784.1 Kb (ftp)(http) BEDPE
Processed data are available on Series record
Raw data not provided for this record

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