| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Beta-catenin (1/2000) | BD bioscience | Cat# 610153; RRID:AB_397554 |
| Collagen 4 (1/100) | Millipore | AB756P; RRID:AB_2276457 |
| DCX (1/500) | Millipore | Cat# AB2253; RRID:AB_1586992 |
| GFAP (rb) (1/500) | DAKO | Cat# Z0334; RRID:AB_10013382 |
| GFAP (ms) (1/500) | Sigma | Cat# G3893; RRID:AB_477010 |
| GFAP (goat) (1/500) | abcam | Cat# ab53554; RRID:AB_880202 |
| GFP (1/1000) | Millipore | Cat# MAB3580; RRID:AB_94936 |
| GFP (1/2000-4000) | Aves lab | Cat# GFP-1020; RRID:AB_10000240 |
| MAG (1/400) | Millipore | Cat# MAB1567; RRID:AB_2137847 |
| MAP2 (1/1000) | Sigma | Cat# M4403; RRID:AB_477193 |
| Nestin (1/100) | Millipore | Cat# MAB353; RRID:AB_94911 |
| NeuN (1/100) | Millipore | Cat# MAB377; RRID:AB_2298772 |
| S100a6 (1/500) | Abcam | Cat# ab181975 |
| S100B (ms) 1/500) | Sigma | Cat# S2532; RRID:AB_477499 |
| Tgm2 (1/100) | Labvision | Cat# MS-224-B0; RRID:AB_62201 |
| WFA (biotin conjugated) (1/500) | Sigma | Cat# L1516-2MG; RRID:AB_2620171 |
| Secondary antibodies | ||
| Alexa Fluor® secondary antibodies (488, 555, 647) (1/1000) | ThermoFisher Scientific | Cat# A-11001; RRID:AB_2534069 |
| 555 Alexa Fluor® conjugated streptavidin | ThermoFisher Scientific | Cat# S32355; RRID:AB_2571525 |
| FACS antibodies | ||
| CD133-PE (1/250) | eBioscience | Cat# 12-1331-82; RRID:AB_465849 |
| EGF–Alexa Fluor 647 (1/300) | Molecular Probes | Cat# E-35351 |
| Anti-PSA-NCAM-PE (1/250) | Miltenyi | Cat# 130-093-274; RRID:AB_1036069 |
| Rat IgG1 K isotype control PE (1/250) | eBioscience | Cat# 12-4301-81; RRID:AB_470046 |
| Mouse IgM-PE antibody (isotype control (1/250)) | Miltenyi | Cat# 130-093-177; RRID:AB_871723 |
| Chemicals, Peptides, Recombinant Proteins and Kits | ||
| IGPAL-CA-630 | Sigma | Cat# I8896 |
| Phosphatase inhibitors | Roche | Cat# 04906837001 |
| Benzonase | Merck | Cat# 70746-3 |
| Protease inhibitors (+EDTA) | LifeTech | Cat# 78430 |
| Sodium deoxycholate | Sigma | Cat# D6750 |
| TCEP | Sigma | Cat# 646547 |
| 2-Chloroacetamide | Sigma | Cat# C0267 |
| Ammonium acetate | Sigma | Cat# V800034 |
| Formic acid | Sigma | Cat# 543804 |
| Gaudinium | Sigma | Cat# G4505 |
| Thio-urea | Sigma | Cat# T8656 |
| SDS | Sigma | Cat# L4509 |
| HEPES | Sigma | Cat# H3375 |
| Trypsin | Sigma | Cat# T9201 |
| Hyaluronidase | Sigma | Cat# H3884 |
| DMEM/F12 | Life Technologies | Cat# 21331020 |
| B27 Supplement | Life Technologies | Cat# 17504044 |
| Poly-D-lysine hydrobromide | Sigma | Cat# P0899 |
| GlutaMax | Life Technologies | Cat# 35050038 |
| Trypsin-EDTA (0.05%) | ThermoFisher Scientific | Cat# 25300054 |
| Poly-L-ornithin | Sigma | Cat# P4957 |
| Laminin | Roche | Cat# 11243217001 |
| TSA Tetramethylrhodamine kit | PerkinElmer | Cat# NEL702001KT |
| Acetonitrile | Sigma | Cat# 271004 |
| Trifluoroacetic acid | Sigma | Cat# 302031 |
| Micro BCA protein assay kit | ThermoFisher Scientific | Cat# 23235 |
| Goat Serum | ThermoFisher Scientific | Cat# 16210072 |
| RLT lysis buffer | QIAGEN | Cat# 79216 |
| Triton X-100 | Sigma | Cat# T8787 |
| RLT lysis buffer | QIAGEN | Cat# 79216 |
| RNeasy Micro Kit | QIAGEN | Cat# 74004 |
| RNeasy Mini Kit | QIAGEN | Cat# 74104 |
| SuperScript III | Invitrogen | Cat# 18080093 |
| iQ SYBR Green Supermix | BIO-RAD | Cat# 1708880 |
| IsoFlo | Abbott Laboratories | Cat# NDC 0044-5260-03 |
| DMSO | Sigma | Cat# D2438-10ML |
| ZDON | Zedira | Cat# Z006 |
| BocDON | Zedira | Cat# B003 |
| EdU | ThermoFisher Scientific | Cat# E10187 |
| Click-iT EdU Alexa fluor 647 Imaging kit | Invitrogen | Cat# C10340 |
| HiPerFect® transfection reagent | QIAGEN | Cat# 301704 |
| Allstars Negative control siRNA | QIAGEN | Cat# 1027280 |
| FlexiTube GeneSolution for Tgm2 | QIAGEN | Cat# GS21817 |
| Glutaraldehyde | Sigma | Cat# G5882 |
| (3-Aminopropyl) trimethoxysilane (APTMS) | Sigma | Cat# 281775 |
| Acrylamide | Sigma | Cat# A4058 |
| N-Hydroxyethyl-acrylamide | Sigma | Cat# 697931 |
| Bis-acrylamide | Fisher Scientific | Cat# BP1404-250 |
| Experimental Models: Organisms/Strains | ||
| C57Bl6/J mice | In-house breeding | N/A |
| C1ql3flox; C1ql3tm1.1Sud | Martinelli et al., 2016 | RRID: MGI_5779515 |
| hGFAP-GFP mice (Tg(GFAP-EGFP)1Hket) | Nolte et al., 2001 | MGI:6188855 |
| Deposited Data | ||
| Proteome dataset | ProteomeXchange Consortium at http://proteomecentral.proteomexchange.org | PXD016632 |
| Supplementary tables (of in-article analyzed data) | The journal | N/A |
| Proteome dataset | https://neuronicheproteome.org | N/A |
| Microarray dataset | Gene Expression Omnibus at https://www.ncbi.nlm.nih.gov/geo/ | accession number GPL15692 |
| Software and Algorithms | ||
| MATLAB, including custom-written scripts to analyze AFM data | Mathworks: https://www.mathworks.com/products/matlab/Custom MATLAB scripts: https://github.com/FranzeLab | Version R2018b |
| Maxquant | http://www.coxdocs.org/doku.php?id=maxquant:start | Version 1.6.0.16 |
| Perseus | http://www.coxdocs.org/doku.php?id=perseus:start | Version 1.6.0.7 |
| Prism | Graphpad | Version 5 |
| Microarray analysis | GeneSpring GX v11.5.1 software package | Agilent Technologies |
| String | https://string-db.org/ | N/A |
| ZEN imaging software | Carl Zeiss | N/A |
| Other | ||
| CellHesion 200 AFM head | JPK Instruments | N/A |
| PetriDishHeater for maintaining constant temperature during AFM-based stiffness measurements | JPK Instruments | N/A |
| Tipless silicon cantilevers for AFM-based stiffness measurements | NanoWorld | Arrow TL-1 |
| Spherical probes for AFM cantilevers | microParticles GMBH | 37.28 μm polystyrene beads, PS-R-37.0 |
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