KEY RESOURCES TABLE
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| VCP | Abcam | Cat# ab11433 |
| VCP | Fitzgerald | Cat# 10R-P104A |
| Pan-14-3-3 | Santa Cruz | Cat# Sc1657 |
| NEUN | CST | Cat# 12943S |
| Gfap | Abcam | Cat# Ab7260 |
| Iba1 | Walko Chem | Cat# 019-19741 |
| C1Q | Abcam | Cat# ab182451 |
| TDP-43 | Proteintech | Cat# 10782-2-AP |
| p-TDP-43 | BioLegend | Cat# 829901 |
| Ubiquitin | Abcam | Cat# ab134953 |
| SQSTM1/p62 | Sigma | Cat# P0067 |
| LAMP1 | BD Transduction Labs | Cat# 553792 |
| LC3 | Sigma | Cat# L7543 |
| LAMP2 | Thermo/Invitrogen | Cat# PA1-655 |
| p-IRE1 | Invitrogen | Cat# PA116927 |
| GAPDH | CST | Cat# 2118 |
| IRE1 | Abcam | Cat# ab37073 |
| HSP70 | Enzo | Cat# ADI-SPA-812 |
| PERK | CST | Cat# 3192 |
| BIP/Grp78 | BD Transduction Labs | Cat# 610979 |
| BIP/Grp78 | Millipore | Cat# 4392 |
| ATG5 | CST | Cat# 12994 |
| FK2 (mono & poly ubiquitin) | Enzo | Cat# pw8810-050 |
| TOM20 | Santa Cruz | Cat# sz1415 |
| PSD-95 | Invitrogen | Cat# 516900 |
| Synapsin 1/2 | Synaptic Systems | Cat# 10600 |
| PSD-95 | Invitrogen | Cat# 51-6900 |
| Bax | CST | Cat# 14796s |
| CHOP | CST | Cat# 2895S |
| LC3 | Nanotools | Cat# 0231-100 |
| Goat anti-Guinea Pig IgG-Alexa 488 | Invitrogen | Cat# A11073 |
| Goat anti-Rabbit IgG-Alexa 594 | Invitrogen | Cat# A11037 |
| Chemicals, peptides, and recombinant proteins | ||
| ProLong Diamond DAPI mounting media | Invitrogen | Cat# P36971 |
| Critical commercial assays | ||
| Thermo EasyPep Mini MS Sample Prep Kit | Thermo Fischer | REF A4006 |
| ApopTag® Fluorescein In Situ Apoptosis Detection Kit | Millipore | REF S7110 |
| Tissue Lyser LT and RNeasy Mini Kit | QIAGEN | N/A |
| Deposited data | ||
| Raw proteomic data related to Figure 4 and Table S2 | This Paper | Data are available via ProteomeXchange with identifier PXD026685 |
| Code for analysis of transcriptomic and proteomic overlay related to Figures 7 and S7 | This Paper | Code available via Github https://zenodo.org/record/4957857 |
| Raw single nuclei RNA sequence data from cVCP KO mice cortex related to Figure 4 and Table S3 | This paper | GEO: GSE178257 |
| RNA sequencing and phenotypic data of patients and brain samples from patients with dementia related to Figures 7 and S7 and Table S4 | This paper | Data deposited in Synapse portal (handle syn25882533) at https://www.synapse.org/#!Synapse:syn25882533/. |
| Experimental models: Organisms/strains | ||
| C57BL/6 | Jackson Labs | Stock No: 000664 |
| CamKIIa-cre | Jackson Labs | Stock No: 005359 |
| B6;129S-Vcptm1Itl/J (VCP R155H knockin) | Jackson Labs | Stock No. 021968 |
| VCP R155C CaMKIIα-Cre | This Paper | N/A |
| ATG5fl/fl | University of Tokyo | Noburu Mizushima |
| VCPfl/fl | Washington University in saint louis | Chris Weihl |
| VCPfl/fl CaMKIIα-Cre | This paper | N/A |
| ATG5fl/fl CaMKIIα-Cre | This paper | N/A |
| Oligonucleotides | ||
| Primers for LoxP site #1 in VCP floxed mice Forward 5′-GGTCTTGTTGTAGAGCCCTGTTCTGTAG-3′ | This paper | N/A |
| Primers for LoxP site #1 in VCP floxed mice Reverse 3′-CCTGGGACAAGGACACCACGCTGTTATC-5′ | This paper | N/A |
| Primers for LoxP site #2 in VCP floxed mice Forward 5′-GTGAGGGGGAGCCAATCAAGCGAGAGG-3′ | This paper | N/A |
| Primers for LoxP site #2 in VCP floxed mice Reverse 3′-CAATATTCCCACCTCCACCTCCTAAGC-5′ | This paper | N/A |
| Primers for Cre Forward 5′-GCATTACCGGTCGATGCAACGAGTGATGAG-3′ | This paper | N/A |
| Primers for Cre Reverse 3′-GAGTGAACGAACCTGGTCGAAATCAGTGCG-5′ | This paper | N/A |
| Primers for VCP-R155C allele Forward 5′-CAGTTCTCATGCCTCTCTGAAGGATAATGT-3′ | This paper | N/A |
| Primers for VCP-R155C allele Reverse 3′-TCTACAACTTTGAACTCCACAGCACGC-5′ | This paper | N/A |
| Software and algorithms | ||
| ImageJ | NIH open access | https://imagej.nih.gov/ij/ |
| NIS Elements Viewer | Nikon | https://www.microscope.healthcare.nikon.com/products/software/nis-elements |
| FV10-ASW 4.2 viewer | Olympus | https://www.olympus-lifescience.com/en/support/downloads/fv10i_vw_license/ |
| Seurat V3.1 R package | Butler et al., 2018 | |
| Ingenuity Pathway Analysis | QIAGEN | |
| GraphPad Prism 7.0 | GraphPad | https://www.graphpad.com/scientific-software/prism/ |
| IMARIS 9.5 | Oxford Instruments | https://imaris.oxinst.com/versions/9-5 |
| Hamilton-Kinder | ||
| ANY-maze | Stoelting Co | https://www.any-maze.com |
| Xcalibur | Thermo Fisher Scientific | https://www.thermofisher.com/order/catalog/product/OPTON-30965#/OPTON-30965 |
| Cell Ranger Single-Cell Software Suite | 10x Genomics | https://support.10xgenomics.com/single-cell-gene-expression/software/overview/welcome |
| R packages ggplot2 (version 3.3.2) | N/A | |
| gplots (version 3.04) | N/A | |