multiplex stained tissue microarray section (Akoya Biosciences)
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Akoya Biosciences
multiplex stained tissue microarray section
Multiplex Stained Tissue Microarray Section, supplied by Akoya Biosciences, used in various techniques. Bioz Stars score: 99/100, based on 5463 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/microarray+multiplex/PhenoImager+HT/pm41385179-63-1-13
Average 99 stars, based on 5463 article reviews
Multiplex Stained Tissue Microarray Section, supplied by Akoya Biosciences, used in various techniques. Bioz Stars score: 99/100, based on 5463 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
https://www.bioz.com/product/microarray+multiplex/PhenoImager+HT/pm41385179-63-1-13
Average 99 stars, based on 5463 article reviews
multiplex stained tissue microarray section - by Bioz Stars,
2026-10
99/100 stars
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Cell Isolation:Article Title: Adiponectin reduces immune checkpoint inhibitor-induced inflammation without blocking anti-tumor immunity. Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER NK cell Isolation Kit (mouse) Miltenyi Cat# 130-115-818 Isolation:Article Title: Adiponectin reduces immune checkpoint inhibitor-induced inflammation without blocking anti-tumor immunity. Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER NK cell Isolation Kit (mouse) Miltenyi Cat# 130-115-818 Bicinchoninic Acid Protein Assay:Article Title: Adiponectin reduces immune checkpoint inhibitor-induced inflammation without blocking anti-tumor immunity. Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER NK cell Isolation Kit (mouse) Miltenyi Cat# 130-115-818 Lysis:Article Title: Adiponectin reduces immune checkpoint inhibitor-induced inflammation without blocking anti-tumor immunity. Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER NK cell Isolation Kit (mouse) Miltenyi Cat# 130-115-818 Flow Cytometry:Article Title: Adiponectin reduces immune checkpoint inhibitor-induced inflammation without blocking anti-tumor immunity. Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER NK cell Isolation Kit (mouse) Miltenyi Cat# 130-115-818 Sequencing:Article Title: Adiponectin reduces immune checkpoint inhibitor-induced inflammation without blocking anti-tumor immunity. Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER NK cell Isolation Kit (mouse) Miltenyi Cat# 130-115-818 Microarray:Article Title: Adiponectin reduces immune checkpoint inhibitor-induced inflammation without blocking anti-tumor immunity. Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER NK cell Isolation Kit (mouse) Miltenyi Cat# 130-115-818 Article Title: APOBEC3B-driven mutations negatively regulated by P53 promote tumor progression and immunosuppressive microenvironment in prostate cancer. Article Snippet: .. The Article Title: DLK signaling in axotomized neurons triggers complement activation and loss of upstream synapses. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Goat anti-Mouse - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A32723, RRID:AB_2633275) Goat anti- Mouse IgG1 - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21121, RRID:AB_2535764) Goat anti- Mouse IgG2a - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21131, RRID:AB_2535771) Goat anti- Mouse IgG2a - 647 Fisher Scientific (Thermo Fisher Scientific Cat# A-21241, RRID:AB_2535810) Goat anti- Mouse IgG1 - 647 Fisher Scientific A21246 Goat anti Rabbit - 405 Abcam (Abcam Cat# ab175652, RRID:AB_2687498) Donkey anti Rabbit - 405 Abcam (Abcam Cat# ab175649, RRID:AB_2715515) Donkey anti Mouse - 543 Biotium (Biotium Cat# 20305, RRID:AB_2923245) Donkey anti Rabbit - 543 Biotium 20308 Donkey anti Mouse - 488 Biotium (Biotium Cat# 20014, RRID:AB_10561327) Alexa Fluor 488 AffiniPure Donkey Anti-Guinea Pig IgG (H + L) Jackson Immuno (Jackson ImmunoResearch Labs Cat# 706-545-148, RRID:AB_2340472) Donkey Anti-Rabbit IgG 488 Biotium (Biotium Cat# 20015-1, RRID:AB_10854232) Chemicals, peptides, and recombinant proteins SMART-Seq v4 Ultra Low Input RNA Kit Takara Bio 634889 TSMARTer DNA Unique Dual Index Kit for library Prep Takara Bio R400665 R400668 RNasin Plus RNase Inhibitor Promega N2615 Cycloheximide Sigma C7698-5G Protease Inhibitor Cocktail Sigma P8340-5mL Heparin sodium salt from porcine intestinal mucosa Sigma H3393-50KU Superscript III First-Strand Synthesis SuperMix Invitrogen 11752–250 FastStart Universal SYBR Green Master Mix (ROX) Fisher Scientific 4913850001 M.O.M blocking reagent Vector Laboratories 27090 Molecular Biology Grade Ethanol Fisher Scientific BP2818100 Paraformaldehyde EMS 15710 Normal Goat serum Fisher Scientific 16210064 Normal Donkey Serum Fisher Scientific NC9624464 Beta Mercaptoethanol Sigma M6250 RNeasy RLT buffer Qiagen 79216 Tissue Plus OCT compound Clear Fisher Scientific 4585 Deposited data Raw RNA sequencing Files GEO: GSE213987 https://www.ncbi.nlm.nih.gov/geo Experimental models: Organisms/strains Dlkfx/fx (Miller et al. 2009)28 RiboTag: B6N.129-Rpl122tm1.1Psam/J Jackson laboratories 011029 ChAT-IRES-Cre: B6; 129S6-ChATtm(Cre)/Lowl/J Jackson laboratories 006410 Rosa-tdTomato line (Ai14) Jackson laboratories 007914 Tmem119-2A-EGFP reporter mouse line Jackson laboratories 031823 C3 Knockout: B6.129S4-C3tm1Crr/J Jackson laboratories 029661 (Continued on next page) Cell Reports 43, 113801, February 27, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides See Table S1 Software and algorithms R R Foundation for Statistical Computing, Vienna, Austria R Foundation for Statistical Computing, Vienna, Austria R.Studio posit https://posit.co/download/rstudio-desktop/ GraphPad Prism 9 GraphPad Software, La Jolla, CA https://www.graphpad.com/ scientific-software/prism/ FastQC Babraham Institute Bioinformatics https://github.com/s-andrews/FastQC BBDuK from BBtools BBMap – Bushnell B. sourceforge.net/projects/bbmap/ STAR/2.5.2a aligner (Dobin et al. 2013)72 https://github.com/alexdobin/STAR Samtools 73 https://samtools.sourceforge.net/ QoRTs (Hartley and Mullikin 2015)74 https://github.com/hartleys/QoRTs DESeq2 (Love, Anders, and Huber 2014)75 https://github.com/mikelove/DESeq2 ggplot2 (Wickham 2011)76 https://github.com/tidyverse/ggplot2 EnhancedVolcano (Blighe, Rana, and Lewis 2019)77 https://github.com/kevinblighe/ EnhancedVolcano DAVID (The Database for Annotation, Visualization and Integrated Discovery) (‘‘DAVID Functional Annotation Bioinformatics Microarray Analysis’’) https://david.ncifcrf.gov/ GeneSCF (Subhash and Kanduri 2016)78 https://github.com/genescf/GeneSCF GoPlot (Walter, Sánchez-Cabo, and Ricote 2015)79 https://wencke.github.io/ Volocity Image analysis software (6.3.1) Perkin Elmer/Quarum Technologies Volocity 3D Image Analysis Software (RRID:SCR_002668) Other Mm- Chat - C2 (in situ probe) ACD 408731-C2 Mm- Atf3 - C3 (in situ probe) ACD 426891-C3 Mm- Article Title: BRAP Promotes the Tumorigenesis of Hepatocellular Carcinoma by Corrupting Cancer Cell Cycle Regulation and Enhancing Immune Evasion Article Snippet: .. The Multiplex Assay:Article Title: Adiponectin reduces immune checkpoint inhibitor-induced inflammation without blocking anti-tumor immunity. Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER NK cell Isolation Kit (mouse) Miltenyi Cat# 130-115-818 Article Title: APOBEC3B-driven mutations negatively regulated by P53 promote tumor progression and immunosuppressive microenvironment in prostate cancer. Article Snippet: .. The Article Title: DLK signaling in axotomized neurons triggers complement activation and loss of upstream synapses. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Goat anti-Mouse - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A32723, RRID:AB_2633275) Goat anti- Mouse IgG1 - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21121, RRID:AB_2535764) Goat anti- Mouse IgG2a - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21131, RRID:AB_2535771) Goat anti- Mouse IgG2a - 647 Fisher Scientific (Thermo Fisher Scientific Cat# A-21241, RRID:AB_2535810) Goat anti- Mouse IgG1 - 647 Fisher Scientific A21246 Goat anti Rabbit - 405 Abcam (Abcam Cat# ab175652, RRID:AB_2687498) Donkey anti Rabbit - 405 Abcam (Abcam Cat# ab175649, RRID:AB_2715515) Donkey anti Mouse - 543 Biotium (Biotium Cat# 20305, RRID:AB_2923245) Donkey anti Rabbit - 543 Biotium 20308 Donkey anti Mouse - 488 Biotium (Biotium Cat# 20014, RRID:AB_10561327) Alexa Fluor 488 AffiniPure Donkey Anti-Guinea Pig IgG (H + L) Jackson Immuno (Jackson ImmunoResearch Labs Cat# 706-545-148, RRID:AB_2340472) Donkey Anti-Rabbit IgG 488 Biotium (Biotium Cat# 20015-1, RRID:AB_10854232) Chemicals, peptides, and recombinant proteins SMART-Seq v4 Ultra Low Input RNA Kit Takara Bio 634889 TSMARTer DNA Unique Dual Index Kit for library Prep Takara Bio R400665 R400668 RNasin Plus RNase Inhibitor Promega N2615 Cycloheximide Sigma C7698-5G Protease Inhibitor Cocktail Sigma P8340-5mL Heparin sodium salt from porcine intestinal mucosa Sigma H3393-50KU Superscript III First-Strand Synthesis SuperMix Invitrogen 11752–250 FastStart Universal SYBR Green Master Mix (ROX) Fisher Scientific 4913850001 M.O.M blocking reagent Vector Laboratories 27090 Molecular Biology Grade Ethanol Fisher Scientific BP2818100 Paraformaldehyde EMS 15710 Normal Goat serum Fisher Scientific 16210064 Normal Donkey Serum Fisher Scientific NC9624464 Beta Mercaptoethanol Sigma M6250 RNeasy RLT buffer Qiagen 79216 Tissue Plus OCT compound Clear Fisher Scientific 4585 Deposited data Raw RNA sequencing Files GEO: GSE213987 https://www.ncbi.nlm.nih.gov/geo Experimental models: Organisms/strains Dlkfx/fx (Miller et al. 2009)28 RiboTag: B6N.129-Rpl122tm1.1Psam/J Jackson laboratories 011029 ChAT-IRES-Cre: B6; 129S6-ChATtm(Cre)/Lowl/J Jackson laboratories 006410 Rosa-tdTomato line (Ai14) Jackson laboratories 007914 Tmem119-2A-EGFP reporter mouse line Jackson laboratories 031823 C3 Knockout: B6.129S4-C3tm1Crr/J Jackson laboratories 029661 (Continued on next page) Cell Reports 43, 113801, February 27, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides See Table S1 Software and algorithms R R Foundation for Statistical Computing, Vienna, Austria R Foundation for Statistical Computing, Vienna, Austria R.Studio posit https://posit.co/download/rstudio-desktop/ GraphPad Prism 9 GraphPad Software, La Jolla, CA https://www.graphpad.com/ scientific-software/prism/ FastQC Babraham Institute Bioinformatics https://github.com/s-andrews/FastQC BBDuK from BBtools BBMap – Bushnell B. sourceforge.net/projects/bbmap/ STAR/2.5.2a aligner (Dobin et al. 2013)72 https://github.com/alexdobin/STAR Samtools 73 https://samtools.sourceforge.net/ QoRTs (Hartley and Mullikin 2015)74 https://github.com/hartleys/QoRTs DESeq2 (Love, Anders, and Huber 2014)75 https://github.com/mikelove/DESeq2 ggplot2 (Wickham 2011)76 https://github.com/tidyverse/ggplot2 EnhancedVolcano (Blighe, Rana, and Lewis 2019)77 https://github.com/kevinblighe/ EnhancedVolcano DAVID (The Database for Annotation, Visualization and Integrated Discovery) (‘‘DAVID Functional Annotation Bioinformatics Microarray Analysis’’) https://david.ncifcrf.gov/ GeneSCF (Subhash and Kanduri 2016)78 https://github.com/genescf/GeneSCF GoPlot (Walter, Sánchez-Cabo, and Ricote 2015)79 https://wencke.github.io/ Volocity Image analysis software (6.3.1) Perkin Elmer/Quarum Technologies Volocity 3D Image Analysis Software (RRID:SCR_002668) Other Mm- Chat - C2 (in situ probe) ACD 408731-C2 Mm- Atf3 - C3 (in situ probe) ACD 426891-C3 Mm- Article Title: BRAP Promotes the Tumorigenesis of Hepatocellular Carcinoma by Corrupting Cancer Cell Cycle Regulation and Enhancing Immune Evasion Article Snippet: .. The Immunofluorescence:Article Title: Adiponectin reduces immune checkpoint inhibitor-induced inflammation without blocking anti-tumor immunity. Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER NK cell Isolation Kit (mouse) Miltenyi Cat# 130-115-818 Imaging:Article Title: Adiponectin reduces immune checkpoint inhibitor-induced inflammation without blocking anti-tumor immunity. Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER NK cell Isolation Kit (mouse) Miltenyi Cat# 130-115-818 Staining:Article Title: Adiponectin reduces immune checkpoint inhibitor-induced inflammation without blocking anti-tumor immunity. Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER NK cell Isolation Kit (mouse) Miltenyi Cat# 130-115-818 Western Blot:Article Title: Adiponectin reduces immune checkpoint inhibitor-induced inflammation without blocking anti-tumor immunity. Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER NK cell Isolation Kit (mouse) Miltenyi Cat# 130-115-818 Marker:Article Title: Adiponectin reduces immune checkpoint inhibitor-induced inflammation without blocking anti-tumor immunity. Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER NK cell Isolation Kit (mouse) Miltenyi Cat# 130-115-818 Microscopy:Article Title: APOBEC3B-driven mutations negatively regulated by P53 promote tumor progression and immunosuppressive microenvironment in prostate cancer. Article Snippet: .. The Article Title: BRAP Promotes the Tumorigenesis of Hepatocellular Carcinoma by Corrupting Cancer Cell Cycle Regulation and Enhancing Immune Evasion Article Snippet: .. The other:Article Title: Adiponectin reduces immune checkpoint inhibitor-induced inflammation without blocking anti-tumor immunity. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Software and algorithms Cell Ranger 6.1.2 10x Genomics N/A clusterProfiler 4.12.6 Bioconductor N/A decoupleR 2.10 Bioconductor N/A FlowJo V10 BD Biosciences N/A Fusion v2.1.0 scan software Akoya Biosciences N/A FACSDiva Software V6 BD Biosciences N/A GeneMapper Software 6 Thermo Fisher Scientific Cat# 4475073 GraphPad Prism GraphPad N/A inform v3.0 Akoya Biosciences N/A LabImage 1D KAPELAN Bio-Imaging Solutions N/A Living Image Revvity Cat# 128110 OMIQ Dotmatics N/A Phenochart v.2.0.0 Akoya Biosciences N/A R 4.3.2 CRAN N/A SAS 9.4 SAS Analytics Software N/A Seurat v4.3.0 Bioconductor N/A Other 123count eBeads Counting Beads ThermoFisher Scientific Cat# 01-1234-42 alfalfa-free diet AIN-93 ResearchDiets Cat# D10012G BD Trucount counting Tubes BD Biosciences Cat# 663028 BS-02 UV irradiation chamber equipped with UVA Opsytec Dr. Gröbel Cat# 860902; 860820 Dynabeads Mouse T-Activator CD3/CD28 ThermoFisher Scientific Cat# 11453D gentleMACS C Tubes Miltenyi Cat# 130-093-237 MHC Dextramer , H-2 Kb / SIINFEKL / PE Immudex Cat# JD02163 PE Nunc Lab-Tek II Chamber Slide System ThermoFisher Scientific Cat# 154453 NuPAGE Bis-Tris Mini Protein Gels, 4–12% ThermoFisher Scientific Cat# NP0336BOX Software:Article Title: DLK signaling in axotomized neurons triggers complement activation and loss of upstream synapses. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Goat anti-Mouse - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A32723, RRID:AB_2633275) Goat anti- Mouse IgG1 - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21121, RRID:AB_2535764) Goat anti- Mouse IgG2a - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21131, RRID:AB_2535771) Goat anti- Mouse IgG2a - 647 Fisher Scientific (Thermo Fisher Scientific Cat# A-21241, RRID:AB_2535810) Goat anti- Mouse IgG1 - 647 Fisher Scientific A21246 Goat anti Rabbit - 405 Abcam (Abcam Cat# ab175652, RRID:AB_2687498) Donkey anti Rabbit - 405 Abcam (Abcam Cat# ab175649, RRID:AB_2715515) Donkey anti Mouse - 543 Biotium (Biotium Cat# 20305, RRID:AB_2923245) Donkey anti Rabbit - 543 Biotium 20308 Donkey anti Mouse - 488 Biotium (Biotium Cat# 20014, RRID:AB_10561327) Alexa Fluor 488 AffiniPure Donkey Anti-Guinea Pig IgG (H + L) Jackson Immuno (Jackson ImmunoResearch Labs Cat# 706-545-148, RRID:AB_2340472) Donkey Anti-Rabbit IgG 488 Biotium (Biotium Cat# 20015-1, RRID:AB_10854232) Chemicals, peptides, and recombinant proteins SMART-Seq v4 Ultra Low Input RNA Kit Takara Bio 634889 TSMARTer DNA Unique Dual Index Kit for library Prep Takara Bio R400665 R400668 RNasin Plus RNase Inhibitor Promega N2615 Cycloheximide Sigma C7698-5G Protease Inhibitor Cocktail Sigma P8340-5mL Heparin sodium salt from porcine intestinal mucosa Sigma H3393-50KU Superscript III First-Strand Synthesis SuperMix Invitrogen 11752–250 FastStart Universal SYBR Green Master Mix (ROX) Fisher Scientific 4913850001 M.O.M blocking reagent Vector Laboratories 27090 Molecular Biology Grade Ethanol Fisher Scientific BP2818100 Paraformaldehyde EMS 15710 Normal Goat serum Fisher Scientific 16210064 Normal Donkey Serum Fisher Scientific NC9624464 Beta Mercaptoethanol Sigma M6250 RNeasy RLT buffer Qiagen 79216 Tissue Plus OCT compound Clear Fisher Scientific 4585 Deposited data Raw RNA sequencing Files GEO: GSE213987 https://www.ncbi.nlm.nih.gov/geo Experimental models: Organisms/strains Dlkfx/fx (Miller et al. 2009)28 RiboTag: B6N.129-Rpl122tm1.1Psam/J Jackson laboratories 011029 ChAT-IRES-Cre: B6; 129S6-ChATtm(Cre)/Lowl/J Jackson laboratories 006410 Rosa-tdTomato line (Ai14) Jackson laboratories 007914 Tmem119-2A-EGFP reporter mouse line Jackson laboratories 031823 C3 Knockout: B6.129S4-C3tm1Crr/J Jackson laboratories 029661 (Continued on next page) Cell Reports 43, 113801, February 27, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides See Table S1 Software and algorithms R R Foundation for Statistical Computing, Vienna, Austria R Foundation for Statistical Computing, Vienna, Austria R.Studio posit https://posit.co/download/rstudio-desktop/ GraphPad Prism 9 GraphPad Software, La Jolla, CA https://www.graphpad.com/ scientific-software/prism/ FastQC Babraham Institute Bioinformatics https://github.com/s-andrews/FastQC BBDuK from BBtools BBMap – Bushnell B. sourceforge.net/projects/bbmap/ STAR/2.5.2a aligner (Dobin et al. 2013)72 https://github.com/alexdobin/STAR Samtools 73 https://samtools.sourceforge.net/ QoRTs (Hartley and Mullikin 2015)74 https://github.com/hartleys/QoRTs DESeq2 (Love, Anders, and Huber 2014)75 https://github.com/mikelove/DESeq2 ggplot2 (Wickham 2011)76 https://github.com/tidyverse/ggplot2 EnhancedVolcano (Blighe, Rana, and Lewis 2019)77 https://github.com/kevinblighe/ EnhancedVolcano DAVID (The Database for Annotation, Visualization and Integrated Discovery) (‘‘DAVID Functional Annotation Bioinformatics Microarray Analysis’’) https://david.ncifcrf.gov/ GeneSCF (Subhash and Kanduri 2016)78 https://github.com/genescf/GeneSCF GoPlot (Walter, Sánchez-Cabo, and Ricote 2015)79 https://wencke.github.io/ Volocity Image analysis software (6.3.1) Perkin Elmer/Quarum Technologies Volocity 3D Image Analysis Software (RRID:SCR_002668) Other Mm- Chat - C2 (in situ probe) ACD 408731-C2 Mm- Atf3 - C3 (in situ probe) ACD 426891-C3 Mm- Functional Assay:Article Title: DLK signaling in axotomized neurons triggers complement activation and loss of upstream synapses. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Goat anti-Mouse - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A32723, RRID:AB_2633275) Goat anti- Mouse IgG1 - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21121, RRID:AB_2535764) Goat anti- Mouse IgG2a - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21131, RRID:AB_2535771) Goat anti- Mouse IgG2a - 647 Fisher Scientific (Thermo Fisher Scientific Cat# A-21241, RRID:AB_2535810) Goat anti- Mouse IgG1 - 647 Fisher Scientific A21246 Goat anti Rabbit - 405 Abcam (Abcam Cat# ab175652, RRID:AB_2687498) Donkey anti Rabbit - 405 Abcam (Abcam Cat# ab175649, RRID:AB_2715515) Donkey anti Mouse - 543 Biotium (Biotium Cat# 20305, RRID:AB_2923245) Donkey anti Rabbit - 543 Biotium 20308 Donkey anti Mouse - 488 Biotium (Biotium Cat# 20014, RRID:AB_10561327) Alexa Fluor 488 AffiniPure Donkey Anti-Guinea Pig IgG (H + L) Jackson Immuno (Jackson ImmunoResearch Labs Cat# 706-545-148, RRID:AB_2340472) Donkey Anti-Rabbit IgG 488 Biotium (Biotium Cat# 20015-1, RRID:AB_10854232) Chemicals, peptides, and recombinant proteins SMART-Seq v4 Ultra Low Input RNA Kit Takara Bio 634889 TSMARTer DNA Unique Dual Index Kit for library Prep Takara Bio R400665 R400668 RNasin Plus RNase Inhibitor Promega N2615 Cycloheximide Sigma C7698-5G Protease Inhibitor Cocktail Sigma P8340-5mL Heparin sodium salt from porcine intestinal mucosa Sigma H3393-50KU Superscript III First-Strand Synthesis SuperMix Invitrogen 11752–250 FastStart Universal SYBR Green Master Mix (ROX) Fisher Scientific 4913850001 M.O.M blocking reagent Vector Laboratories 27090 Molecular Biology Grade Ethanol Fisher Scientific BP2818100 Paraformaldehyde EMS 15710 Normal Goat serum Fisher Scientific 16210064 Normal Donkey Serum Fisher Scientific NC9624464 Beta Mercaptoethanol Sigma M6250 RNeasy RLT buffer Qiagen 79216 Tissue Plus OCT compound Clear Fisher Scientific 4585 Deposited data Raw RNA sequencing Files GEO: GSE213987 https://www.ncbi.nlm.nih.gov/geo Experimental models: Organisms/strains Dlkfx/fx (Miller et al. 2009)28 RiboTag: B6N.129-Rpl122tm1.1Psam/J Jackson laboratories 011029 ChAT-IRES-Cre: B6; 129S6-ChATtm(Cre)/Lowl/J Jackson laboratories 006410 Rosa-tdTomato line (Ai14) Jackson laboratories 007914 Tmem119-2A-EGFP reporter mouse line Jackson laboratories 031823 C3 Knockout: B6.129S4-C3tm1Crr/J Jackson laboratories 029661 (Continued on next page) Cell Reports 43, 113801, February 27, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides See Table S1 Software and algorithms R R Foundation for Statistical Computing, Vienna, Austria R Foundation for Statistical Computing, Vienna, Austria R.Studio posit https://posit.co/download/rstudio-desktop/ GraphPad Prism 9 GraphPad Software, La Jolla, CA https://www.graphpad.com/ scientific-software/prism/ FastQC Babraham Institute Bioinformatics https://github.com/s-andrews/FastQC BBDuK from BBtools BBMap – Bushnell B. sourceforge.net/projects/bbmap/ STAR/2.5.2a aligner (Dobin et al. 2013)72 https://github.com/alexdobin/STAR Samtools 73 https://samtools.sourceforge.net/ QoRTs (Hartley and Mullikin 2015)74 https://github.com/hartleys/QoRTs DESeq2 (Love, Anders, and Huber 2014)75 https://github.com/mikelove/DESeq2 ggplot2 (Wickham 2011)76 https://github.com/tidyverse/ggplot2 EnhancedVolcano (Blighe, Rana, and Lewis 2019)77 https://github.com/kevinblighe/ EnhancedVolcano DAVID (The Database for Annotation, Visualization and Integrated Discovery) (‘‘DAVID Functional Annotation Bioinformatics Microarray Analysis’’) https://david.ncifcrf.gov/ GeneSCF (Subhash and Kanduri 2016)78 https://github.com/genescf/GeneSCF GoPlot (Walter, Sánchez-Cabo, and Ricote 2015)79 https://wencke.github.io/ Volocity Image analysis software (6.3.1) Perkin Elmer/Quarum Technologies Volocity 3D Image Analysis Software (RRID:SCR_002668) Other Mm- Chat - C2 (in situ probe) ACD 408731-C2 Mm- Atf3 - C3 (in situ probe) ACD 426891-C3 Mm- In Situ:Article Title: DLK signaling in axotomized neurons triggers complement activation and loss of upstream synapses. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Goat anti-Mouse - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A32723, RRID:AB_2633275) Goat anti- Mouse IgG1 - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21121, RRID:AB_2535764) Goat anti- Mouse IgG2a - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21131, RRID:AB_2535771) Goat anti- Mouse IgG2a - 647 Fisher Scientific (Thermo Fisher Scientific Cat# A-21241, RRID:AB_2535810) Goat anti- Mouse IgG1 - 647 Fisher Scientific A21246 Goat anti Rabbit - 405 Abcam (Abcam Cat# ab175652, RRID:AB_2687498) Donkey anti Rabbit - 405 Abcam (Abcam Cat# ab175649, RRID:AB_2715515) Donkey anti Mouse - 543 Biotium (Biotium Cat# 20305, RRID:AB_2923245) Donkey anti Rabbit - 543 Biotium 20308 Donkey anti Mouse - 488 Biotium (Biotium Cat# 20014, RRID:AB_10561327) Alexa Fluor 488 AffiniPure Donkey Anti-Guinea Pig IgG (H + L) Jackson Immuno (Jackson ImmunoResearch Labs Cat# 706-545-148, RRID:AB_2340472) Donkey Anti-Rabbit IgG 488 Biotium (Biotium Cat# 20015-1, RRID:AB_10854232) Chemicals, peptides, and recombinant proteins SMART-Seq v4 Ultra Low Input RNA Kit Takara Bio 634889 TSMARTer DNA Unique Dual Index Kit for library Prep Takara Bio R400665 R400668 RNasin Plus RNase Inhibitor Promega N2615 Cycloheximide Sigma C7698-5G Protease Inhibitor Cocktail Sigma P8340-5mL Heparin sodium salt from porcine intestinal mucosa Sigma H3393-50KU Superscript III First-Strand Synthesis SuperMix Invitrogen 11752–250 FastStart Universal SYBR Green Master Mix (ROX) Fisher Scientific 4913850001 M.O.M blocking reagent Vector Laboratories 27090 Molecular Biology Grade Ethanol Fisher Scientific BP2818100 Paraformaldehyde EMS 15710 Normal Goat serum Fisher Scientific 16210064 Normal Donkey Serum Fisher Scientific NC9624464 Beta Mercaptoethanol Sigma M6250 RNeasy RLT buffer Qiagen 79216 Tissue Plus OCT compound Clear Fisher Scientific 4585 Deposited data Raw RNA sequencing Files GEO: GSE213987 https://www.ncbi.nlm.nih.gov/geo Experimental models: Organisms/strains Dlkfx/fx (Miller et al. 2009)28 RiboTag: B6N.129-Rpl122tm1.1Psam/J Jackson laboratories 011029 ChAT-IRES-Cre: B6; 129S6-ChATtm(Cre)/Lowl/J Jackson laboratories 006410 Rosa-tdTomato line (Ai14) Jackson laboratories 007914 Tmem119-2A-EGFP reporter mouse line Jackson laboratories 031823 C3 Knockout: B6.129S4-C3tm1Crr/J Jackson laboratories 029661 (Continued on next page) Cell Reports 43, 113801, February 27, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides See Table S1 Software and algorithms R R Foundation for Statistical Computing, Vienna, Austria R Foundation for Statistical Computing, Vienna, Austria R.Studio posit https://posit.co/download/rstudio-desktop/ GraphPad Prism 9 GraphPad Software, La Jolla, CA https://www.graphpad.com/ scientific-software/prism/ FastQC Babraham Institute Bioinformatics https://github.com/s-andrews/FastQC BBDuK from BBtools BBMap – Bushnell B. sourceforge.net/projects/bbmap/ STAR/2.5.2a aligner (Dobin et al. 2013)72 https://github.com/alexdobin/STAR Samtools 73 https://samtools.sourceforge.net/ QoRTs (Hartley and Mullikin 2015)74 https://github.com/hartleys/QoRTs DESeq2 (Love, Anders, and Huber 2014)75 https://github.com/mikelove/DESeq2 ggplot2 (Wickham 2011)76 https://github.com/tidyverse/ggplot2 EnhancedVolcano (Blighe, Rana, and Lewis 2019)77 https://github.com/kevinblighe/ EnhancedVolcano DAVID (The Database for Annotation, Visualization and Integrated Discovery) (‘‘DAVID Functional Annotation Bioinformatics Microarray Analysis’’) https://david.ncifcrf.gov/ GeneSCF (Subhash and Kanduri 2016)78 https://github.com/genescf/GeneSCF GoPlot (Walter, Sánchez-Cabo, and Ricote 2015)79 https://wencke.github.io/ Volocity Image analysis software (6.3.1) Perkin Elmer/Quarum Technologies Volocity 3D Image Analysis Software (RRID:SCR_002668) Other Mm- Chat - C2 (in situ probe) ACD 408731-C2 Mm- Atf3 - C3 (in situ probe) ACD 426891-C3 Mm- RNAscope:Article Title: DLK signaling in axotomized neurons triggers complement activation and loss of upstream synapses. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Goat anti-Mouse - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A32723, RRID:AB_2633275) Goat anti- Mouse IgG1 - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21121, RRID:AB_2535764) Goat anti- Mouse IgG2a - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21131, RRID:AB_2535771) Goat anti- Mouse IgG2a - 647 Fisher Scientific (Thermo Fisher Scientific Cat# A-21241, RRID:AB_2535810) Goat anti- Mouse IgG1 - 647 Fisher Scientific A21246 Goat anti Rabbit - 405 Abcam (Abcam Cat# ab175652, RRID:AB_2687498) Donkey anti Rabbit - 405 Abcam (Abcam Cat# ab175649, RRID:AB_2715515) Donkey anti Mouse - 543 Biotium (Biotium Cat# 20305, RRID:AB_2923245) Donkey anti Rabbit - 543 Biotium 20308 Donkey anti Mouse - 488 Biotium (Biotium Cat# 20014, RRID:AB_10561327) Alexa Fluor 488 AffiniPure Donkey Anti-Guinea Pig IgG (H + L) Jackson Immuno (Jackson ImmunoResearch Labs Cat# 706-545-148, RRID:AB_2340472) Donkey Anti-Rabbit IgG 488 Biotium (Biotium Cat# 20015-1, RRID:AB_10854232) Chemicals, peptides, and recombinant proteins SMART-Seq v4 Ultra Low Input RNA Kit Takara Bio 634889 TSMARTer DNA Unique Dual Index Kit for library Prep Takara Bio R400665 R400668 RNasin Plus RNase Inhibitor Promega N2615 Cycloheximide Sigma C7698-5G Protease Inhibitor Cocktail Sigma P8340-5mL Heparin sodium salt from porcine intestinal mucosa Sigma H3393-50KU Superscript III First-Strand Synthesis SuperMix Invitrogen 11752–250 FastStart Universal SYBR Green Master Mix (ROX) Fisher Scientific 4913850001 M.O.M blocking reagent Vector Laboratories 27090 Molecular Biology Grade Ethanol Fisher Scientific BP2818100 Paraformaldehyde EMS 15710 Normal Goat serum Fisher Scientific 16210064 Normal Donkey Serum Fisher Scientific NC9624464 Beta Mercaptoethanol Sigma M6250 RNeasy RLT buffer Qiagen 79216 Tissue Plus OCT compound Clear Fisher Scientific 4585 Deposited data Raw RNA sequencing Files GEO: GSE213987 https://www.ncbi.nlm.nih.gov/geo Experimental models: Organisms/strains Dlkfx/fx (Miller et al. 2009)28 RiboTag: B6N.129-Rpl122tm1.1Psam/J Jackson laboratories 011029 ChAT-IRES-Cre: B6; 129S6-ChATtm(Cre)/Lowl/J Jackson laboratories 006410 Rosa-tdTomato line (Ai14) Jackson laboratories 007914 Tmem119-2A-EGFP reporter mouse line Jackson laboratories 031823 C3 Knockout: B6.129S4-C3tm1Crr/J Jackson laboratories 029661 (Continued on next page) Cell Reports 43, 113801, February 27, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides See Table S1 Software and algorithms R R Foundation for Statistical Computing, Vienna, Austria R Foundation for Statistical Computing, Vienna, Austria R.Studio posit https://posit.co/download/rstudio-desktop/ GraphPad Prism 9 GraphPad Software, La Jolla, CA https://www.graphpad.com/ scientific-software/prism/ FastQC Babraham Institute Bioinformatics https://github.com/s-andrews/FastQC BBDuK from BBtools BBMap – Bushnell B. sourceforge.net/projects/bbmap/ STAR/2.5.2a aligner (Dobin et al. 2013)72 https://github.com/alexdobin/STAR Samtools 73 https://samtools.sourceforge.net/ QoRTs (Hartley and Mullikin 2015)74 https://github.com/hartleys/QoRTs DESeq2 (Love, Anders, and Huber 2014)75 https://github.com/mikelove/DESeq2 ggplot2 (Wickham 2011)76 https://github.com/tidyverse/ggplot2 EnhancedVolcano (Blighe, Rana, and Lewis 2019)77 https://github.com/kevinblighe/ EnhancedVolcano DAVID (The Database for Annotation, Visualization and Integrated Discovery) (‘‘DAVID Functional Annotation Bioinformatics Microarray Analysis’’) https://david.ncifcrf.gov/ GeneSCF (Subhash and Kanduri 2016)78 https://github.com/genescf/GeneSCF GoPlot (Walter, Sánchez-Cabo, and Ricote 2015)79 https://wencke.github.io/ Volocity Image analysis software (6.3.1) Perkin Elmer/Quarum Technologies Volocity 3D Image Analysis Software (RRID:SCR_002668) Other Mm- Chat - C2 (in situ probe) ACD 408731-C2 Mm- Atf3 - C3 (in situ probe) ACD 426891-C3 Mm- Magnetic Beads:Article Title: DLK signaling in axotomized neurons triggers complement activation and loss of upstream synapses. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Goat anti-Mouse - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A32723, RRID:AB_2633275) Goat anti- Mouse IgG1 - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21121, RRID:AB_2535764) Goat anti- Mouse IgG2a - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21131, RRID:AB_2535771) Goat anti- Mouse IgG2a - 647 Fisher Scientific (Thermo Fisher Scientific Cat# A-21241, RRID:AB_2535810) Goat anti- Mouse IgG1 - 647 Fisher Scientific A21246 Goat anti Rabbit - 405 Abcam (Abcam Cat# ab175652, RRID:AB_2687498) Donkey anti Rabbit - 405 Abcam (Abcam Cat# ab175649, RRID:AB_2715515) Donkey anti Mouse - 543 Biotium (Biotium Cat# 20305, RRID:AB_2923245) Donkey anti Rabbit - 543 Biotium 20308 Donkey anti Mouse - 488 Biotium (Biotium Cat# 20014, RRID:AB_10561327) Alexa Fluor 488 AffiniPure Donkey Anti-Guinea Pig IgG (H + L) Jackson Immuno (Jackson ImmunoResearch Labs Cat# 706-545-148, RRID:AB_2340472) Donkey Anti-Rabbit IgG 488 Biotium (Biotium Cat# 20015-1, RRID:AB_10854232) Chemicals, peptides, and recombinant proteins SMART-Seq v4 Ultra Low Input RNA Kit Takara Bio 634889 TSMARTer DNA Unique Dual Index Kit for library Prep Takara Bio R400665 R400668 RNasin Plus RNase Inhibitor Promega N2615 Cycloheximide Sigma C7698-5G Protease Inhibitor Cocktail Sigma P8340-5mL Heparin sodium salt from porcine intestinal mucosa Sigma H3393-50KU Superscript III First-Strand Synthesis SuperMix Invitrogen 11752–250 FastStart Universal SYBR Green Master Mix (ROX) Fisher Scientific 4913850001 M.O.M blocking reagent Vector Laboratories 27090 Molecular Biology Grade Ethanol Fisher Scientific BP2818100 Paraformaldehyde EMS 15710 Normal Goat serum Fisher Scientific 16210064 Normal Donkey Serum Fisher Scientific NC9624464 Beta Mercaptoethanol Sigma M6250 RNeasy RLT buffer Qiagen 79216 Tissue Plus OCT compound Clear Fisher Scientific 4585 Deposited data Raw RNA sequencing Files GEO: GSE213987 https://www.ncbi.nlm.nih.gov/geo Experimental models: Organisms/strains Dlkfx/fx (Miller et al. 2009)28 RiboTag: B6N.129-Rpl122tm1.1Psam/J Jackson laboratories 011029 ChAT-IRES-Cre: B6; 129S6-ChATtm(Cre)/Lowl/J Jackson laboratories 006410 Rosa-tdTomato line (Ai14) Jackson laboratories 007914 Tmem119-2A-EGFP reporter mouse line Jackson laboratories 031823 C3 Knockout: B6.129S4-C3tm1Crr/J Jackson laboratories 029661 (Continued on next page) Cell Reports 43, 113801, February 27, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides See Table S1 Software and algorithms R R Foundation for Statistical Computing, Vienna, Austria R Foundation for Statistical Computing, Vienna, Austria R.Studio posit https://posit.co/download/rstudio-desktop/ GraphPad Prism 9 GraphPad Software, La Jolla, CA https://www.graphpad.com/ scientific-software/prism/ FastQC Babraham Institute Bioinformatics https://github.com/s-andrews/FastQC BBDuK from BBtools BBMap – Bushnell B. sourceforge.net/projects/bbmap/ STAR/2.5.2a aligner (Dobin et al. 2013)72 https://github.com/alexdobin/STAR Samtools 73 https://samtools.sourceforge.net/ QoRTs (Hartley and Mullikin 2015)74 https://github.com/hartleys/QoRTs DESeq2 (Love, Anders, and Huber 2014)75 https://github.com/mikelove/DESeq2 ggplot2 (Wickham 2011)76 https://github.com/tidyverse/ggplot2 EnhancedVolcano (Blighe, Rana, and Lewis 2019)77 https://github.com/kevinblighe/ EnhancedVolcano DAVID (The Database for Annotation, Visualization and Integrated Discovery) (‘‘DAVID Functional Annotation Bioinformatics Microarray Analysis’’) https://david.ncifcrf.gov/ GeneSCF (Subhash and Kanduri 2016)78 https://github.com/genescf/GeneSCF GoPlot (Walter, Sánchez-Cabo, and Ricote 2015)79 https://wencke.github.io/ Volocity Image analysis software (6.3.1) Perkin Elmer/Quarum Technologies Volocity 3D Image Analysis Software (RRID:SCR_002668) Other Mm- Chat - C2 (in situ probe) ACD 408731-C2 Mm- Atf3 - C3 (in situ probe) ACD 426891-C3 Mm- Control:Article Title: DLK signaling in axotomized neurons triggers complement activation and loss of upstream synapses. Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER Goat anti-Mouse - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A32723, RRID:AB_2633275) Goat anti- Mouse IgG1 - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21121, RRID:AB_2535764) Goat anti- Mouse IgG2a - 488 Fisher Scientific (Thermo Fisher Scientific Cat# A-21131, RRID:AB_2535771) Goat anti- Mouse IgG2a - 647 Fisher Scientific (Thermo Fisher Scientific Cat# A-21241, RRID:AB_2535810) Goat anti- Mouse IgG1 - 647 Fisher Scientific A21246 Goat anti Rabbit - 405 Abcam (Abcam Cat# ab175652, RRID:AB_2687498) Donkey anti Rabbit - 405 Abcam (Abcam Cat# ab175649, RRID:AB_2715515) Donkey anti Mouse - 543 Biotium (Biotium Cat# 20305, RRID:AB_2923245) Donkey anti Rabbit - 543 Biotium 20308 Donkey anti Mouse - 488 Biotium (Biotium Cat# 20014, RRID:AB_10561327) Alexa Fluor 488 AffiniPure Donkey Anti-Guinea Pig IgG (H + L) Jackson Immuno (Jackson ImmunoResearch Labs Cat# 706-545-148, RRID:AB_2340472) Donkey Anti-Rabbit IgG 488 Biotium (Biotium Cat# 20015-1, RRID:AB_10854232) Chemicals, peptides, and recombinant proteins SMART-Seq v4 Ultra Low Input RNA Kit Takara Bio 634889 TSMARTer DNA Unique Dual Index Kit for library Prep Takara Bio R400665 R400668 RNasin Plus RNase Inhibitor Promega N2615 Cycloheximide Sigma C7698-5G Protease Inhibitor Cocktail Sigma P8340-5mL Heparin sodium salt from porcine intestinal mucosa Sigma H3393-50KU Superscript III First-Strand Synthesis SuperMix Invitrogen 11752–250 FastStart Universal SYBR Green Master Mix (ROX) Fisher Scientific 4913850001 M.O.M blocking reagent Vector Laboratories 27090 Molecular Biology Grade Ethanol Fisher Scientific BP2818100 Paraformaldehyde EMS 15710 Normal Goat serum Fisher Scientific 16210064 Normal Donkey Serum Fisher Scientific NC9624464 Beta Mercaptoethanol Sigma M6250 RNeasy RLT buffer Qiagen 79216 Tissue Plus OCT compound Clear Fisher Scientific 4585 Deposited data Raw RNA sequencing Files GEO: GSE213987 https://www.ncbi.nlm.nih.gov/geo Experimental models: Organisms/strains Dlkfx/fx (Miller et al. 2009)28 RiboTag: B6N.129-Rpl122tm1.1Psam/J Jackson laboratories 011029 ChAT-IRES-Cre: B6; 129S6-ChATtm(Cre)/Lowl/J Jackson laboratories 006410 Rosa-tdTomato line (Ai14) Jackson laboratories 007914 Tmem119-2A-EGFP reporter mouse line Jackson laboratories 031823 C3 Knockout: B6.129S4-C3tm1Crr/J Jackson laboratories 029661 (Continued on next page) Cell Reports 43, 113801, February 27, 2024 17 .. REAGENT or RESOURCE SOURCE IDENTIFIER Oligonucleotides See Table S1 Software and algorithms R R Foundation for Statistical Computing, Vienna, Austria R Foundation for Statistical Computing, Vienna, Austria R.Studio posit https://posit.co/download/rstudio-desktop/ GraphPad Prism 9 GraphPad Software, La Jolla, CA https://www.graphpad.com/ scientific-software/prism/ FastQC Babraham Institute Bioinformatics https://github.com/s-andrews/FastQC BBDuK from BBtools BBMap – Bushnell B. sourceforge.net/projects/bbmap/ STAR/2.5.2a aligner (Dobin et al. 2013)72 https://github.com/alexdobin/STAR Samtools 73 https://samtools.sourceforge.net/ QoRTs (Hartley and Mullikin 2015)74 https://github.com/hartleys/QoRTs DESeq2 (Love, Anders, and Huber 2014)75 https://github.com/mikelove/DESeq2 ggplot2 (Wickham 2011)76 https://github.com/tidyverse/ggplot2 EnhancedVolcano (Blighe, Rana, and Lewis 2019)77 https://github.com/kevinblighe/ EnhancedVolcano DAVID (The Database for Annotation, Visualization and Integrated Discovery) (‘‘DAVID Functional Annotation Bioinformatics Microarray Analysis’’) https://david.ncifcrf.gov/ GeneSCF (Subhash and Kanduri 2016)78 https://github.com/genescf/GeneSCF GoPlot (Walter, Sánchez-Cabo, and Ricote 2015)79 https://wencke.github.io/ Volocity Image analysis software (6.3.1) Perkin Elmer/Quarum Technologies Volocity 3D Image Analysis Software (RRID:SCR_002668) Other Mm- Chat - C2 (in situ probe) ACD 408731-C2 Mm- Atf3 - C3 (in situ probe) ACD 426891-C3 Mm- |
