KEY RESOUCES TABLE:
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| PKR | Abcam | Cat#ab184257 |
| phospho-PKR | GeneTex | Cat#GTX32348 |
| NeuN | MilliporeSigma | Cat#MAB377; RRID: AB_2298772 |
| Eif4a2 | Abcam | Cat#ab31218; RRID: AB_732123 |
| TOMM70 | Abcam | Cat#ab83841; RRID: AB_1861453 |
| VDAC | Cell Signaling Technology | Cat#4866; RRID: AB_2272627 |
| PPP1R1B | Cell Signaling Technology | Cat#2302; RRID: AB_2169007 |
| H3C1 | Abcam | Cat#ab1791; RRID: AB_302613 |
| anti-GFP 19C8 TRAP purification antibody | Antibody and Bioresource Core Facility at the Memorial Sloan Kettering Cancer Center | Cat#HtzGFP-19C8_as_BRS; RRID:AB_2716737 |
| anti-GFP 19F7 TRAP purification antibody | Antibody and Bioresource Core Facility at the Memorial Sloan Kettering Cancer Center | Cat#HtzGFP-19F7_as_BRS; RRID:AB_2716736 |
| AlexaFluor647 goat anti-mouse secondary antibody | ThermoFisher Scientific | Cat#A32728; RRID: AB_2633277 |
| Alexafluor594 chicken anti-rabbit secondary antibody | ThermoFisher Scientific | Cat#A21442; RRID: AB_2535860 |
| ImmPRESS anti-rabbit-HRP secondary antibody | Vector Laboratories | Cat#MP-7451; RRID: AB_2631198 |
| Bacterial and Virus Strains | ||
| Biological Samples | ||
| Human Control samples | The Alabama Brain Collection (ABC) and The NIH NeuroBioBank (The Human Brain and Spinal Fluid Resource Center) | https://www.uab.edu/medicine/psychiatry/research/resources-0/alabama-brain-collection and https://neurobiobank.nih.gov |
| Human HD grade 2–4 samples | The NIH NeuroBioBank (The Human Brain and Spinal Fluid Resource Center) | https://neurobiobank.nih.gov |
| Chemicals, Peptides, and Recombinant Proteins | ||
| Critical Commercial Assays | ||
| Interferon alpha-2 ELISA assay kit | Abcam | Cat#ab211648 |
| TaqMan Fast Advanced Master Mix | ThermoFisher Scientific | Cat# 4444963 |
| Mitochondria Isolation Kit, mouse tissue | Miltenyi Biotec Inc. | Cat#130-096-946 |
| Chromium Single Cell 3′ Library & Gel Bead Kit v3 | 10x Genomics | Cat#1000075 |
| Chromium Chip B Single Cell Kit | 10x Genomics | Cat#1000074 |
| Chromium i7 Multiplex Kit | 10x Genomics | Cat#120262 |
| Deposited Data | ||
| HD and HD mouse model sequencing data | This Paper | NCBI GEO: GSE152058 |
| Experimental Models: Cell Lines | ||
| Experimental Models: Organisms/Strains | ||
| Mouse: R6/2 hemizygous transgenic: B6CBA-Tg(HDexon1)62Gpb/1J hemi |
The Jackson Laboratory | RRID:IMSR_JAX: 002810 |
| Mouse: R6/2 non-carrier: B6CBA-Tg(HDexon1)62Gpb/1J non carrier controls |
The Jackson Laboratory | RRID:IMSR_JAX: 002810 |
| Mouse: Drd1a::TRAP: Tg(Drd1a-EGFP/Rpl10a)CP73Htz |
The Jackson Laboratory | RRID:IMSR_JAX:030254 |
| Mouse: Drd2::TRAP: Tg(Drd2-EGFP/Rpl10a)CP101Htz |
The Jackson Laboratory | RRID:IMSR_JAX:030255 |
| Mouse: Aldh1l1::TRAP: Tg(Aldh1l1-EGFP/Rpl10a)JD130Htz |
The Jackson Laboratory | RRID:IMSR_JAX:030247 |
| Mouse: Chat::TRAP: Tg(Chat-EGFP/Rpl10a,Slc18a3)DW167Htz/J |
The Jackson Laboratory | RRID:IMSR_JAX:030250 |
| Mouse: Q20 KI: B6J.HdhQ20 | The Jackson Laboratory | RRID:IMSR_JAX: 370504 |
| Mouse: Q50 KI: B6J.HdhQ50 | The Jackson Laboratory | RRID:IMSR_JAX: 303454 |
| Mouse: Q111 KI: B6J.HdhQ111 | The Jackson Laboratory | RRID:IMSR_JAX: 370624 |
| Mouse: Q170 KI: B6J.HdhQ170 | The Jackson Laboratory | RRID:IMSR_JAX: 400706 |
| Mouse: zQ175DN: B6J.zQ175DN | The Jackson Laboratory | RRID:IMSR_JAX: 370832 |
| Mouse: C57BL/6J WT controls | The Jackson Laboratory | RRID:IMSR_JAX:000664 |
| Oligonucleotides | ||
| Taqman gene expression Mouse Actb, Mm02619580_g1 | ThermoFisher Scientific | Cat#4331182 |
| Taqman gene expression Mouse mt-Co1, Mm04225243_g1 | ThermoFisher Scientific | Cat#4331182 |
| Taqman gene expression Mouse mt-Nd1, Mm04225274_s1 | ThermoFisher Scientific | Cat#4331182 |
| Taqman gene expression Mouse mt-Nd4/4l, Mm04225294_s1 | ThermoFisher Scientific | Cat#4331182 |
| Taqman gene expression Mouse mt-Nd5/6, Mm04225315_s1 | ThermoFisher Scientific | Cat#4331182 |
| Taqman gene expression Mouse mt-Rnr1, Mm04260177_s1 | ThermoFisher Scientific | Cat#4331182 |
| Recombinant DNA | ||
| Software and Algorithms | ||
| MACS2 | Zhang et al., 2008 | https://github.com/taoliu/MACS |
| EnrichR | Chen et. al. 2013, Kuleshov et al., 2016 | https://amp.pharm.mssm.edu/Enrichr/; RRID:SCR_001575 |
| WGCNA | Langfelder and Horvath, 2008 | https://horvath.genetics.ucla.edu/html/CoexpressionNetwork/Rpackages/WGCNA/; RRID:SCR_003302 |
| Limma | Ritchie et al., 2015 | http://bioconductor.org/packages/release/bioc/html/limma.html |
| Batchelor | Haghverdi et al., 2018 | https://bioconductor.org/packages/release/bioc/html/batchelor.html |
| ACTIONet | Mohammadi et al., 2019 | https://github.com/shmohammadi86/ACTIONet |
| STAR | Dobin et al., 2013 | https://github.com/alexdobin/STAR |
| DESeq2 | Love et al., 2014 | https://bioconductor.org/packages/release/bioc/html/DESeq2.html |