Key resources table
| REAGENT or RESOURCE | SOURCE | IDENTIFIER |
|---|---|---|
| Antibodies | ||
| Anti-human CD10 FITC (clone HI10a) | Biolegend | Cat#312207 RRID:AB_314918 |
| Anti-human CD101 PE (clone BB27) | Biolegend | Cat#331011 RRID:AB_2716106 |
| Anti-human CD11c PE (clone 3.9) | Biolegend | Cat#301605 RRID:AB_314175 |
| Anti-human CD14 APC (clone M5E2) | Biolegend | Cat#301807 RRID:AB_314189 |
| Anti-human CD14 BV785 (clone M5E2) | Biolegend | Cat#301839 RRID:AB_2561366 |
| Anti-human CD15 BV605 (clone W6D3) | Biolegend | Cat#323031 RRID:AB_2562131 |
| Anti-human CD15 BV650 (clone W6D3) | Biolegend | Cat#323033 RRID:AB_2562499 |
| Anti-human CD16 APC (clone 3G8) | Biolegend | Cat#302011 RRID:AB_314211 |
| Anti-human CD16 APC/Cy7 (clone 3G8) | Biolegend | Cat#302017 RRID:AB_314217 |
| Anti-human CD19 APC (clone HIB19) | Biolegend | Cat#302211 RRID:AB_314241 |
| Anti-human CD206 Alexa Fluor 700 (clone 15-2) | Biolegend | Cat#321131 RRID:AB_2616868 |
| Anti-human CD25 APC/Fire 810 (clone M-A251) | Biolegend | Cat#356149 RRID:AB_2876679 |
| Anti-human CD25 PE/Dazzle 594 (clone M-A251) | Biolegend | Cat#356125 RRID:AB_2563561 |
| Anti-human CD3 BV421 (clone UCHT1) | Biolegend | Cat#300433 RRID:AB_10897105 |
| Anti-human CD31 (polyclonal) | Abcam | Cat#ab28364 RRID:AB_726362 |
| Anti-human CD4 BV711 (clone OKT4) | Biolegend | Cat#317439 RRID:AB_11219404 |
| Anti-human CD4 PE/Fire 700 (clone SK3) | Biolegend | Cat#344665 RRID:AB_2876651 |
| Anti-human CD45 APC/Cy7 (clone 2D1) | Biolegend | Cat#368515 RRID:AB_2566375 |
| Anti-human CD45 BV711 (clone HI30) | Biolegend | Cat#304049 RRID:AB_2563465 |
| Anti-human CD49d PerCP/Cy5.5 (clone 9F10) | Biolegend | Cat#304311 RRID:AB_10640735 |
| Anti-human CD56 APC (clone HCD56) | Biolegend | Cat#318309 RRID:AB_604098 |
| Anti-human CD56 PE/Fire 700 (clone QA17A16) | Biolegend | Cat#392427 RRID:AB_2876708 |
| Anti-human CD66b BV421 (clone 6/40c) | Biolegend | Cat#392915 RRID:AB_2888722 |
| Anti-human CD69 BV785 (clone FN50) | Biolegend | Cat#310931 RRID:AB_2561370 |
| Anti-human CD8 APC (clone SK1) | Biolegend | Cat#980904 RRID:AB_2616624 |
| Anti-human CD8 PE/Cy7 (clone SK1) | Biolegend | Cat#344711 RRID:AB_2044007 |
| Anti-human CD8 PE/Dazzle 594 (clone SK1) | Biolegend | Cat#344743 RRID:AB_2566514 |
| Anti-human Fc (clone Fc1) | BD Biosciences | Cat#564219 RRID:AB_2728082 |
| Anti-human GM-CSF (clone BVD2-23B6) | Biolegend | Cat#502201 RRID:AB_315211 |
| Anti-human HLA-DR/DP/DQ (clone Tü39) | Biolegend | Cat#361702 RRID:AB_2563139 |
| Anti-human HLA-DR/DP/DQ APC/Fire 750 (clone Tü39) | Biolegend | Cat#361711 RRID:AB_2750313 |
| Anti-human HLA-DR/DP/DQ FITC (clone Tü39) | Biolegend | Cat#361705 RRID:AB_2563191 |
| Anti-human HLA-DR/DP/DQ PE/Cy7 (clone Tü39) | Biolegend | Cat#361707 RRID:AB_2564278 |
| Anti-human myeloperoxidase (clone 2C7) | Abcam | Cat#ab25989 RRID:AB_448948 |
| Anti-human Nestin (clone 10C2) | Abcam | Cat#ab22035 RRID:AB_446723 |
| Anti-human OPN (polyclonal) | R&D Systems | Cat#AF1433 RRID:AB_354791 |
| Anti-human Siglec8 APC (clone 7C9) | Biolegend | Cat#347105 RRID:AB_2561401 |
| Anti-mouse CD105 (MJ7/18) Alexa Fluor 488 | Biolegend | Cat#120405 RRID:AB_961056 |
| Anti-mouse CD106 (429) Alexa Fluor 488 | Biolegend | Cat#105710 RRID:AB_493427 |
| Anti-mouse CD11c BV605 (clone N418) | Biolegend | Cat#117333 RRID:AB_11204262 |
| Anti-mouse CD11c PE/Cy7 (clone N418) | Biolegend | Cat#117317 RRID:AB_493569 |
| Anti-mouse CD133 (315-2C11) PE/Dazzle 594 | Biolegend | Cat#141211 RRID:AB_2566009 |
| Anti-mouse CD133 APC (clone 315-2C11) | Biolegend | Cat#141207 RRID:AB_10898121 |
| Anti-mouse CD140a (APA5) PE/Cy7 | Biolegend | Cat#135911 RRID:AB_2715973 |
| Anti-mouse CD140b (APB5) APC | Biolegend | Cat#136007 RRID:AB_2043971 |
| Anti-mouse CD16/32 (clone 2.4G2) | BD Biosciences | Cat#553142 RRID:AB_394657 |
| Anti-mouse CD16/32 BV421 (clone 190909) | BD Biosciences | Cat#747952 RRID:AB_2872413 |
| Anti-mouse CD183 (CXCR3) (CXCR3-173) | Biolegend | Cat#126554 RRID:AB_2832456 |
| Anti-mouse CD206 APC (clone C068C2) | Biolegend | Cat#141707 RRID:AB_10896057 |
| Anti-mouse CD206 PE/Cy7 (clone C068C2) | Biolegend | Cat#141719 RRID:AB_2562247 |
| Anti-mouse CD25 APC/Cy7 (clone 3C7) | Biolegend | Cat#101917 RRID:AB_2650981 |
| Anti-mouse CD3 APC (clone 17A2) | Biolegend | Cat#100235 RRID:AB_2561455 |
| Anti-mouse CD3 PE (clone 17A2) | Biolegend | Cat#100205 RRID:AB_312662 |
| Anti-mouse CD31 (390) BV421 | Biolegend | Cat#102423 RRID:AB_2562186 |
| Anti-mouse CD326 (EpCAM) (G8.8) BV650 | Biolegend | Cat#118241 RRID:AB_2876432 |
| Anti-mouse CD4 BV421 (clone GK1.5) | Biolegend | Cat#100437 RRID:AB_10900241 |
| Anti-mouse CD4 BV605 (clone GK1.5) | Biolegend | Cat#100451 RRID:AB_2564591 |
| Anti-mouse CD45 (30-F11) BV510 | Biolegend | Cat#103137 RRID:AB_2561392 |
| Anti-mouse CD45 Alexa Fluor 488 (clone 30-F11) | Biolegend | Cat#103121 RRID:AB_493532 |
| Anti-mouse CD45 Alexa Fluor 700 (clone 30-F11) | Biolegend | Cat#103127 RRID:AB_493714 |
| Anti-mouse CD45 APC/Cy7 (clone 30-F11) | Biolegend | Cat#103115 RRID:AB_312980 |
| Anti-mouse CD45 FITC (clone I3/2.3) | Biolegend | Cat#147709 RRID:AB_2563541 |
| Anti-mouse CD45 PerCP/Cy5.5 (clone 30-F11) | Biolegend | Cat#103131 RRID:AB_893344 |
| Anti-mouse CD62L Alexa Fluor 488 (clone MEL-14) | Biolegend | Cat#104419 RRID:AB_493377 |
| Anti-mouse CD62L PE/Cy7 (clone MEL-14) | Biolegend | Cat#104417 RRID:AB_313102 |
| Anti-mouse CD69 APC (clone H1.2F3) | Biolegend | Cat#104513 RRID:AB_492844 |
| Anti-mouse CD69 PE/Cy7 (clone H1.2F3) | Biolegend | Cat#104511 RRID:AB_493565 |
| Anti-mouse CD8a BV711 (clone 53-6.7) | Biolegend | Cat#100747 RRID:AB_11219594 |
| Anti-mouse CD8a PE (clone 53-6.7) | Biolegend | Cat#100707 RRID:AB_312746 |
| Anti-mouse CD8a PE/Cy7 (clone 53-6.7) | Biolegend | Cat#100721 RRID:AB_312760 |
| Anti-mouse CD90.2 APC (clone 30-H12) | Biolegend | Cat#105311 RRID:AB_313182 |
| Anti-mouse CD90.2 APC/Cy7 (clone 30-H12) | Biolegend | Cat#105327 RRID:AB_10613280 |
| Anti-mouse c-Kit Alexa Fluor 488 (clone 2B8) | Biolegend | Cat#105815 RRID:AB_493473 |
| Anti-mouse c-Kit PE (clone 2B8) | Biolegend | Cat#105807 RRID:AB_313216 |
| Anti-mouse c-Kit PE/Dazzle 594 (clone 2B8) | Biolegend | Cat#105833 RRID:AB_2564054 |
| Anti-mouse CSF1R APC/Cy7 (clone AFS98) | Biolegend | Cat#135531 RRID:AB_2632739 |
| Anti-mouse CSF1R BV605 (clone AFS98) | Biolegend | Cat#135517 RRID:AB_2562760 |
| Anti-mouse CSF1R PE (clone AFS98) | Biolegend | Cat#135505 RRID:AB_1937254 |
| Anti-mouse CSF1R PE/Cy7 (clone AFS98) | Biolegend | Cat#135523 RRID:AB_2566459 |
| Anti-mouse CSF1R PE/Dazzle 594 (clone AFS98) | Biolegend | Cat#135527 RRID:AB_2566522 |
| Anti-mouse CX3CR1 Alexa Fluor 647 (clone SA011F11) | Biolegend | Cat#848003 RRID:AB_2721644 |
| Anti-mouse CX3CR1 BV711 (clone SA011F11) | Biolegend | Cat#149031 RRID:AB_2565939 |
| Anti-mouse CXCR2 BV421 (clone V48-2310) | BD Biosciences | Cat#566622 RRID:AB_2864336 |
| Anti-mouse CXCR2 BV605 (clone V48-2310) | BD Biosciences | Cat#747814 RRID:AB_2872278 |
| Anti-mouse CXCR2 PE (clone SA044G4) | Biolegend | Cat#149303 RRID:AB_2565691 |
| Anti-mouse CXCR2 PerCP/Cy5.5 (clone SA044G4) | Biolegend | Cat#149307 RRID:AB_2565695 |
| Anti-mouse F4/80 BV650 (clone BM8) | Biolegend | Cat#123149 RRID:AB_2564589 |
| Anti-mouse GM-CSF (MP1-22E9) | Biolegend | Cat#505415 RRID:AB_2810635 |
| Anti-mouse Gr-1 Alexa Fluor 488 (clone RB6-8C5) | Biolegend | Cat#108419 RRID:AB_493480 |
| Anti-mouse Gr-1 Alexa Fluor 700 (clone RB6-8C5) | Biolegend | Cat#108421 RRID:AB_493728 |
| Anti-mouse Gr-1 PE (clone RB6-8C5) | Biolegend | Cat#108407 RRID:AB_313372 |
| Anti-mouse Gr-1 PE/Dazzle 594 (clone RB6-8C5) | Biolegend | Cat#108451 RRID:AB_2564248 |
| Anti-mouse Gr-1 PerCP/Cy5.5 (clone RB6-8C5) | Biolegend | Cat#108427 RRID:AB_893561 |
| Anti-mouse HLA-IA/E AF488 (clone M5/114.15.2) | Biolegend | Cat#107615 RRID:AB_493524 |
| Anti-mouse HLA-IA/E BV785 (clone M5/114.15.2) | Biolegend | Cat#107645 RRID:AB_2565977 |
| Anti-mouse HLA-IA/E PE (clone M5/114.15.2) | Biolegend | Cat#107607 RRID:AB_313322 |
| Anti-mouse IFN-γ (XMG1.2) | Biolegend | Cat#505833 RRID:AB_11147371 |
| Anti-mouse IFN-γ BV421 (clone XMG1.2) | Biolegend | Cat#505829 RRID:AB_10897937 |
| Anti-mouse IL-10 (1B1.3a) | Biolegend | Cat#504907 RRID:AB_2810629 |
| Anti-mouse IL-12/IL-23 p40 (C17.8) | Biolegend | Cat#505307 RRID:AB_11150770 |
| Anti-mouse IL21 (S20017B) | Biolegend | Cat#122202 RRID:AB_2941414 |
| Anti-mouse Ly6A/E (Sca1) (D7) BV785 | Biolegend | Cat#108139 RRID:AB_2565957 |
| Anti-mouse Ly6C APC (clone HK1.4) | Biolegend | Cat#128015 RRID:AB_1732087 |
| Anti-mouse Ly6G BV421 (clone 1A8) | Biolegend | Cat#127627 RRID:AB_10897944 |
| Anti-mouse Ly6G PE/Dazzle 594 (clone 1A8) | Biolegend | Cat#127647 RRID:AB_2566318 |
| Anti-mouse Ly6G PerCP/Cy5.5 (clone 1A8) | Biolegend | Cat#127615 RRID:AB_1877272 |
| Anti-mouse NK1.1 APC (clone S17016D) | Biolegend | Cat#156505 RRID:AB_2876525 |
| Anti-mouse NK1.1 APC/Cy7 (clone S17016D) | Biolegend | Cat#156509 RRID:AB_2876527 |
| Anti-mouse P2RY12 PE (clone S16007D) | Biolegend | Cat#848003 RRID:AB_2721644 |
| Anti-mouse Podoplanin (8.1.1) PerCP/Cy5.5 | Biolegend | Cat#127421 RRID:AB_2814015 |
| Anti-mouse SiglecF APC (clone S17007L) | Biolegend | Cat#155507 RRID:AB_2750236 |
| Anti-mouse SiglecF APC/Cy7 (clone S17007L) | Biolegend | Cat#155531 RRID:AB_2904295 |
| Anti-mouse SOX2 PE (clone 14A6A34) | Biolegend | Cat#656103 RRID:AB_2562852 |
| Anti-mouse/human B220 APC (clone RA3-6B2) | Biolegend | Cat#103211 RRID:AB_312996 |
| Anti-mouse/human B220 APC/Cy7 (clone RA3-6B2) | Biolegend | Cat#103223 RRID:AB_313006 |
| Anti-mouse/human CD11b APC (M1/70) | Biolegend | Cat#101211 RRID:AB_2044007 |
| Anti-mouse/human CD11b APC/Cy7 (clone M1/70) | Biolegend | Cat#101225 RRID:AB_830641 |
| Anti-mouse/human CD11b BV421 (clone M1/70) | Biolegend | Cat#101235 RRID:AB_10897942 |
| Anti-mouse/human CD11b FITC (clone M1/70) | Biolegend | Cat#101205 RRID:AB_312788 |
| Anti-mouse/human CD11b PE (clone M1/70) | Biolegend | Cat#101207 RRID:AB_312790 |
| Anti-mouse/human CD44 Alexa Fluor 488 (clone IM7) | Biolegend | Cat#103015 RRID:AB_493678 |
| Anti-mouse/human CD44 APC (clone IM7) | Biolegend | Cat#103011 RRID:AB_312962 |
| Anti-mouse/human CD44 BV785 (clone IM7) | Biolegend | Cat#103041 RRID:AB_11218802 |
| Donkey anti-Rabbit IgG (H+L) Highly Cross-Adsorbed Secondary Antibody, Alexa Fluor 555 | Thermo Fisher Invitrogen | Cat#A31572 RRID:AB_162543 |
| Goat anti-Mouse IgG (H+L) Superclonal Secondary Antibody, Alexa Fluor 488 | Thermo Fisher Invitrogen | Cat#A28175 RRID:AB_2536161 |
| InVivoMAb anti-mouse CD4 (clone GK1.5) | BioXCell | Cat#BE0003-1 RRID:AB_1107636 |
| InVivoMAb anti-mouse CD8α (clone 53-6.7) | BioXCell | Cat#BE0004-1 RRID:AB_1107671 |
| InVivoMAb anti-mouse CD90.2 (Thy1.2) (clone 30H12) | BioXCell | Cat#BE0066 RRID:AB_1107682 |
| InVivoMAb anti-mouse Ly6G (clone 1A8) | BioXCell | Cat#BE0075-1 RRID:AB_1107721 |
| InVivoMAb rat IgG2a isotype control, anti-trinitrophenol (clone 2A3) | BioXCell | Cat#BE0089 RRID:AB_1107769 |
| InVivoMAb rat IgG2b isotype control, anti-keyhole limpet hemocyanin (clone LTF-2) | BioXCell | Cat#BE0090 RRID:AB_1107780 |
| Isotype, mouse IgG2a κ (clone MOPC-173) | Biolegend | Cat#400202 RRID:AB_2927399 |
| Isotype, normal goat IgG (polyclonal) | R&D Systems | Cat#AB-108-C RRID:AB_354267 |
| Isotype, rat IgG2a κ (clone RTK2758) | Biolegend | Cat#400501 RRID:AB_326523 |
| Biological samples | ||
| Human: Fresh GBM tissue from time of initial resection | UCSF Brain Tumor Center | N/A |
| Human: Patient and control blood | UCSF Brain Tumor Center | N/A |
| Chemicals, peptides, and recombinant proteins | ||
| Accutase Cell Detachment Reagent | Innovative Cell Technologies | Cat#AT104 |
| Alloxate™ (Meloxicam) Solution for Injection 10 ml | Patterson Veterinary Supply | Cat#078931368 |
| AMD3100 octahydrochloride, CXCR4 antagonist | Abcam | Cat#ab120718 CAS: 155148-31-5 |
| Animal-Free Recombinant Human EGF | Peprotech | Cat#AF-100-15 |
| Apotracker™ Green | Biolegend | Cat#427401 |
| Bovine Serum Albumin, heat shock fraction, protease free, low endotoxin, suitable for cell culture, pH 7, ≥98% | Sigma-Aldrich | Cat#A4919 CAS: 9048-46-8 |
| Bupivacaine 0.255, 10ml vials | Patterson Veterinary Supply | Cat#078904881 |
| Buprenex buprenorphine HCL, 0.3 mg/mL | Patterson Veterinary Supply | Cat#078502280 |
| Dimethyl sulfoxide ACS reagent, >=99.9% | Sigma-Aldrich | Cat#472301 CAS: 67-68-5 |
| D-Luciferin, Potassium Salt | Gold Biotechnology | Cat#LUCK-2G CAS: 115144-35-9 |
| DNase 1 100MG | Worthington Biochemical Corporation | Cat#LS002007 |
| Epredia™ Cytoseal™ Mountant 60 | Fisher Scientific | Cat#83104 |
| Gem21 NeuroPlex™ Supplement without Vitamin A | GeminiBio | Cat#400-161-010 |
| Gibco 2-Mercaptoethanol | Thermo Fisher | Cat#21985023 |
| Gibco ACK Lysing Buffer | Thermo Fisher | Cat#A1049201 |
| Gibco Collagenase, Type IV, powder | Thermo Fisher | Cat#17104019 |
| Gibco DMEM, high glucose, no glutamine | Thermo Fisher | Cat#11960044 |
| Gibco DMEM/F-12 | Thermo Fisher | Cat#11320033 |
| Gibco DPBS, no calcium, no magnesium | Thermo Fisher | Cat#14190144 |
| Gibco GlutaMAX™ Supplement | Thermo Fisher | Cat#35050061 |
| Gibco HEPES (1M) | Thermo Fisher | Cat#15630130 |
| Gibco Hibernate™-A Medium | Thermo Fisher | Cat#A1247501 |
| Gibco MEM Non-Essential Amino Acids Solution (100X) | Thermo Fisher | Cat#11140050 |
| Gibco Penicillin-Streptomycin (10,000 U/mL) | Thermo Fisher | Cat#15140122 |
| Gibco RPMI 1640 Medium | Thermo Fisher | Cat#11875093 |
| Gibco Sodium Pyruvate (100 mM) | Thermo Fisher | Cat#11360070 |
| Gibco TrypLE™ Express Enzyme (1X), phenol red | Thermo Fisher | Cat#12605010 |
| ImmunoCult™ Human CD3/CD28 T Cell Activator | Stem Cell | Cat#10971 |
| Invitrogen CellTracker™ Green CMFDA Dye | Thermo Fisher | Cat#C2925 |
| Invitrogen DQ™ Ovalbumin | Thermo Fisher | Cat#D12053 |
| Invitrogen eBioscience™ Lipopolysaccharide (LPS) Solution (500X) | Thermo Fisher | Cat#00-4976-93 |
| Invitrogen SYTOX™ Dead Cell Stain Sampler Kit | Thermo Fisher | Cat#S34862 |
| IRDye® 800CW Streptavidin | LI-COR | Cat#926-32230 |
| Isoflurane, USP Inhalation Anesthetic | Dechra | Cat#DP7000 |
| Liquid Cyanoacrylate Glue | Avantor VWR | Cat# 470024-626 |
| Normal Goat Serum, Unconjugated, 10ml | Jackson Immuno Research Labs | Cat#005000121 |
| OVA 323-339 | InvivoGen | Cat#vac-isq |
| Recombinant Human FGF-basic (154 a.a.) | Peprotech | Cat#100-18B |
| Recombinant mouse IL-2 protein (Active) | Abcam | Cat# ab259380 |
| RICCA Chemical R9380000-500C Wright-Giemsa Stain Mixture | Genesee Scientific | Cat#72-850 CAS: 67-56-1 |
| Scrub Surgical Betadine PVP Iodine 7.5% Pump | Purdue Frederick Co | Cat#67618-151-17 |
| Seradigm Premium Grade Fetal Bovine Serum (FBS) | Avantor VWR | Cat#97068-085 |
| Sodium Chloride 0.9% Injection Preservative Free SDV | Henry Schein | Cat#1049943 |
| Southern Biotech DAPI Fluoromount-G® | Avantor VWR | DAPI Fluoromount-G® |
| Thermo Scientific Chemicals D(+)-Sucrose, 99+%, for biochemistry, DNAse, RNAse and protease free | Thermo Fisher | Cat#419762500 CAS: 57-50-1 |
| Thermo Scientific Chemicals Paraformaldehyde Solution, 4% in PBS | Thermo Fisher | Cat#J19943.K2 |
| Triton™ X-100 | Sigma-Aldrich | Cat#T8787 CAS: 9036-19-5 |
| Zombie Aqua™ Fixable Viability Kit | Biolegend | Cat#423101 |
| Zombie NIR™ Fixable Viability Kit | Biolegend | Cat#423105 |
| Critical commercial assays | ||
| Applied Biosystems PowerUp SYBR Green Master Mix | Thermo Fisher | Cat#A25776 |
| CFSE Cell Division Tracker Kit | Biolegend | Cat#423801 |
| Chromium Next GEM Chip G Single Cell Kit | 10X Genomics | PN-1000127 |
| Chromium Next GEM Single Cell 3’ GEM, Library & Gel Bead Kit v3.1 | 10X Genomics | PN-1000121 |
| EasySep™ Direct Human Neutrophil Isolation Kit | Stem Cell | Cat#19666 |
| EasySep™ Direct Human T Cell Isolation Kit | Stem Cell | Cat#19661 |
| Human Myeloid v2 Primers | Nanotring | Cat#115000177 |
| Human Myeloid v2 Profiling Codeset (XT_PGX_HuV2_Myeloid_CSO) | Nanotring | Cat#115000171 |
| Human Osteopontin (OPN) Quantikine ELISA Kit | R&D Systems | Cat#DOST00 |
| Invitrogen eBioscience™ Foxp3 / Transcription Factor Staining Buffer Set | Thermo Fisher | Cat#00-5523-00 |
| MojoSort™ Mouse CD4 T Cell Isolation Kit | Biolegend | Cat#480005 |
| MojoSort™ Mouse Neutrophil Isolation Kit | Biolegend | Cat#480057 |
| Mouse Tumor 360 Profiling Codeset + Primers (XT Mm Tumor Sig 360 CSO+PS) | Nanotring | Cat#115000426 |
| nCounter Sprint Cartridge | Nanostring | Cat#100078 |
| Proteome Profiler Mouse Cytokine Array Kit, Panel A | R&D Systems | Cat#ARY006 |
| Qiashredder | Qiagen | Cat#78654 |
| qScript™ XLT cDNA SuperMix | Quanta Bio | Cat#95161-500 |
| RNeasy Mini Kit | Qiagen | Cat#74104 |
| Single Index Kit T Set A | 10X Genomics | PN-1000213 |
| Deposited data | ||
| Human GBM PBN scRNAseq dataset | GEO | GSM8380727 |
| Human GBM TAN scRNAseq dataset | GEO | GSM8380728 |
| Human GBM TAN and PBN scRNAseq analysis code | FigShare | DOI: 10.6084 |
| TCGA mRNA normalized and miRNA data | Genomic Data Commons | https://gdc.cancer.gov/about-data/publications/pancanatlas |
| TCGA clinical and subtype data | Genomic Data Commons; Sanchez-Vega et al., 2018; Robertson et al., 2017 | https://gdc.cancer.gov/about-data/publications/pancanatlas |
| Experimental models: Cell lines | ||
| Human: DBTRG-05MG | ATCC | ATCC: CRL-2020 RRID:CVCL_1169 |
| Human: GBM43 | Mayo Clinic Brain Tumor Xenograft National Resource | Human: GBM43 |
| Human: GBM6 | Mayo Clinic Brain Tumor Xenograft National Resource | Human: GBM6 |
| Human: U-251MG | Sigma-Aldrich | Cat#09063001 RRID: CVCL_0021 |
| Mouse: BGL1 | Dr. Hideho Okada, UCSF Ahn et al., 2015 |
N/A |
| Mouse: GL261 | US National Cancer Institute | RRID: CVCL_Y003 |
| Mouse: SB28 | Dr. Hideho Okada, UCSF Genoud et al., 2018 |
N/A |
| Experimental models: Organisms/strains | ||
| Mouse: B6.Cg-Tg(TcraTcrb)425Cbn/J [OT-II] | The Jackson Laboratory | Stock No.: 004194 |
| Mouse: BalbC/J | The Jackson Laboratory | Stock No.: 000651 |
| Mouse: C57BL/6J | The Jackson Laboratory | Stock No.: 000664 |
| Mouse: UBC-GFP: C57BL/6-Tg(UBC-GFP)30Scha/J | Dr. Harold Chapman, Dr. Martin C Valdearcos, and Dr. Suneil Koliwad (UCSF) | N/A |
| Software and algorithms | ||
| BioRender | BioRender.com | https://www.biorender.com/ |
| cellranger | 10X Genomics | https://support.10xgenomics.com/ |
| ClusterExplorer (v1.7.6) | FlowJo Exchange | https://www.flowjo.com/exchange/ |
| clusterProfiler v4.4.4 | N/A | https://bioconductor.org/packages/release/bioc/html/clusterProfiler.html |
| Destiny 3.10.0 | N/A | https://bioconductor.org/packages/release/bioc/html/destiny.html |
| Downsample (v3.3.1) | FlowJo Exchange | https://www.flowjo.com/exchange/ |
| EnhancedVolcano v1.14.0 | N/A | https://bioconductor.org/packages/release/bioc/html/EnhancedVolcano.html |
| enrichR | N/A | https://maayanlab.cloud/Enrichr/ |
| Fiji | Schindelin et al. | https://fiji.sc/ |
| FlowJo v10.8.1 | FlowJo Corp. | https://www.flowjo.com/ |
| FlowSOM (v4.1.0) | FlowJo Exchange | https://www.flowjo.com/exchange/ |
| ggplot 4.2.0 | N/A | https://github.com/tidyverse/ggplot2 |
| ImageJ | Schneider et al. | https://imagej.nih.gov/ij/ |
| Living Image 4.2 | Caliper Life Sciences | https://www.perkinelmer.com/category/in-vivo-imaging-software |
| Monocle3 v1.2.9 | N/A | https://cole-trapnell-lab.github.io/monocle3/ |
| nSolver v4.0.70 | Nanostring | https://nanostring.com/products/analysis-solutions/nsolver-advanced-analysis-software/ |
| Pathview v1.36.1 | N/A | https://bioconductor.org/packages/release/bioc/html/pathview.html |
| Prism v9.5.1 | GraphPad | https://www.graphpad.com/ |
| Python 3.9 | Python Software Foundation | https://www.python.org |
| R v4.2.0 | The R Foundation | https://cran.r-project.org/src/base/R-4/ |
| Real Statistics Resource Pack Release 7.6 | Charles Zaiontz, © 2013-2021 | https://real-statistics.com/ |
| Rosalind v3.36.1.2 | OnRamp Bio | https://www.rosalind.bio/ |
| scVelo v0.2.4 | N/A | https://scvelo.readthedocs.io/en/stable/installation/ |
| Seurat v4.3.0 | N/A | https://github.com/satijalab/seurat |
| UMAP (v4.0.4) | FlowJo Exchange | https://www.flowjo.com/exchange/ |
| velocyto v0.17.17 | N/A | http://velocyto.org |
| Other | ||
| 0.5 mm x 2.3 mm Tungsten Carbide Burr for Micro Drill | Fine Science Tools | Cat#19009-05 |
| 10 μL, Model 901 Removable Needle (RN) Syringe | Hamilton | Cat#7648-01 |
| 26 gauge, Small Hub RN Needle, 1”, PS4 | Hamilton | Cat#7804-03 |
| 34 gauge, Small Hub RN Needle, 0.375”, PS3 | Hamilton | Cat#207434 |
| 7mm Reflex Clip Applier | Braintree Scientific | Cat#RF7APL |
| Cellstar® Suspension Culture Flask, 50 mL, PS, White Filter Screw Cap | Greiner Bio-One | Cat#690195 |
| Cellstar® TC Cell Culture Flask, 50 mL, PS, Red Filter Screw Cap | Greiner Bio-One | Cat#658175 |
| Costar® 96-well Clear Flat Bottom Ultra-Low Attachment Microplate | Corning | Cat#3474 |
| Costar® 96-well Clear Round Bottom Ultra-Low Attachment Microplate | Corning | Cat#7007 |
| Ethicon bone wax: 2.5G | Ethicon Endo-surgery | Cat#W31G |
| Exel International Disposable Scalpels | Fisher Scientific | Cat#14-840-01 |
| Falcon® 48-well Clear Flat Bottom TC-treated Cell Culture Plate, with Lid | Corning | Cat#353078 |
| Falcon® Permeable Support for 12-well Plate with 3.0 μm Transparent PET Membrane | Corning | Cat#353181 |
| Falcon™ Cell Strainer 70 μm | Corning | Cat#352350 |
| Falcon™ Round-Bottom Polystyrene Test Tubes | Corning | Cat#352058 |
| Fisherbrand™ Cover Glasses: Rectangles | Fisher Scientific | Cat#12-545G |
| Fisherbrand™ Wood Handled 6” Cotton Swab | Fisher Scientific | Cat#22363157 |
| GenClone 12-Well Non-Treated Plates Flat Bottom | Genesee Scientific | Cat#25-101 |
| Luer-Lok™ Syringe sterile, single use, 5 mL | BD Biosciences | Cat#309646 |
| Miltex™ Mid Grade Eye Dressing Forceps | Integra LifeSciences | Cat#V918-780 |
| Nunc™ Lab-Tek™ 8-well Chamber Slide w/ removable wells | Thermo Fisher | Cat#177402 |
| PrecisionGlide™ 25 G X 5/8” Hypodermic Needles | BD Biosciences | Cat#305122 |
| Reflex Wound Clips 7 mm | CellPoint Scientific | Cat#203-1000 |
| Roche Protector RNase Inhibitor | Sigma-Aldrich | Cat#3335402001 |
| SAFE-T-FILL® Capillary Blood Collection Tubes - EDTA | RAM Scientific | Cat#07-7051 |
| Scissors, Fine, Excelta Corp® | VWR | Cat#75880-906 |
| Size 1 Head Exposure Shield Size 1 | Precision X-Ray | Cat#XD1907-2015 |
| Size 1 Holding Fixture, No Flank | Precision X-Ray | Cat#XD1907-1014 |
| Steriflip-HV Sterile Centrifuge Tube Top Filter Unit, 0.45 μm pore size, PVDF | Millipore Sigma | Cat#SE1M003M00 |
| Tissue-Plus™ O.C.T. Compound Tissue-Plus™ O.C.T. Compound, Clear | Fisher Scientific | Cat#FIS23-730-571 |
| Vacutainer™ 10mL Plastic Blood Collection Tubes with Sodium Heparin: Conventional Stopper | BD Biosciences | Cat#367874 |
| Vacutainer™ Plastic Blood Collection Tubes with K2 EDTA: Hemogard™ Closure | BD Biosciences | Cat#366643 |
| VistaVision™ HistoBond® Adhesive Microscope Slides, Premium | Avantor VWR | Cat# 16004-408 |