KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Mouse monoclonal anti-Aβ antibody, mHJ3.4 | David M. Holtzman | |
| Rabbit polyclonal anti-Iba1 antibody | Wako | Cat #019–19741; RRID:AB_839504 |
| Guinea pig anti vGLUT1 | Synaptic Systems | Cat #135304; RRID:AB_887878 |
| Mouse monoclonal (IgG2a) anti PSD95 | Upstate | Cat #05–494; RRID:AB_2315219 |
| Rabbit monoclonal anti-synaptophysin | Synaptic Systems | Cat #101203; RRID:AB_2810218) |
| Rabbit monoclonal anti C1q | Abcam | Cat. #ab227072; N.A |
| Rat monoclonal anti-CD68 | Bio-Rad Lab | Cat #MCA1957; RRID:AB_322219 |
| Mouse monoclonal anti GFAP | Millipore | Cat #MAB360, RRID:AB_11212597 |
| Mouse monoclonal anti PSD95 | Millipore | Cat #MAB1596, RRID:AB_2092365 |
| Rabbit monoclonal anti-synaptophysin | Abcam | Cat #ab16659; RRID:AB_443419 |
| Mouse monoclonal anti β tubulin | Sigma-Aldrich | Cat # T6074; RRID:AB_477582 |
| mouse monoclonal anti-C9orf72 | GeneTex | Cat #. GTX634482, RRID:AB_2784545 |
| Rabbit polyclonal anti PSD95 | Thermo Fisher Scientific | Catalog # 51–6900; RRID:AB_2533914 |
| Rabbit monoclonal anti STING | Cell Signaling | Catalog # 13647 RRID:AB_ 2732796 |
| Rabbit polyclonal anti-Homer 1 | Synaptic Systems | Cat# 160 002, RRID:AB 2120990 |
| Guinea pig anti Bassoon | Synaptic Systems | Cat# 141 004, RRID:AB_2290619 |
| IRDye® 800CW Goat anti-Rabbit IgG Secondary Antibody | Licor | P/N: 926–32211; RRID:AB_621843 |
| IRDye® 680RD Goat anti-Mouse IgG Secondary Antibody | Licor | P/N: 926–68070; RRID:AB_10956588 |
| Alexa Fluor 488 goat anti-mouse IgG (H+L) | Thermo Fisher Scientific | Cat #A11029; RRID:AB_138404 |
| Alexa Fluor 555 goat anti-rabbit IgG (H+L) | Thermo Fisher Scientific | Cat #A21428; RRID:AB_2535849 |
| Alexa Fluor 488 donkey anti-rat IgG (H+L) | Thermo Fisher Scientific | Cat #A21208; RRID:AB_2535794 |
| Alexa Fluor 647 donkey anti-mouse IgG (H+L) | Thermo Fisher Scientific | Cat #A31571; RRID:AB_162542 |
| Alexa Fluor 647 donkey anti-rabbit IgG (H+L) | Thermo Fisher Scientific | Cat #A31573; RRID:AB_2536183 |
| Alexa Fluor 647 goat anti-rabbit IgG (H+L) | Thermo Fisher Scientific | Cat #A21244; RRID:AB_2535812 |
| Alexa Fluor 555 F(ab’)2 oat anti-mouse IgG (H+L) | Thermo Fisher Scientific | Cat #A21425; RRID:AB_2535846 |
| Prolong Gold Antifade Reagent with DAPI | Thermo Fisher Scientific | Cat # P36931; N.A |
| Bacterial and Virus Strains | ||
| Biological Samples | ||
| Chemicals, Peptides, and Recombinant Proteins | ||
| Cresyl violet | Sigma-Aldrich | Cat #C5042 |
| cOmplete, Roche protease inhibitor cocktail | Sigma-Aldrich | Cat #5892970001 |
| PhosSTOP phosphatase inhibitor cocktail | Sigma-Aldrich | Cat #4906837001 |
| Critical Commercial Assays | ||
| FD Rapid GolgiStain™ Kit | FD Neuro Technologies, Inc. | Cat #PK401 |
| Mouse IgG ELISpot kit (HRP) | Mabtech | Cat #3825–2H |
| Mouse IFNg ELISPOT Set | BD Biosciences | Cat #551083 |
| Neural Tissue dissociation kit | Miltenyi Biotech | Cat #130–092-628 |
| Myelin Removal Beads II | Miltenyi Biotech | Cat # 30–096-433 |
| CD11b+ magnetic beads | Miltenyi Biotech | Cat #130–093-634 |
| TruSeq Stranded mRNA Library Prep kit | Illumina | Cat #20020594 |
| TruSeq RNA Single Indexes Set A | Illumina | Cat #20020492 |
| TruSeq RNA Single Indexes Set B | Illumina | Cat # 20020493 |
| VECTASTAIN Elite ABC Kit | Vector labs | Cat #PK-6100 |
| Pierce™ BCA Protein Assay Kit | Thermo Fisher Scientific | Cat #23225 |
| Mini-PROTEAN® TGX™ Precast Gels | Bio-Rad | Cat #4561096 |
| Odyssey blocking buffer | Li-Cor | Cat #927–40000 |
| RNeasy Micro Kit | Qiagen | Cat #74004 |
| Single Cell 3′ v3.1 Reagent Kits | 10x Genomics | |
| SPRIselect Reagent Kit | Beckman Coulter | B23319 |
| Chromium Single-Cell 3′ Library Kit | 10x Genomics | PN-120237 |
| Collibri Library Quantification Kit | (Thermo Fisher Scientific | A38524100 |
| Deposited Data | ||
| Bulk RNAseq data Single cell RNAseq data |
This paper | GEO Accession numbers: GSE164676 (superseries) GSE164675 (Bulk RNAseq) GSE164674 (Single Cell RNAseq) |
| Experimental Models: Cell Lines | ||
| Experimental Models: Organisms/Strains | ||
| Mouse: C9orf72 (311004O21Rik) knockout mouse | In house | O’Rourke et.al 2016 |
| Mouse: B6SJL-Tg(APPSwFlLon,PSEN1*M146L*L286V)6799Vas/Mmjax | The Jackson Laboratory | MMRRC Stock No: 34840 |
| Mouse: C9orf72fl/fl | Obtained from R Jeroen Pasterkamp | Koppers et al., 2015 |
| Mouse: (B6J.B6N(Cg)-Cx3cr1tm1.1(cre)Jung/J | The Jackson Laboratory | Stock No: 025524 RRID:IMSR_JAX:025524 |
| Oligonucleotides | ||
| Recombinant DNA | ||
| Software and Algorithms | ||
| Fiji ImageJ | https://doi.org/10.1038/nmeth.2019 | https://imagej.net/Fiji |
| GraphPad Prism | GraphPad Software, La Jolla, CA, USA | Version 9.0.0 https://www.graphpad.com/scientific-software/prism/ |
| WGCNA R package | https://doi.org/10.1186/1471-2105-9-559 |
https://horvath.genetics.ucla.edu/html/ CoexpressionNetwork/Rpackages/ WGCNA |
| STRING | https://doi.org/10.1093/nar/gkw937 | https://string-db.org |
| Galaxy | https://doi.org/10.1093/nar/gky379; https://doi.org/10.1093/nar/gkw343 |
http://usegalaxy.org/ |
| FASTQ Groomer (Galaxy Version 1.1.1) | https://doi.org/10.1093/bioinformatics/btq281 | http://usegalaxy.org/ |
| TopHat (Galaxy Version 2.1.1) | https://doi.org/10.1186/gb-2013-14-4-r36 | http://usegalaxy.org/ |
| Bowtie2 (part of TopHat Galaxy Version 2.1.1) | https://doi.org/10.1038/nmeth.1923 | http://usegalaxy.org/ |
| Samtools (part of TopHat Galaxy Version 2.1.1) | https://doi.org/10.1093/bioinformatics/btp352 | http://usegalaxy.org/ |
| Partek Genomic Suite | Partek® Genomics Suite®, Partek Inc., St. Louis, MO, 2018, version 7.17.0918 | Version 7.17.0918 https://www.partek.com/partek-genomics-suite/ |
| Salmon | https://doi.org/10.1038/nmeth.4197 | Version 0.8.2 https://combine-lab.github.io/salmon/ |
| mm10 (GRCm38) mouse reference genome sequence and transcriptome annotation | http://www.genome.org/cgi/doi/10.1101/gr.213611.116 | hosting webpage: https://support.illumina.com/sequencing/sequencing_software/igenome.html |
| mm10 (continued) | download url used: http://igenomes.illumina.com.s3-website-us-east-1.amazonaws.com/Mus_musculus/UCSC/mm10/Mus_musculus_UCSC_mm10.tar.gz | |
| mm10 (continued) | README.txt file found in the downloaded reference sequence in the following directory ./Mus_musculus/UCSC/mm10/Annotation : “The contents of the annotation directories were downloaded from UCSC on: July 17, 2015. SmallRNA annotation files were downloaded from miRBase release 21.” | |
| DESeq2 R package (Bioconductor version: Release 3.11) | https://doi.org/10.1186/s13059-014-0550-8 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |
| STAR | https://doi.org/10.1093/bioinformatics/bts635 | Version 2.5.1 |
| Cell Ranger software | 10X Genomics | Version 4.0.0 |
| GO Ontology database | http://doi.org/10.5281/zenodo.4081749 | Release 2020–10-09 |
| MyGeneSet | https://doi.org/10.1038/ni1008-1091 | http://rstats.immgen.org/MyGeneSet_New/index.html |
| R | https://www.R-project.org/ | Version 4.0.3 |
| Rstudio | http://www.rstudio.com | Version 1.3.1093 |
| Seurat R package |
https://doi.org/10.1038/nbt.4096 https://doi.org/10.1016/j.cell.2019.05.031 https://doi.org/10.1186/s13059-019-1874-1 |
Version 3.2.2 |
| Harmony R package | https://doi.org/10.1101/461954 | Version 1.0.0 |
| Tidyverse R package | https://doi.org/10.21105/joss.01686 | Version 1.3.0 |
| Matrix R package | Douglas Bates and Martin Maechler (2019). Matrix: Sparse and Dense Matrix Classes and Methods. | Version 1.2–18 |
| Cowplot R package | Claus O. Wilke (2020). cowplot: Streamlined Plot Theme and Plot Annotations for ‘ggplot2’ | Version 1.1.0 |
| Viridis R package | Simon Garnier (2018). viridis: Default Color Maps from ‘matplotlib’ | Version 0.5.1 |
| Other | ||
| Leica digital image hub | -N-A- | |
| Li-COR imaging system (Odyssey CLx) | -N-A- | |