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n a imaris 9 5 1 software oxford instruments n a imarisfileconverter 9 5 1 oxford instruments n a metamorph software molecular devices n a gepia2
N A Imaris 9 5 1 Software Oxford Instruments N A Imarisfileconverter 9 5 1 Oxford Instruments N A Metamorph Software Molecular Devices N A Gepia2, supplied by Oxford Instruments, used in various techniques. Bioz Stars score: 99/100, based on 44474 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
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N A Imaris 9 5 1 Software Oxford Instruments N A Imarisfileconverter 9 5 1 Oxford Instruments N A Metamorph Software Molecular Devices N A Gepia2, supplied by Oxford Instruments, used in various techniques. Bioz Stars score: 99/100, based on 44474 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/software+metamorph+software/Imaris/pm41241939-242-101-102
Average 99 stars, based on 44474 article reviews
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Recombinant:Article Title: Intermediate filaments promote glioblastoma cell invasion by controlling nuclear deformations and mechanosensitive expression of MMP14. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Methylene Blue hydrate Sigma-Aldrich M4159 Ultrapure Low melting point agarose Invitrogen 16520–050 DMSO Sigma-Aldrich D2650-100ML GM6001 MMP inhibitor Sigma-Aldrich 38249992 Clear Silicone Rubber Compound kit Momentive RTV 615 Fibronectin Sigma Aldrich F1141-1MG SiR-DNA Spirochrome SC007 CellTracker Red CMTPX Invitrogen C34552 Rat tail collagen I Corning 354236 HEPES Sigma-Aldrich 7365-45-9 poly-L-lysine/polyethylene glycol (PLL-PEG, Graft Ratio 3.5, PLL MW 20000) JemKem PLL20K-G35-PEG2K NaHCO 3 Sigma Aldrich S5761 3-(Trimethoxysilyl)propyl methacrylate Sigma Aldrich 440159 acetic acid Sigma Aldrich A6283 acrylamide solution Sigma Aldrich A4058 bisacrylamide solution Sigma Aldrich 1.01546 ammonium persulfate (APS) Sigma Aldrich 215589 tetramethylethylenediamine (TEMED) Sigma Aldrich 1.10732 Sulpho-SANPAH Thermo Scientific 22589 Paraformaldehyde, 16% w/v aq. soln., methanol free Thermo Scientific 11490570 Triton X-100 Sigma Aldrich 282103 Bovine Serum Albumin (BSA) Sigma Aldrich A9418 Hoechst 33342 Thermo Scientific 62249 Alexa 647 phalloidin Cell Signaling Technologies #8940 Prolong Diamond Invitrogen P36961 SYBR Green Master mix Applied Biosystems 4309155 TRIzol Invitrogen 15596026 Chloroform Sigma Aldrich N/A NuPage LDS sample buffer Invitrogen NP0008 cOmplete TM Protease Inhibitor Cocktail Roche CO-RO NuPAGE TM Bis-Tris Gels, 4–12% NP0321BOX Invitrogen nitrocellulose membrane Thermo Scientific 88018 PVDF Transfer Membranes Thermo Scientific 88518 Clarity Western ECL Blotting Substrate Biorad 1705060S TWEEN® 20 Sigma Aldrich P6585 Deposited data Glioblastoma 10X Visium spatial transcriptomics Greenwald et al. 33 https://doi.org/10.5281/zenodo.8105466 Glioblastoma single cell RNA sequencing Darmanis et al. 26 GEO: GSE84465 Glioblastoma single cell RNA sequencing Yuan et al. 25 GEO: GSE103224 Glioblastoma single cell RNA sequencing integrated dataset Ruiz-Moreno et al. 27 https://cellxgene.cziscience.com/ collections/999f2a15-3d7e-440b-96ae2c806799c08c Experimental models: Cell lines U251-MG, 1 to 20 passages after thawing ECACC 09063001 U3117 glioblastoma cells, 1 to 20 passages https://doi.org/10.1016/j.ebiom.2015.08.026 N/A HEK-293T Merck 12022001 (Continued on next page) Cell Reports 44, 116553, November 25, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains zebrafish larvae Tg(fli1a:EGFP)y1 Herbomel lab Lawson et al. 65 zebrafish larvae Tg(gfap:GFP)mi2001 Herbomel lab Bernardos & Raymond 66 Oligonucleotides See Table S5 for oligonucleotides N/A N/A Recombinant DNA pSpCas9(BB)-2A-GFP Addgene #48138 pLKO.1 puro Addgene #8453 psPAX2 Addgene #12260 pMD2.G Addgene #12259 pRSV-rev Addgene #12253 pMDLg/pRRE Addgene #12251 pLenti PGK mKate2 Addgene #154290 MISSION® shRNA MMP14 1 Sigma-Aldrich® Advanced Genomics TRCN0000050853 MISSION® shRNA MMP14 1 Sigma-Aldrich® Advanced Genomics TRCN0000050854 MISSION® pLKO.1-puro Non-Target shRNA Control Plasmid DNA Sigma-Aldrich® Advanced Genomics SHC016 Software and algorithms Benchling CRISPR Guide RNA Design Tool https://www.benchling.com/crispr N/A SnapGene software www.snapgene.com Article Title: Radial astroglia cooperate with microglia to clear neuronal cell bodies during zebrafish optic tectum development. Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Ronidazole Sigma Cat# R7635-5G AcuI Restriction Enzyme New England Biolabs Cat# R0641S BssSI-v2 Restiction Enzyme New England Biolabs Cat# R0680L Critical commercial assays LysoTracker Deep Red Invitrogen/ThermoFisher Cat# L12492 Acridine Orange hemi (zinc chloride) salt Santa Cruz Biotechnology Cat# sc-214488 Recombinant DNA Reagent Lakritz forward primer (CCGGAATTACATCCCAAGAAC) Kay et al.29; Integrated DNA Technologies Custom Order Lakritz reverse primer (GGCCATGATGTAGCTCAGAG) Kay et al.29; Integrated DNA Technologies Custom Order slc1a3b:myrGFP-P2A-H2AmCherry Chen et al.27; provided by Monk lab RRID: Addgene_170208 p5e-slc1a3b Chen et al.27; provided by Monk lab RRID: Addgene_170205 pMe-myrEGFP Provided by Laura Fontenas N/A Experimental models: Organisms/strains See Table S1 for further strain details AB* (strain/strain background) ZIRC RRID: ZFIN_ZDB-GENO-960809-7 Tg(slc1a3b:myrGFP-P2A-H2AmCherry)vo80 Chen et al.27; provided by Monk lab RRID: ZFIN_ZDB-ALT-200915-2 Tg(slc1a3b:myrEGFP)uva74 This article (HMB, ZC) N/A Tg(slc1a3b:TagRFP-CAAX)uva76 Brown, Barber, & Kucenas68 RRID: ZFIN_ZDB-ALT-250314-6 Tg(slc1a3b:mCerulean)uva84 This article (IW) N/A Tg(fli1a:EGFPF)y288Tg Yu et al.69 RRID: ZFIN_ZDB-ALT-151231-3 atoh7th241 Kelsh et al.30; provided by Schoppik lab RRID: ZFIN_ZDB-ALT-980203-363 Tg(atoh7:gap43-RFP)cu2 Zolessi et al.70; provided by Schoppik lab RRID: ZFIN_ZDB-ALT-070129-2 Tg(elavl3:H2B-GCaMP6s)uva98 This article (RIB) N/A Et(e1b:GAL4)s1101t Szobota et al.42 RRID: ZFIN_ZDB-ALT-070716-2 Tg(UAS:secHsa.ANXA5-YFP,myl7:RFP)f12 van Ham et al.43 RRID: ZFIN_ZDB-ALT-110603-3 Tg(slc1a3b:mCherry-2xFYVE;cry:mCherry)uva72Tg This article (IW) N/A Tg(mfap4.1:mTurquoise)xt27 Oehlers et al.71 RRID: ZFIN_ZDB-ALT-150424-9 Tg(mpeg1:Gal4-VP16)gl24 Ellet et al.72 RRID: ZFIN_ZDB-ALT-120117-3 Tg(5xUAS:GAP-TagYFP-2A-NTR2.0)jh513 Sharrock et al.73 RRID: ZFIN_ZDB-ALT-240130-3 csf1raj4e1 Parichy et al.74 RRID: ZFIN_ZDB-ALT-001205-14 Software and shRNA:Article Title: Intermediate filaments promote glioblastoma cell invasion by controlling nuclear deformations and mechanosensitive expression of MMP14. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Methylene Blue hydrate Sigma-Aldrich M4159 Ultrapure Low melting point agarose Invitrogen 16520–050 DMSO Sigma-Aldrich D2650-100ML GM6001 MMP inhibitor Sigma-Aldrich 38249992 Clear Silicone Rubber Compound kit Momentive RTV 615 Fibronectin Sigma Aldrich F1141-1MG SiR-DNA Spirochrome SC007 CellTracker Red CMTPX Invitrogen C34552 Rat tail collagen I Corning 354236 HEPES Sigma-Aldrich 7365-45-9 poly-L-lysine/polyethylene glycol (PLL-PEG, Graft Ratio 3.5, PLL MW 20000) JemKem PLL20K-G35-PEG2K NaHCO 3 Sigma Aldrich S5761 3-(Trimethoxysilyl)propyl methacrylate Sigma Aldrich 440159 acetic acid Sigma Aldrich A6283 acrylamide solution Sigma Aldrich A4058 bisacrylamide solution Sigma Aldrich 1.01546 ammonium persulfate (APS) Sigma Aldrich 215589 tetramethylethylenediamine (TEMED) Sigma Aldrich 1.10732 Sulpho-SANPAH Thermo Scientific 22589 Paraformaldehyde, 16% w/v aq. soln., methanol free Thermo Scientific 11490570 Triton X-100 Sigma Aldrich 282103 Bovine Serum Albumin (BSA) Sigma Aldrich A9418 Hoechst 33342 Thermo Scientific 62249 Alexa 647 phalloidin Cell Signaling Technologies #8940 Prolong Diamond Invitrogen P36961 SYBR Green Master mix Applied Biosystems 4309155 TRIzol Invitrogen 15596026 Chloroform Sigma Aldrich N/A NuPage LDS sample buffer Invitrogen NP0008 cOmplete TM Protease Inhibitor Cocktail Roche CO-RO NuPAGE TM Bis-Tris Gels, 4–12% NP0321BOX Invitrogen nitrocellulose membrane Thermo Scientific 88018 PVDF Transfer Membranes Thermo Scientific 88518 Clarity Western ECL Blotting Substrate Biorad 1705060S TWEEN® 20 Sigma Aldrich P6585 Deposited data Glioblastoma 10X Visium spatial transcriptomics Greenwald et al. 33 https://doi.org/10.5281/zenodo.8105466 Glioblastoma single cell RNA sequencing Darmanis et al. 26 GEO: GSE84465 Glioblastoma single cell RNA sequencing Yuan et al. 25 GEO: GSE103224 Glioblastoma single cell RNA sequencing integrated dataset Ruiz-Moreno et al. 27 https://cellxgene.cziscience.com/ collections/999f2a15-3d7e-440b-96ae2c806799c08c Experimental models: Cell lines U251-MG, 1 to 20 passages after thawing ECACC 09063001 U3117 glioblastoma cells, 1 to 20 passages https://doi.org/10.1016/j.ebiom.2015.08.026 N/A HEK-293T Merck 12022001 (Continued on next page) Cell Reports 44, 116553, November 25, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains zebrafish larvae Tg(fli1a:EGFP)y1 Herbomel lab Lawson et al. 65 zebrafish larvae Tg(gfap:GFP)mi2001 Herbomel lab Bernardos & Raymond 66 Oligonucleotides See Table S5 for oligonucleotides N/A N/A Recombinant DNA pSpCas9(BB)-2A-GFP Addgene #48138 pLKO.1 puro Addgene #8453 psPAX2 Addgene #12260 pMD2.G Addgene #12259 pRSV-rev Addgene #12253 pMDLg/pRRE Addgene #12251 pLenti PGK mKate2 Addgene #154290 MISSION® shRNA MMP14 1 Sigma-Aldrich® Advanced Genomics TRCN0000050853 MISSION® shRNA MMP14 1 Sigma-Aldrich® Advanced Genomics TRCN0000050854 MISSION® pLKO.1-puro Non-Target shRNA Control Plasmid DNA Sigma-Aldrich® Advanced Genomics SHC016 Software and algorithms Benchling CRISPR Guide RNA Design Tool https://www.benchling.com/crispr N/A SnapGene software www.snapgene.com Control:Article Title: Intermediate filaments promote glioblastoma cell invasion by controlling nuclear deformations and mechanosensitive expression of MMP14. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Methylene Blue hydrate Sigma-Aldrich M4159 Ultrapure Low melting point agarose Invitrogen 16520–050 DMSO Sigma-Aldrich D2650-100ML GM6001 MMP inhibitor Sigma-Aldrich 38249992 Clear Silicone Rubber Compound kit Momentive RTV 615 Fibronectin Sigma Aldrich F1141-1MG SiR-DNA Spirochrome SC007 CellTracker Red CMTPX Invitrogen C34552 Rat tail collagen I Corning 354236 HEPES Sigma-Aldrich 7365-45-9 poly-L-lysine/polyethylene glycol (PLL-PEG, Graft Ratio 3.5, PLL MW 20000) JemKem PLL20K-G35-PEG2K NaHCO 3 Sigma Aldrich S5761 3-(Trimethoxysilyl)propyl methacrylate Sigma Aldrich 440159 acetic acid Sigma Aldrich A6283 acrylamide solution Sigma Aldrich A4058 bisacrylamide solution Sigma Aldrich 1.01546 ammonium persulfate (APS) Sigma Aldrich 215589 tetramethylethylenediamine (TEMED) Sigma Aldrich 1.10732 Sulpho-SANPAH Thermo Scientific 22589 Paraformaldehyde, 16% w/v aq. soln., methanol free Thermo Scientific 11490570 Triton X-100 Sigma Aldrich 282103 Bovine Serum Albumin (BSA) Sigma Aldrich A9418 Hoechst 33342 Thermo Scientific 62249 Alexa 647 phalloidin Cell Signaling Technologies #8940 Prolong Diamond Invitrogen P36961 SYBR Green Master mix Applied Biosystems 4309155 TRIzol Invitrogen 15596026 Chloroform Sigma Aldrich N/A NuPage LDS sample buffer Invitrogen NP0008 cOmplete TM Protease Inhibitor Cocktail Roche CO-RO NuPAGE TM Bis-Tris Gels, 4–12% NP0321BOX Invitrogen nitrocellulose membrane Thermo Scientific 88018 PVDF Transfer Membranes Thermo Scientific 88518 Clarity Western ECL Blotting Substrate Biorad 1705060S TWEEN® 20 Sigma Aldrich P6585 Deposited data Glioblastoma 10X Visium spatial transcriptomics Greenwald et al. 33 https://doi.org/10.5281/zenodo.8105466 Glioblastoma single cell RNA sequencing Darmanis et al. 26 GEO: GSE84465 Glioblastoma single cell RNA sequencing Yuan et al. 25 GEO: GSE103224 Glioblastoma single cell RNA sequencing integrated dataset Ruiz-Moreno et al. 27 https://cellxgene.cziscience.com/ collections/999f2a15-3d7e-440b-96ae2c806799c08c Experimental models: Cell lines U251-MG, 1 to 20 passages after thawing ECACC 09063001 U3117 glioblastoma cells, 1 to 20 passages https://doi.org/10.1016/j.ebiom.2015.08.026 N/A HEK-293T Merck 12022001 (Continued on next page) Cell Reports 44, 116553, November 25, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains zebrafish larvae Tg(fli1a:EGFP)y1 Herbomel lab Lawson et al. 65 zebrafish larvae Tg(gfap:GFP)mi2001 Herbomel lab Bernardos & Raymond 66 Oligonucleotides See Table S5 for oligonucleotides N/A N/A Recombinant DNA pSpCas9(BB)-2A-GFP Addgene #48138 pLKO.1 puro Addgene #8453 psPAX2 Addgene #12260 pMD2.G Addgene #12259 pRSV-rev Addgene #12253 pMDLg/pRRE Addgene #12251 pLenti PGK mKate2 Addgene #154290 MISSION® shRNA MMP14 1 Sigma-Aldrich® Advanced Genomics TRCN0000050853 MISSION® shRNA MMP14 1 Sigma-Aldrich® Advanced Genomics TRCN0000050854 MISSION® pLKO.1-puro Non-Target shRNA Control Plasmid DNA Sigma-Aldrich® Advanced Genomics SHC016 Software and algorithms Benchling CRISPR Guide RNA Design Tool https://www.benchling.com/crispr N/A SnapGene software www.snapgene.com Plasmid Preparation:Article Title: Intermediate filaments promote glioblastoma cell invasion by controlling nuclear deformations and mechanosensitive expression of MMP14. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Methylene Blue hydrate Sigma-Aldrich M4159 Ultrapure Low melting point agarose Invitrogen 16520–050 DMSO Sigma-Aldrich D2650-100ML GM6001 MMP inhibitor Sigma-Aldrich 38249992 Clear Silicone Rubber Compound kit Momentive RTV 615 Fibronectin Sigma Aldrich F1141-1MG SiR-DNA Spirochrome SC007 CellTracker Red CMTPX Invitrogen C34552 Rat tail collagen I Corning 354236 HEPES Sigma-Aldrich 7365-45-9 poly-L-lysine/polyethylene glycol (PLL-PEG, Graft Ratio 3.5, PLL MW 20000) JemKem PLL20K-G35-PEG2K NaHCO 3 Sigma Aldrich S5761 3-(Trimethoxysilyl)propyl methacrylate Sigma Aldrich 440159 acetic acid Sigma Aldrich A6283 acrylamide solution Sigma Aldrich A4058 bisacrylamide solution Sigma Aldrich 1.01546 ammonium persulfate (APS) Sigma Aldrich 215589 tetramethylethylenediamine (TEMED) Sigma Aldrich 1.10732 Sulpho-SANPAH Thermo Scientific 22589 Paraformaldehyde, 16% w/v aq. soln., methanol free Thermo Scientific 11490570 Triton X-100 Sigma Aldrich 282103 Bovine Serum Albumin (BSA) Sigma Aldrich A9418 Hoechst 33342 Thermo Scientific 62249 Alexa 647 phalloidin Cell Signaling Technologies #8940 Prolong Diamond Invitrogen P36961 SYBR Green Master mix Applied Biosystems 4309155 TRIzol Invitrogen 15596026 Chloroform Sigma Aldrich N/A NuPage LDS sample buffer Invitrogen NP0008 cOmplete TM Protease Inhibitor Cocktail Roche CO-RO NuPAGE TM Bis-Tris Gels, 4–12% NP0321BOX Invitrogen nitrocellulose membrane Thermo Scientific 88018 PVDF Transfer Membranes Thermo Scientific 88518 Clarity Western ECL Blotting Substrate Biorad 1705060S TWEEN® 20 Sigma Aldrich P6585 Deposited data Glioblastoma 10X Visium spatial transcriptomics Greenwald et al. 33 https://doi.org/10.5281/zenodo.8105466 Glioblastoma single cell RNA sequencing Darmanis et al. 26 GEO: GSE84465 Glioblastoma single cell RNA sequencing Yuan et al. 25 GEO: GSE103224 Glioblastoma single cell RNA sequencing integrated dataset Ruiz-Moreno et al. 27 https://cellxgene.cziscience.com/ collections/999f2a15-3d7e-440b-96ae2c806799c08c Experimental models: Cell lines U251-MG, 1 to 20 passages after thawing ECACC 09063001 U3117 glioblastoma cells, 1 to 20 passages https://doi.org/10.1016/j.ebiom.2015.08.026 N/A HEK-293T Merck 12022001 (Continued on next page) Cell Reports 44, 116553, November 25, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains zebrafish larvae Tg(fli1a:EGFP)y1 Herbomel lab Lawson et al. 65 zebrafish larvae Tg(gfap:GFP)mi2001 Herbomel lab Bernardos & Raymond 66 Oligonucleotides See Table S5 for oligonucleotides N/A N/A Recombinant DNA pSpCas9(BB)-2A-GFP Addgene #48138 pLKO.1 puro Addgene #8453 psPAX2 Addgene #12260 pMD2.G Addgene #12259 pRSV-rev Addgene #12253 pMDLg/pRRE Addgene #12251 pLenti PGK mKate2 Addgene #154290 MISSION® shRNA MMP14 1 Sigma-Aldrich® Advanced Genomics TRCN0000050853 MISSION® shRNA MMP14 1 Sigma-Aldrich® Advanced Genomics TRCN0000050854 MISSION® pLKO.1-puro Non-Target shRNA Control Plasmid DNA Sigma-Aldrich® Advanced Genomics SHC016 Software and algorithms Benchling CRISPR Guide RNA Design Tool https://www.benchling.com/crispr N/A SnapGene software www.snapgene.com Software:Article Title: Intermediate filaments promote glioblastoma cell invasion by controlling nuclear deformations and mechanosensitive expression of MMP14. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Methylene Blue hydrate Sigma-Aldrich M4159 Ultrapure Low melting point agarose Invitrogen 16520–050 DMSO Sigma-Aldrich D2650-100ML GM6001 MMP inhibitor Sigma-Aldrich 38249992 Clear Silicone Rubber Compound kit Momentive RTV 615 Fibronectin Sigma Aldrich F1141-1MG SiR-DNA Spirochrome SC007 CellTracker Red CMTPX Invitrogen C34552 Rat tail collagen I Corning 354236 HEPES Sigma-Aldrich 7365-45-9 poly-L-lysine/polyethylene glycol (PLL-PEG, Graft Ratio 3.5, PLL MW 20000) JemKem PLL20K-G35-PEG2K NaHCO 3 Sigma Aldrich S5761 3-(Trimethoxysilyl)propyl methacrylate Sigma Aldrich 440159 acetic acid Sigma Aldrich A6283 acrylamide solution Sigma Aldrich A4058 bisacrylamide solution Sigma Aldrich 1.01546 ammonium persulfate (APS) Sigma Aldrich 215589 tetramethylethylenediamine (TEMED) Sigma Aldrich 1.10732 Sulpho-SANPAH Thermo Scientific 22589 Paraformaldehyde, 16% w/v aq. soln., methanol free Thermo Scientific 11490570 Triton X-100 Sigma Aldrich 282103 Bovine Serum Albumin (BSA) Sigma Aldrich A9418 Hoechst 33342 Thermo Scientific 62249 Alexa 647 phalloidin Cell Signaling Technologies #8940 Prolong Diamond Invitrogen P36961 SYBR Green Master mix Applied Biosystems 4309155 TRIzol Invitrogen 15596026 Chloroform Sigma Aldrich N/A NuPage LDS sample buffer Invitrogen NP0008 cOmplete TM Protease Inhibitor Cocktail Roche CO-RO NuPAGE TM Bis-Tris Gels, 4–12% NP0321BOX Invitrogen nitrocellulose membrane Thermo Scientific 88018 PVDF Transfer Membranes Thermo Scientific 88518 Clarity Western ECL Blotting Substrate Biorad 1705060S TWEEN® 20 Sigma Aldrich P6585 Deposited data Glioblastoma 10X Visium spatial transcriptomics Greenwald et al. 33 https://doi.org/10.5281/zenodo.8105466 Glioblastoma single cell RNA sequencing Darmanis et al. 26 GEO: GSE84465 Glioblastoma single cell RNA sequencing Yuan et al. 25 GEO: GSE103224 Glioblastoma single cell RNA sequencing integrated dataset Ruiz-Moreno et al. 27 https://cellxgene.cziscience.com/ collections/999f2a15-3d7e-440b-96ae2c806799c08c Experimental models: Cell lines U251-MG, 1 to 20 passages after thawing ECACC 09063001 U3117 glioblastoma cells, 1 to 20 passages https://doi.org/10.1016/j.ebiom.2015.08.026 N/A HEK-293T Merck 12022001 (Continued on next page) Cell Reports 44, 116553, November 25, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains zebrafish larvae Tg(fli1a:EGFP)y1 Herbomel lab Lawson et al. 65 zebrafish larvae Tg(gfap:GFP)mi2001 Herbomel lab Bernardos & Raymond 66 Oligonucleotides See Table S5 for oligonucleotides N/A N/A Recombinant DNA pSpCas9(BB)-2A-GFP Addgene #48138 pLKO.1 puro Addgene #8453 psPAX2 Addgene #12260 pMD2.G Addgene #12259 pRSV-rev Addgene #12253 pMDLg/pRRE Addgene #12251 pLenti PGK mKate2 Addgene #154290 MISSION® shRNA MMP14 1 Sigma-Aldrich® Advanced Genomics TRCN0000050853 MISSION® shRNA MMP14 1 Sigma-Aldrich® Advanced Genomics TRCN0000050854 MISSION® pLKO.1-puro Non-Target shRNA Control Plasmid DNA Sigma-Aldrich® Advanced Genomics SHC016 Software and algorithms Benchling CRISPR Guide RNA Design Tool https://www.benchling.com/crispr N/A SnapGene software www.snapgene.com Article Title: On-demand delivery of fibulin-1 protects the basement membrane during cyclic stretching in C. elegans. Article Snippet: Article Article Title: Radial astroglia cooperate with microglia to clear neuronal cell bodies during zebrafish optic tectum development. Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Chemicals, peptides, and recombinant proteins Ronidazole Sigma Cat# R7635-5G AcuI Restriction Enzyme New England Biolabs Cat# R0641S BssSI-v2 Restiction Enzyme New England Biolabs Cat# R0680L Critical commercial assays LysoTracker Deep Red Invitrogen/ThermoFisher Cat# L12492 Acridine Orange hemi (zinc chloride) salt Santa Cruz Biotechnology Cat# sc-214488 Recombinant DNA Reagent Lakritz forward primer (CCGGAATTACATCCCAAGAAC) Kay et al.29; Integrated DNA Technologies Custom Order Lakritz reverse primer (GGCCATGATGTAGCTCAGAG) Kay et al.29; Integrated DNA Technologies Custom Order slc1a3b:myrGFP-P2A-H2AmCherry Chen et al.27; provided by Monk lab RRID: Addgene_170208 p5e-slc1a3b Chen et al.27; provided by Monk lab RRID: Addgene_170205 pMe-myrEGFP Provided by Laura Fontenas N/A Experimental models: Organisms/strains See Table S1 for further strain details AB* (strain/strain background) ZIRC RRID: ZFIN_ZDB-GENO-960809-7 Tg(slc1a3b:myrGFP-P2A-H2AmCherry)vo80 Chen et al.27; provided by Monk lab RRID: ZFIN_ZDB-ALT-200915-2 Tg(slc1a3b:myrEGFP)uva74 This article (HMB, ZC) N/A Tg(slc1a3b:TagRFP-CAAX)uva76 Brown, Barber, & Kucenas68 RRID: ZFIN_ZDB-ALT-250314-6 Tg(slc1a3b:mCerulean)uva84 This article (IW) N/A Tg(fli1a:EGFPF)y288Tg Yu et al.69 RRID: ZFIN_ZDB-ALT-151231-3 atoh7th241 Kelsh et al.30; provided by Schoppik lab RRID: ZFIN_ZDB-ALT-980203-363 Tg(atoh7:gap43-RFP)cu2 Zolessi et al.70; provided by Schoppik lab RRID: ZFIN_ZDB-ALT-070129-2 Tg(elavl3:H2B-GCaMP6s)uva98 This article (RIB) N/A Et(e1b:GAL4)s1101t Szobota et al.42 RRID: ZFIN_ZDB-ALT-070716-2 Tg(UAS:secHsa.ANXA5-YFP,myl7:RFP)f12 van Ham et al.43 RRID: ZFIN_ZDB-ALT-110603-3 Tg(slc1a3b:mCherry-2xFYVE;cry:mCherry)uva72Tg This article (IW) N/A Tg(mfap4.1:mTurquoise)xt27 Oehlers et al.71 RRID: ZFIN_ZDB-ALT-150424-9 Tg(mpeg1:Gal4-VP16)gl24 Ellet et al.72 RRID: ZFIN_ZDB-ALT-120117-3 Tg(5xUAS:GAP-TagYFP-2A-NTR2.0)jh513 Sharrock et al.73 RRID: ZFIN_ZDB-ALT-240130-3 csf1raj4e1 Parichy et al.74 RRID: ZFIN_ZDB-ALT-001205-14 Software and CRISPR:Article Title: Intermediate filaments promote glioblastoma cell invasion by controlling nuclear deformations and mechanosensitive expression of MMP14. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Methylene Blue hydrate Sigma-Aldrich M4159 Ultrapure Low melting point agarose Invitrogen 16520–050 DMSO Sigma-Aldrich D2650-100ML GM6001 MMP inhibitor Sigma-Aldrich 38249992 Clear Silicone Rubber Compound kit Momentive RTV 615 Fibronectin Sigma Aldrich F1141-1MG SiR-DNA Spirochrome SC007 CellTracker Red CMTPX Invitrogen C34552 Rat tail collagen I Corning 354236 HEPES Sigma-Aldrich 7365-45-9 poly-L-lysine/polyethylene glycol (PLL-PEG, Graft Ratio 3.5, PLL MW 20000) JemKem PLL20K-G35-PEG2K NaHCO 3 Sigma Aldrich S5761 3-(Trimethoxysilyl)propyl methacrylate Sigma Aldrich 440159 acetic acid Sigma Aldrich A6283 acrylamide solution Sigma Aldrich A4058 bisacrylamide solution Sigma Aldrich 1.01546 ammonium persulfate (APS) Sigma Aldrich 215589 tetramethylethylenediamine (TEMED) Sigma Aldrich 1.10732 Sulpho-SANPAH Thermo Scientific 22589 Paraformaldehyde, 16% w/v aq. soln., methanol free Thermo Scientific 11490570 Triton X-100 Sigma Aldrich 282103 Bovine Serum Albumin (BSA) Sigma Aldrich A9418 Hoechst 33342 Thermo Scientific 62249 Alexa 647 phalloidin Cell Signaling Technologies #8940 Prolong Diamond Invitrogen P36961 SYBR Green Master mix Applied Biosystems 4309155 TRIzol Invitrogen 15596026 Chloroform Sigma Aldrich N/A NuPage LDS sample buffer Invitrogen NP0008 cOmplete TM Protease Inhibitor Cocktail Roche CO-RO NuPAGE TM Bis-Tris Gels, 4–12% NP0321BOX Invitrogen nitrocellulose membrane Thermo Scientific 88018 PVDF Transfer Membranes Thermo Scientific 88518 Clarity Western ECL Blotting Substrate Biorad 1705060S TWEEN® 20 Sigma Aldrich P6585 Deposited data Glioblastoma 10X Visium spatial transcriptomics Greenwald et al. 33 https://doi.org/10.5281/zenodo.8105466 Glioblastoma single cell RNA sequencing Darmanis et al. 26 GEO: GSE84465 Glioblastoma single cell RNA sequencing Yuan et al. 25 GEO: GSE103224 Glioblastoma single cell RNA sequencing integrated dataset Ruiz-Moreno et al. 27 https://cellxgene.cziscience.com/ collections/999f2a15-3d7e-440b-96ae2c806799c08c Experimental models: Cell lines U251-MG, 1 to 20 passages after thawing ECACC 09063001 U3117 glioblastoma cells, 1 to 20 passages https://doi.org/10.1016/j.ebiom.2015.08.026 N/A HEK-293T Merck 12022001 (Continued on next page) Cell Reports 44, 116553, November 25, 2025 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Experimental models: Organisms/strains zebrafish larvae Tg(fli1a:EGFP)y1 Herbomel lab Lawson et al. 65 zebrafish larvae Tg(gfap:GFP)mi2001 Herbomel lab Bernardos & Raymond 66 Oligonucleotides See Table S5 for oligonucleotides N/A N/A Recombinant DNA pSpCas9(BB)-2A-GFP Addgene #48138 pLKO.1 puro Addgene #8453 psPAX2 Addgene #12260 pMD2.G Addgene #12259 pRSV-rev Addgene #12253 pMDLg/pRRE Addgene #12251 pLenti PGK mKate2 Addgene #154290 MISSION® shRNA MMP14 1 Sigma-Aldrich® Advanced Genomics TRCN0000050853 MISSION® shRNA MMP14 1 Sigma-Aldrich® Advanced Genomics TRCN0000050854 MISSION® pLKO.1-puro Non-Target shRNA Control Plasmid DNA Sigma-Aldrich® Advanced Genomics SHC016 Software and algorithms Benchling CRISPR Guide RNA Design Tool https://www.benchling.com/crispr N/A SnapGene software www.snapgene.com |
