KEY RESOURCES TABLE.
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
|
| ||
| Antibodies | ||
|
| ||
| H3K27me3 | Cell Signaling 9733S; rabbit | RRID:AB_2616029 |
| H3K4me3 | Diagenode C15410003-50; rabbit | RRID:AB_2616052 |
| H3K27ac | Abcam ab177178; rabbit | RRID:AB_2828007 |
| CTCF | Cell Signaling 3418S; rabbit | RRID:AB_2086791 |
| GAPDH | rabbit monoclonal, 5174S, Cell Signaling | RRID:AB_10622025 |
| STAT1 | Cell Signaling 14994S; rabbit, monoclonal | RRID:AB_2737027 |
| secondary antibody anti-rabbit | A6667, Sigma | RRID:AB_258307 |
| GFP | FITC conjugated, Ab6662, Abcam | RRID:AB_305635 |
|
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| Chemicals, peptides, and recombinant proteins | ||
|
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| EZH2 inhibitor EPZ011989 | Selleckchem | S7805 |
| Protein A-MNase | Schmid et al., 2004 | N/A |
|
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| Critical commercial assays | ||
|
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| emulsion of MOG35-55 peptide in complete Freud’s adjuvant | Hooke laboratories | EK-2110 |
| adult brain dissociation kit | Miltenyi | 130-107-677 |
| neural tissue dissociation kit | Miltenyi | 130-092-628 |
| Cd140a microbead kit | Miltenyi | 130-101-547 |
| Chromium Single Cell ATAC v1 Chemistry | 10× Genomics | N/A |
| Chromium Next GEM Single Cell Multiome ATAC + Gene Expression v1 | 10× Genomics | N/A |
|
| ||
| Deposited data | ||
|
| ||
| Raw sequencing data (scATAC-Seq, CUT&RUN, HiChIP, RNA-Seq, single cell multiome) | This paper | GEO: GSE166179, EGA: EGAS00001005911 |
| scRNA-Seq EAE mouse model | Falcão et al., 2019 | GEO: GSE113973 |
| Human brain snATAC-Seq | Corces et al., 2020 | GEO: GSE147672 |
|
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| Experimental models: Organisms/strains | ||
|
| ||
| Mouse: RCE: loxP | Jens Herjling-Lefler, Karolinska Institutet, Gord Fishell, Harvard Medical School | Gt(ROSA)26Sortm1.1(CAG-EGFP)Fsh in CD1 background; RRID:MMRRC_032037-JAX |
| Mouse Sox10:Cre | The Jackson Laboratory | 025807 |
|
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| Oligonucleotides | ||
|
| ||
|
Ubc qRT-PCR primers 5’-agg tca aac agg aag aca gac gta-3’ 5’-tca cac cca aga aca agc aca-3’ |
This paper | N/A |
|
b-Act qRT-PCR primers 5’-ctc tgg ctc cta gca cca tga aga-3’ 5’-gta aaa cgc agc tca gta aca gtc cg-3’ |
This paper | N/A |
|
Nlrc5 qRT-PCR primers 5’-ccg tgg tac tca cat ttg cc-3’ 5’-cct tcg aga tct ctg gga ca-3’ |
This paper | N/A |
|
Psmb8 qRT-PCR primers 5’-cct tac ctg ctt ggc acc at-3’ 5’-atg ctg cag aca cgg aga tg-3’ |
This paper | N/A |
|
H2-q7 qRT-PCR primers 5’-ata cct gca gct cgg gaa g-3’ 5’-agc acc ata aga cct ggg gt-3’ |
This paper | N/A |
|
Ciita qRT-PCR primers 5’-ctg gca cag gtc tct cca gt-3’ 5’-tac tga ggc tgc ttg aag gg-3’ |
This paper | N/A |
|
H2-aa qRT-PCR primers 5’-gct cag cct ctg tgg agg t-3’ 5’-tgt act ggc caa tgt ctc ca-3’ |
This paper | N/A |
|
H2-ab1 qRT-PCR primers 5’-gca gac aca act acg agg gg-3’ 5’-agt gtt gtg gtg gtt gag gg-3’ |
This paper | N/A |
|
Cd74 qRT-PCR primers 5’-ctg gat gaa gca gtg gct ct-3’ 5’-ccc agg cca gaa gat agg tc-3’ |
This paper | N/A |
|
Stat1 qRT-PCR primers 5’-aac atg ctg gtg aca gag cc-3’ 5’-tgc caa ctc aac acc tct ga-3’ |
This paper | N/A |
|
Bach1 qRT-PCR primers 5’-tcg aga atc gta ggc cag ac-3’ 5’-tgg cag tgt agg caa act ga-3’ |
This paper | N/A |
|
Hmox1 qRT-PCR primers 5’-gcc gag aat gct gag ttc at-3’ 5’-tcc agg gcc gtg tag ata tg-3’ |
This paper | N/A |
| SiGENOME SMARTpool siRNA Ctr 5’-uag cga cua aac aca uca a-3’ 5’-uaa ggc uau gaa gag aua c-3’ 5’-aug uau ugg ccu gua uua g-3’ 5’-aug aac gug aau ugc uca a-3’ |
Dharmacon | D-001206-13-05 |
| SiGENOME SMARTpool siRNA Stat1 5’-gga cgu ucc ugc uua gau u-3’ 5’-aca cug uga ugu uag aua a-3’ 5’-gca uag agc agg aaa uca a-3’ 5’-cca ucg agc uca cuc aga a-3’ |
Dharmacon | M-058881-02-0005 |
| SiGENOME SMARTpool siRNA Bach1 5’- gca gga gcc uug ccc gua u-3’ 5’- gag ugu ccc ugg uug ggu a-3’ 5’- aaa cua cga uua ugu cuc g-3’ 5’-cga cug ccc gcu uuc cuu u-3’ |
Dharmacon | M-042956-01-0005 |
|
| ||
| Software and algorithms | ||
|
| ||
| Cell Ranger ATAC (version 1.2.0) | 10× Genomics | https://support.10xgenomics.com/single-cell-atac/software/pipelines/1.2/what-is-cell-ranger-atac |
| Cell Ranger ARC v.2.0 | 10× Genomics | https://support.10xgenomics.com/single-cell-multiome-atac-gex/software/pipelines/latest/installation |
| DEseq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| EdgeR | Robinson et al., 2010 | https://bioconductor.org/packages/release/bioc/html/edgeR.html |
| DeeptTools | Ramírez et al., 2016 | https://deeptools.readthedocs.io/en/develop/content/installation.html |
| ComplexHeatmap | Gu etal., 2016 | https://github.com/jokergoo/ComplexHeatmap |
| EnhancedVolcano | Blighe et al., 2018. “EnhancedVolcano: Publication-ready volcano plots with enhanced colouring and labeling.” | https://github.com/kevinblighe/EnhancedVolcano |
| Bedtools | Quinlan and Hall, 2010 | https://bedtools.readthedocs.io/en/latest/ |
| Pyicos | Althammer et al., 2011 | http://regulatorygenomics.upf.edu/Software/Pyicoteo/pyicos.html |
| UpsetR | Conway et al., 2017 | https://github.com/hms-dbmi/UpSetR |
| Signac | Stuart et al., 2020 | https://satijalab.org/signac/. |
| De Bore pipeline | de Boer and Regev, 2018 | https://carldeboer.github.io/brockman.html |
| Salmon | Patro et al., 2017 | https://salmon.readthedocs.io/en/latest/index.html |
| Bowtie2 | (Langmead and Salzberg, 2012) | http://bowtie-bio.sourceforge.net/bowtie2/index.shtml |
| MACS2 | (Zhang et al., 2008) | https://github.com/macs3-project/MACS |
| chromVAR | (Schep et al., 2017) | https://greenleaflab.github.io/chromVAR/articles/Introduction.html |
| ClueGO (version 2.5.5) | (Bindea et al., 2009) | https://apps.cytoscape.org/apps/cluego |
| Cytoscape (version 3.7.2) | (Smoot et al., 2011) | https://cytoscape.org/ |
| HOMER v4.11 | (Heinz et al., 2010) | http://homer.ucsd.edu/homer/index.html |
| Cell type specific (CTS) LD score regression | (Finucane et al., 2018) | https://github.com/bulik/ldsc/wiki/Cell-type-specific-analyses |
| MAGMA v1.06 | (de Leeuw et al., 2015) | https://ctg.cncr.nl/software/magma |
| GREGOR | (Schmidt et al., 2015) | http://csg.sph.umich.edu/GREGOR/ |
| Seurat | (Butler et al., 2018) | https://github.com/satijalab/seurat |
| SAMtools | (Li et al., 2009) | http://www.htslib.org/ |
| MarkDuplicates | Picard - latest version 1.126 | http://broadinstitute.github.io/picard/ |
| STAR 2.7 | (Dobin et al., 2013) | https://github.com/alexdobin/STAR |
| Juicebox | (Robinson et al., 2018) | https://www.aidenlab.org/juicebox/ |
| ABC model | (Fulco etal., 2019) | https://github.com/broadinstitute/ABC-Enhancer-Gene-Prediction |
| ArchR | (Granja et al., 2020) | https://www.archrproject.com |
| CTS LD score regression | (Finucane et al., 2018) | https://github.com/bulik/ldsc |
| CUT&RUNTools | (Zhu et al., 2019) | https://bitbucket.org/qzhudfci/cutruntools/ |
|
| ||
| Other | ||
|
| ||
| scATAC-Seq data webresources (also available at https://ki.se/en/mbb/oligointernode) | This paper |
https://castelobranco.shinyapps.io/SCATAC10X_2020/. http://cells.ucsc.edu/?ds=olg-eae-ms |
| Sc-multiome data webresources (also available at https://ki.se/en/mbb/oligointernode) | This paper |
https://castelobranco.shinyapps.io/eae_multi_act
https://castelobranco.shinyapps.io/eae_multi_rna https://castelobranco.shinyapps.io/hs_ctr_multi_act https://castelobranco.shinyapps.io/hs_ctr_multi_rna |
| Genome tracks for all datasets | This paper | GEO: GSE166179 |
| Code availability | This paper | DOI 10.5281/zenodo.5781403 |