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| Status |
Public on Jan 28, 2022 |
| Title |
A primed immune transcriptional programme is activated in oligodendroglia in multiple sclerosisn [RNA-Seq] |
| Organism |
Mus musculus |
| Experiment type |
Expression 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 |
We have performed bulk RNA-seq of Stat1 and Bach1 transcription factors knockdown upon IFNG treatment in primary OPCs.
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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 |
| |
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| Platforms (1) |
| GPL24247 |
Illumina NovaSeq 6000 (Mus musculus) |
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| Samples (32)
|
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| This SubSeries is part of SuperSeries: |
| GSE166179 |
A primed immune transcriptional program is activated in oligodendroglia in multiple sclerosis |
|
| Relations |
| BioProject |
PRJNA795465 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE193236_Bach1_Ctrl_DGE_edgeR_table_Gene_res.csv.gz |
1.4 Mb |
(ftp)(http) |
CSV |
| GSE193236_Bach1_IFNg_DGE_edgeR_table_Gene_res.csv.gz |
1.5 Mb |
(ftp)(http) |
CSV |
| GSE193236_Ctrl_STAT1_B_merged.peaks.wig.gz |
31.6 Mb |
(ftp)(http) |
WIG |
| GSE193236_IFNg_STAT1_B_merged.peaks.wig.gz |
14.7 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1015_S64_fwd_rpkm.wig.gz |
29.4 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1015_S64_rev_rpkm.wig.gz |
28.5 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1016_S65_fwd_rpkm.wig.gz |
31.8 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1016_S65_rev_rpkm.wig.gz |
31.0 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1017_S66_fwd_rpkm.wig.gz |
19.5 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1017_S66_rev_rpkm.wig.gz |
18.8 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1018_S67_fwd_rpkm.wig.gz |
36.0 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1018_S67_rev_rpkm.wig.gz |
35.2 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1021_S70_fwd_rpkm.wig.gz |
21.2 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1021_S70_rev_rpkm.wig.gz |
20.5 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1022_S71_fwd_rpkm.wig.gz |
22.5 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1022_S71_rev_rpkm.wig.gz |
21.7 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1023_S72_fwd_rpkm.wig.gz |
18.6 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1023_S72_rev_rpkm.wig.gz |
17.8 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1024_S73_fwd_rpkm.wig.gz |
15.3 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1024_S73_rev_rpkm.wig.gz |
14.8 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1027_S76_fwd_rpkm.wig.gz |
17.8 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1027_S76_rev_rpkm.wig.gz |
17.2 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1028_S77_fwd_rpkm.wig.gz |
11.5 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1028_S77_rev_rpkm.wig.gz |
11.1 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1029_S78_fwd_rpkm.wig.gz |
13.6 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1029_S78_rev_rpkm.wig.gz |
13.1 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1030_S79_fwd_rpkm.wig.gz |
12.9 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1030_S79_rev_rpkm.wig.gz |
12.5 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1033_S82_fwd_rpkm.wig.gz |
25.7 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1033_S82_rev_rpkm.wig.gz |
24.9 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1034_S83_fwd_rpkm.wig.gz |
25.2 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1034_S83_rev_rpkm.wig.gz |
24.4 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1035_S84_fwd_rpkm.wig.gz |
26.4 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1035_S84_rev_rpkm.wig.gz |
25.5 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1036_S85_fwd_rpkm.wig.gz |
28.9 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1036_S85_rev_rpkm.wig.gz |
27.9 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1039_S88_fwd_rpkm.wig.gz |
18.6 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1039_S88_rev_rpkm.wig.gz |
17.9 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1040_S89_fwd_rpkm.wig.gz |
19.4 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1040_S89_rev_rpkm.wig.gz |
18.6 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1043_S92_fwd_rpkm.wig.gz |
21.3 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1043_S92_rev_rpkm.wig.gz |
20.3 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1044_S93_fwd_rpkm.wig.gz |
14.0 Mb |
(ftp)(http) |
WIG |
| GSE193236_P21206_1044_S93_rev_rpkm.wig.gz |
13.7 Mb |
(ftp)(http) |
WIG |
| GSE193236_Stat1_Ctrl_DGE_edgeR_table_Gene_res.csv.gz |
1.5 Mb |
(ftp)(http) |
CSV |
| GSE193236_Stat1_IFNg_DGE_edgeR_table_Gene_res.csv.gz |
1.5 Mb |
(ftp)(http) |
CSV |
| GSE193236_s210506M1_fwd_RPKM.wig.gz |
31.3 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210506M1_rev_RPKM.wig.gz |
29.9 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210506M2_fwd_RPKM.wig.gz |
32.4 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210506M2_rev_RPKM.wig.gz |
30.9 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210506M5_fwd_RPKM.wig.gz |
18.8 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210506M5_rev_RPKM.wig.gz |
17.9 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210506M6_fwd_RPKM.wig.gz |
27.9 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210506M6_rev_RPKM.wig.gz |
17.9 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210511M1_fwd_RPKM.wig.gz |
16.1 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210511M1_rev_RPKM.wig.gz |
15.3 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210511M2_fwd_RPKM.wig.gz |
8.4 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210511M2_rev_RPKM.wig.gz |
8.1 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210511M7_fwd_RPKM.wig.gz |
19.6 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210511M7_rev_RPKM.wig.gz |
18.7 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210511M8_fwd_RPKM.wig.gz |
29.4 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210511M8_rev_RPKM.wig.gz |
28.2 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210526M1_fwd_RPKM.wig.gz |
29.2 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210526M1_rev_RPKM.wig.gz |
28.1 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210526M2_fwd_RPKM.wig.gz |
31.9 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210526M2_rev_RPKM.wig.gz |
30.8 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210526M5_fwd_RPKM.wig.gz |
24.1 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210526M5_rev_RPKM.wig.gz |
23.1 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210526M6_fwd_RPKM.wig.gz |
37.8 Mb |
(ftp)(http) |
WIG |
| GSE193236_s210526M6_rev_RPKM.wig.gz |
36.5 Mb |
(ftp)(http) |
WIG |
| GSE193236_siBach1_Control_merged.bam.sorted.bam.fwd.bam.RPKM.wig.gz |
40.2 Mb |
(ftp)(http) |
WIG |
| GSE193236_siBach1_Control_merged.bam.sorted.bam.rev.bam.RPKM.wig.gz |
39.1 Mb |
(ftp)(http) |
WIG |
| GSE193236_siBach1_IFNg_merged.bam.sorted.bam.fwd.bam.RPKM.wig.gz |
35.5 Mb |
(ftp)(http) |
WIG |
| GSE193236_siBach1_IFNg_merged.bam.sorted.bam.rev.bam.RPKM.wig.gz |
49.6 Mb |
(ftp)(http) |
WIG |
| GSE193236_siStat1_Ctr_merged.bam.fwd.bam.RPKM.wig.gz |
39.4 Mb |
(ftp)(http) |
WIG |
| GSE193236_siStat1_Ctr_merged.bam.rev.bam.RPKM.wig.gz |
37.9 Mb |
(ftp)(http) |
WIG |
| GSE193236_siStat1_IFNg_merged.bam.fwd.bam.RPKM.wig.gz |
50.9 Mb |
(ftp)(http) |
WIG |
| GSE193236_siStat1_IFNg_merged.bam.rev.bam.RPKM.wig.gz |
49.2 Mb |
(ftp)(http) |
WIG |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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