|
| 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.
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| |
|
| Overall design |
Two 10X Genomics single cell multiomics Grey matter brain control samples one from 2 donors.
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Access to raw fastq and bam files through https://ega-archive.org/ portal, accession ID EGAD00001008457 .
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| |
|
| 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)
|
|
| This SubSeries is part of SuperSeries: |
| GSE166179 |
A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis |
|
| Relations |
| BioProject |
PRJNA795471 |
| 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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