other:Article Title: Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver.
Article Snippet: REAGENT or RESOURCE SOURCE IDENTIFIER scVelo 0.2.4 GitHub https://github.com/theislab/scvelo ImageJ 1.53t Schneider et al.53 https://imagej.nih.gov/ij DAVID Bioinformatics Resources Sherman et al., Huang et al.54,55 https://david.ncifcrf.gov/home.jsp Enrichr Chen et al., Kuleshov et al., Xie et al.56–58 https://maayanlab.cloud/Enrichr/ inForm Software 2.6.0 Akoya Biosciences https://www.akoyabio.com/phenoimager/ software/inform-tissue-finder/ Original code for analyses This Study https://zenodo.org/records/11274305 (https://doi.org/10.5281/zenodo.11274305) Others ROCHE Collagenase/Dispase Roche Cat#10269638001 InvitrogenTM eBioscienceTM 1X RBC Lysis Buffer Invitrogen Cat#00-4333-57 RQ1 RNase-Free Dnase Promega Cat#M6101 DirectPCR Lysis Reagent (Ear) Viagen Cat#402-E Recombinant Proteinase K Solution (20 mg/mL) Thermo Fisher Scientific Cat#AM2546 InvitrogenTM PlatinumTM Green Hot Start PCR Master Mix (2X) Thermo Fisher Scientific Cat#13001012 MiniCollect Complete CAT Serum Separator Clot Activator tubes Greiner Cat#450548 SPLInsertTM Hanging SPL Life Sciences Cat#35206 CorningTM FalconTM Cell Culture Inserts Corning Cat#353097 GibcoTM HBSS (10X), no calcium, no magnesium, phenol red Thermo Fisher Scientific Cat#14180046 Collagenase from Clostridium histolyticum, Type IA Sigma-Aldrich Cat#C9891 0.5M EGTA, pH 8.0 1st Base Cat#CUS-1070 GibcoTM ACK Lysing Buffer Thermo Fisher Scientific Cat#A1049201 Percoll Sigma-Aldrich Cat#P1644 Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix Merck Cat#CLS356231 SPRIselect for Size Selection Beckman Coulter Cat#B23317 Qiagen, Inc. RNeasy Mini Kit Qiagen Cat#74106 Advantage RT-for-PCR Kit Takara Cat#639506 GoTaq qPCR Master Mix Promega Cat#A600A cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Roche Cat#11873580001 PhosSTOP Roche Cat#4906845001 LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat#11668019 Clearene Solvent Leica Cat#3803600 CV Ultra Mounting Media Leica Cat#14070936261 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories H-1200-10 Standard Macrophage Depletion Kit (Clodrosome + Encapsome ) Encapsula Nano Sciences SKU# CLD-8901 Paraplast Leica 39603002 CV Ultra Mounting Media Leica cv-ultra-mounting-media Cover glass Size 22 x 22mm Fisher Scientific FIS#12-544-10 Formalin solution, neutral buffered, 10% Sigma-Aldrich HT501128 Clearene Leica 3803600 Target Retrieval Solution, Citrate pH 6.1 (10x) Dako S1699 Peroxidase-Blocking Solution, Dako REAL Dako S2023 (Continued on next page) 22 Cell Reports 43, 114400, July 23, 2024
Single Cell:Article Title: Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER AZD5582 Selleck Chemicals Cat#S7362 Emricasan (IDN-6556) Selleck Chemicals Cat#S7775 Critical commercial assays 10x Genomics Chromium Next GEM Single Cell 30 kit v3.1 (Dual index) 10x Genomics Cat#1000268 Visium spatial gene expression slide & reagent kit 10x Genomics Cat#1000184 Deposited data Mouse Bulk RNA sequencing data GEO GEO: GSE225175 Mouse Single-cell RNA sequencing data GEO GEO: GSE227092 Mouse Spatial Transcriptomics data GEO GEO: GSE228195 Human HCC Single-cell RNA sequencing data GEO GEO: GSE223204 Experimental models: Cell lines AML12 - CRL-2254 - ATCC ATCC Cat#ATCC-CRL-2254; RRID:CVCL_0140 SNU449 - ATCC CRL-2234 ATCC Cat#ATCC CRL-2234; RRID:CVCL_0454 RAW 264.7 - TIB-71 - ATCC ATCC Cat#ATCC TIB-71; RRID:CVCL_0493 Hepa 1–6 [Hepa1-6] ATCC Cat#CRL-1830; RRID:CVCL_0327 B16-F10 ATCC Cat#CRL-6475; RRID:CVCL_0159 Experimental models: Organisms/strains B6.129-Adartm1Knk/Mmjax The Jackson Laboratory MMRRC Strain #034619-JAX RRID:MMRRC_034619-JAX B6.Cg-Ifih1tm1.1Cln/J The Jackson Laboratory Strain #:015812 RRID:IMSR_JAX:015812 B6.Cg-Speer6-ps1Tg(Alb-cre)21Mgn/J The Jackson Laboratory Strain #:003574 RRID:IMSR_JAX:003574 C57BL/6JInv The Jackson Laboratory Strain #:000664 RRID:IMSR_JAX:000664 Oligonucleotides Primers for mouse qPCR data This study Table S6 Primers for human qPCR data This study Table S6 shRNA sequences for ADAR1 knock-down This study Table S7 shRNA sequences for Adar knock-down This study Table S7 sgRNA sequences for Adar knock-out This study Table S7 Software and algorithms GraphPad Prism 9 GraphPad https://www.graphpad.com/ scientific-software/prism/ BioRender BioRender BioRender.com R 4.1.2 The R Foundation https://www.r-project.org UMAP Stuart et al.51 https://satijalab.org/seurat/ Seurat Butler et al.52 https://github.com/satijalab/seurat Cellranger 6.1.1 10X Genomics https://www.10xgenomics.com Python 3.6.15 Python Software Foundation https://www.python.org Anaconda 2019.6 Anaconda https://www.anaconda.com Scanpy 1.7.2 PyPI https://pypi.org anndata 0.7.6 PyPI https://pypi.org numpy 1.19.5 PyPI https://pypi.org scipy 1.5.3 PyPI https://pypi.org pandas 1.1.5 PyPI https://pypi.org NicheNet Github https://github.com/saeyslab/nichenetr RNA Velocity velocyto.py GitHub https://github.com/velocyto-team/velocyto.py (Continued on next page) Cell Reports 43, 114400, July 23, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER scVelo 0.2.4 GitHub https://github.com/theislab/scvelo ImageJ 1.53t Schneider et al.53 https://imagej.nih.gov/ij DAVID Bioinformatics Resources Sherman et al., Huang et al.54,55 https://david.ncifcrf.gov/home.jsp Enrichr Chen et al., Kuleshov et al., Xie et al.56–58 https://maayanlab.cloud/Enrichr/ inForm Software 2.6.0 Akoya Biosciences https://www.akoyabio.com/phenoimager/ software/inform-tissue-finder/ Original code for analyses This Study https://zenodo.org/records/11274305 (https://doi.org/10.5281/zenodo.11274305) Others ROCHE Collagenase/Dispase Roche Cat#10269638001 InvitrogenTM eBioscienceTM 1X RBC Lysis Buffer Invitrogen Cat#00-4333-57 RQ1 RNase-Free Dnase Promega Cat#M6101 DirectPCR Lysis Reagent (Ear) Viagen Cat#402-E Recombinant Proteinase K Solution (20 mg/mL) Thermo Fisher Scientific Cat#AM2546 InvitrogenTM PlatinumTM Green Hot Start PCR Master Mix (2X) Thermo Fisher Scientific Cat#13001012 MiniCollect Complete CAT Serum Separator Clot Activator tubes Greiner Cat#450548 SPLInsertTM Hanging SPL Life Sciences Cat#35206 CorningTM FalconTM Cell Culture Inserts Corning Cat#353097 GibcoTM HBSS (10X), no calcium, no magnesium, phenol red Thermo Fisher Scientific Cat#14180046 Collagenase from Clostridium histolyticum, Type IA Sigma-Aldrich Cat#C9891 0.5M EGTA, pH 8.0 1st Base Cat#CUS-1070 GibcoTM ACK Lysing Buffer Thermo Fisher Scientific Cat#A1049201 Percoll Sigma-Aldrich Cat#P1644 Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix Merck Cat#CLS356231 SPRIselect for Size Selection Beckman Coulter Cat#B23317 Qiagen, Inc. RNeasy Mini Kit Qiagen Cat#74106 Advantage RT-for-PCR Kit Takara Cat#639506 GoTaq qPCR Master Mix Promega Cat#A600A cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Roche Cat#11873580001 PhosSTOP Roche Cat#4906845001 LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat#11668019 Clearene Solvent Leica Cat#3803600 CV Ultra Mounting Media Leica Cat#14070936261 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories H-1200-10 Standard Macrophage Depletion Kit (Clodrosome + Encapsome ) Encapsula Nano Sciences SKU# CLD-8901 Paraplast Leica 39603002 CV Ultra Mounting Media Leica cv-ultra-mounting-media Cover glass Size 22 x 22mm Fisher Scientific FIS#12-544-10 Formalin solution, neutral buffered, 10% Sigma-Aldrich HT501128 Clearene Leica 3803600 Target Retrieval Solution, Citrate pH 6.1 (10x) Dako S1699 Peroxidase-Blocking Solution, Dako REAL Dako S2023 (Continued on next page) 22 Cell Reports 43, 114400, July 23, 2024
Gene Expression:Article Title: Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER AZD5582 Selleck Chemicals Cat#S7362 Emricasan (IDN-6556) Selleck Chemicals Cat#S7775 Critical commercial assays 10x Genomics Chromium Next GEM Single Cell 30 kit v3.1 (Dual index) 10x Genomics Cat#1000268 Visium spatial gene expression slide & reagent kit 10x Genomics Cat#1000184 Deposited data Mouse Bulk RNA sequencing data GEO GEO: GSE225175 Mouse Single-cell RNA sequencing data GEO GEO: GSE227092 Mouse Spatial Transcriptomics data GEO GEO: GSE228195 Human HCC Single-cell RNA sequencing data GEO GEO: GSE223204 Experimental models: Cell lines AML12 - CRL-2254 - ATCC ATCC Cat#ATCC-CRL-2254; RRID:CVCL_0140 SNU449 - ATCC CRL-2234 ATCC Cat#ATCC CRL-2234; RRID:CVCL_0454 RAW 264.7 - TIB-71 - ATCC ATCC Cat#ATCC TIB-71; RRID:CVCL_0493 Hepa 1–6 [Hepa1-6] ATCC Cat#CRL-1830; RRID:CVCL_0327 B16-F10 ATCC Cat#CRL-6475; RRID:CVCL_0159 Experimental models: Organisms/strains B6.129-Adartm1Knk/Mmjax The Jackson Laboratory MMRRC Strain #034619-JAX RRID:MMRRC_034619-JAX B6.Cg-Ifih1tm1.1Cln/J The Jackson Laboratory Strain #:015812 RRID:IMSR_JAX:015812 B6.Cg-Speer6-ps1Tg(Alb-cre)21Mgn/J The Jackson Laboratory Strain #:003574 RRID:IMSR_JAX:003574 C57BL/6JInv The Jackson Laboratory Strain #:000664 RRID:IMSR_JAX:000664 Oligonucleotides Primers for mouse qPCR data This study Table S6 Primers for human qPCR data This study Table S6 shRNA sequences for ADAR1 knock-down This study Table S7 shRNA sequences for Adar knock-down This study Table S7 sgRNA sequences for Adar knock-out This study Table S7 Software and algorithms GraphPad Prism 9 GraphPad https://www.graphpad.com/ scientific-software/prism/ BioRender BioRender BioRender.com R 4.1.2 The R Foundation https://www.r-project.org UMAP Stuart et al.51 https://satijalab.org/seurat/ Seurat Butler et al.52 https://github.com/satijalab/seurat Cellranger 6.1.1 10X Genomics https://www.10xgenomics.com Python 3.6.15 Python Software Foundation https://www.python.org Anaconda 2019.6 Anaconda https://www.anaconda.com Scanpy 1.7.2 PyPI https://pypi.org anndata 0.7.6 PyPI https://pypi.org numpy 1.19.5 PyPI https://pypi.org scipy 1.5.3 PyPI https://pypi.org pandas 1.1.5 PyPI https://pypi.org NicheNet Github https://github.com/saeyslab/nichenetr RNA Velocity velocyto.py GitHub https://github.com/velocyto-team/velocyto.py (Continued on next page) Cell Reports 43, 114400, July 23, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER scVelo 0.2.4 GitHub https://github.com/theislab/scvelo ImageJ 1.53t Schneider et al.53 https://imagej.nih.gov/ij DAVID Bioinformatics Resources Sherman et al., Huang et al.54,55 https://david.ncifcrf.gov/home.jsp Enrichr Chen et al., Kuleshov et al., Xie et al.56–58 https://maayanlab.cloud/Enrichr/ inForm Software 2.6.0 Akoya Biosciences https://www.akoyabio.com/phenoimager/ software/inform-tissue-finder/ Original code for analyses This Study https://zenodo.org/records/11274305 (https://doi.org/10.5281/zenodo.11274305) Others ROCHE Collagenase/Dispase Roche Cat#10269638001 InvitrogenTM eBioscienceTM 1X RBC Lysis Buffer Invitrogen Cat#00-4333-57 RQ1 RNase-Free Dnase Promega Cat#M6101 DirectPCR Lysis Reagent (Ear) Viagen Cat#402-E Recombinant Proteinase K Solution (20 mg/mL) Thermo Fisher Scientific Cat#AM2546 InvitrogenTM PlatinumTM Green Hot Start PCR Master Mix (2X) Thermo Fisher Scientific Cat#13001012 MiniCollect Complete CAT Serum Separator Clot Activator tubes Greiner Cat#450548 SPLInsertTM Hanging SPL Life Sciences Cat#35206 CorningTM FalconTM Cell Culture Inserts Corning Cat#353097 GibcoTM HBSS (10X), no calcium, no magnesium, phenol red Thermo Fisher Scientific Cat#14180046 Collagenase from Clostridium histolyticum, Type IA Sigma-Aldrich Cat#C9891 0.5M EGTA, pH 8.0 1st Base Cat#CUS-1070 GibcoTM ACK Lysing Buffer Thermo Fisher Scientific Cat#A1049201 Percoll Sigma-Aldrich Cat#P1644 Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix Merck Cat#CLS356231 SPRIselect for Size Selection Beckman Coulter Cat#B23317 Qiagen, Inc. RNeasy Mini Kit Qiagen Cat#74106 Advantage RT-for-PCR Kit Takara Cat#639506 GoTaq qPCR Master Mix Promega Cat#A600A cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Roche Cat#11873580001 PhosSTOP Roche Cat#4906845001 LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat#11668019 Clearene Solvent Leica Cat#3803600 CV Ultra Mounting Media Leica Cat#14070936261 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories H-1200-10 Standard Macrophage Depletion Kit (Clodrosome + Encapsome ) Encapsula Nano Sciences SKU# CLD-8901 Paraplast Leica 39603002 CV Ultra Mounting Media Leica cv-ultra-mounting-media Cover glass Size 22 x 22mm Fisher Scientific FIS#12-544-10 Formalin solution, neutral buffered, 10% Sigma-Aldrich HT501128 Clearene Leica 3803600 Target Retrieval Solution, Citrate pH 6.1 (10x) Dako S1699 Peroxidase-Blocking Solution, Dako REAL Dako S2023 (Continued on next page) 22 Cell Reports 43, 114400, July 23, 2024
RNA Sequencing:Article Title: Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER AZD5582 Selleck Chemicals Cat#S7362 Emricasan (IDN-6556) Selleck Chemicals Cat#S7775 Critical commercial assays 10x Genomics Chromium Next GEM Single Cell 30 kit v3.1 (Dual index) 10x Genomics Cat#1000268 Visium spatial gene expression slide & reagent kit 10x Genomics Cat#1000184 Deposited data Mouse Bulk RNA sequencing data GEO GEO: GSE225175 Mouse Single-cell RNA sequencing data GEO GEO: GSE227092 Mouse Spatial Transcriptomics data GEO GEO: GSE228195 Human HCC Single-cell RNA sequencing data GEO GEO: GSE223204 Experimental models: Cell lines AML12 - CRL-2254 - ATCC ATCC Cat#ATCC-CRL-2254; RRID:CVCL_0140 SNU449 - ATCC CRL-2234 ATCC Cat#ATCC CRL-2234; RRID:CVCL_0454 RAW 264.7 - TIB-71 - ATCC ATCC Cat#ATCC TIB-71; RRID:CVCL_0493 Hepa 1–6 [Hepa1-6] ATCC Cat#CRL-1830; RRID:CVCL_0327 B16-F10 ATCC Cat#CRL-6475; RRID:CVCL_0159 Experimental models: Organisms/strains B6.129-Adartm1Knk/Mmjax The Jackson Laboratory MMRRC Strain #034619-JAX RRID:MMRRC_034619-JAX B6.Cg-Ifih1tm1.1Cln/J The Jackson Laboratory Strain #:015812 RRID:IMSR_JAX:015812 B6.Cg-Speer6-ps1Tg(Alb-cre)21Mgn/J The Jackson Laboratory Strain #:003574 RRID:IMSR_JAX:003574 C57BL/6JInv The Jackson Laboratory Strain #:000664 RRID:IMSR_JAX:000664 Oligonucleotides Primers for mouse qPCR data This study Table S6 Primers for human qPCR data This study Table S6 shRNA sequences for ADAR1 knock-down This study Table S7 shRNA sequences for Adar knock-down This study Table S7 sgRNA sequences for Adar knock-out This study Table S7 Software and algorithms GraphPad Prism 9 GraphPad https://www.graphpad.com/ scientific-software/prism/ BioRender BioRender BioRender.com R 4.1.2 The R Foundation https://www.r-project.org UMAP Stuart et al.51 https://satijalab.org/seurat/ Seurat Butler et al.52 https://github.com/satijalab/seurat Cellranger 6.1.1 10X Genomics https://www.10xgenomics.com Python 3.6.15 Python Software Foundation https://www.python.org Anaconda 2019.6 Anaconda https://www.anaconda.com Scanpy 1.7.2 PyPI https://pypi.org anndata 0.7.6 PyPI https://pypi.org numpy 1.19.5 PyPI https://pypi.org scipy 1.5.3 PyPI https://pypi.org pandas 1.1.5 PyPI https://pypi.org NicheNet Github https://github.com/saeyslab/nichenetr RNA Velocity velocyto.py GitHub https://github.com/velocyto-team/velocyto.py (Continued on next page) Cell Reports 43, 114400, July 23, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER scVelo 0.2.4 GitHub https://github.com/theislab/scvelo ImageJ 1.53t Schneider et al.53 https://imagej.nih.gov/ij DAVID Bioinformatics Resources Sherman et al., Huang et al.54,55 https://david.ncifcrf.gov/home.jsp Enrichr Chen et al., Kuleshov et al., Xie et al.56–58 https://maayanlab.cloud/Enrichr/ inForm Software 2.6.0 Akoya Biosciences https://www.akoyabio.com/phenoimager/ software/inform-tissue-finder/ Original code for analyses This Study https://zenodo.org/records/11274305 (https://doi.org/10.5281/zenodo.11274305) Others ROCHE Collagenase/Dispase Roche Cat#10269638001 InvitrogenTM eBioscienceTM 1X RBC Lysis Buffer Invitrogen Cat#00-4333-57 RQ1 RNase-Free Dnase Promega Cat#M6101 DirectPCR Lysis Reagent (Ear) Viagen Cat#402-E Recombinant Proteinase K Solution (20 mg/mL) Thermo Fisher Scientific Cat#AM2546 InvitrogenTM PlatinumTM Green Hot Start PCR Master Mix (2X) Thermo Fisher Scientific Cat#13001012 MiniCollect Complete CAT Serum Separator Clot Activator tubes Greiner Cat#450548 SPLInsertTM Hanging SPL Life Sciences Cat#35206 CorningTM FalconTM Cell Culture Inserts Corning Cat#353097 GibcoTM HBSS (10X), no calcium, no magnesium, phenol red Thermo Fisher Scientific Cat#14180046 Collagenase from Clostridium histolyticum, Type IA Sigma-Aldrich Cat#C9891 0.5M EGTA, pH 8.0 1st Base Cat#CUS-1070 GibcoTM ACK Lysing Buffer Thermo Fisher Scientific Cat#A1049201 Percoll Sigma-Aldrich Cat#P1644 Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix Merck Cat#CLS356231 SPRIselect for Size Selection Beckman Coulter Cat#B23317 Qiagen, Inc. RNeasy Mini Kit Qiagen Cat#74106 Advantage RT-for-PCR Kit Takara Cat#639506 GoTaq qPCR Master Mix Promega Cat#A600A cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Roche Cat#11873580001 PhosSTOP Roche Cat#4906845001 LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat#11668019 Clearene Solvent Leica Cat#3803600 CV Ultra Mounting Media Leica Cat#14070936261 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories H-1200-10 Standard Macrophage Depletion Kit (Clodrosome + Encapsome ) Encapsula Nano Sciences SKU# CLD-8901 Paraplast Leica 39603002 CV Ultra Mounting Media Leica cv-ultra-mounting-media Cover glass Size 22 x 22mm Fisher Scientific FIS#12-544-10 Formalin solution, neutral buffered, 10% Sigma-Aldrich HT501128 Clearene Leica 3803600 Target Retrieval Solution, Citrate pH 6.1 (10x) Dako S1699 Peroxidase-Blocking Solution, Dako REAL Dako S2023 (Continued on next page) 22 Cell Reports 43, 114400, July 23, 2024
Spatial Transcriptomics:Article Title: Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER AZD5582 Selleck Chemicals Cat#S7362 Emricasan (IDN-6556) Selleck Chemicals Cat#S7775 Critical commercial assays 10x Genomics Chromium Next GEM Single Cell 30 kit v3.1 (Dual index) 10x Genomics Cat#1000268 Visium spatial gene expression slide & reagent kit 10x Genomics Cat#1000184 Deposited data Mouse Bulk RNA sequencing data GEO GEO: GSE225175 Mouse Single-cell RNA sequencing data GEO GEO: GSE227092 Mouse Spatial Transcriptomics data GEO GEO: GSE228195 Human HCC Single-cell RNA sequencing data GEO GEO: GSE223204 Experimental models: Cell lines AML12 - CRL-2254 - ATCC ATCC Cat#ATCC-CRL-2254; RRID:CVCL_0140 SNU449 - ATCC CRL-2234 ATCC Cat#ATCC CRL-2234; RRID:CVCL_0454 RAW 264.7 - TIB-71 - ATCC ATCC Cat#ATCC TIB-71; RRID:CVCL_0493 Hepa 1–6 [Hepa1-6] ATCC Cat#CRL-1830; RRID:CVCL_0327 B16-F10 ATCC Cat#CRL-6475; RRID:CVCL_0159 Experimental models: Organisms/strains B6.129-Adartm1Knk/Mmjax The Jackson Laboratory MMRRC Strain #034619-JAX RRID:MMRRC_034619-JAX B6.Cg-Ifih1tm1.1Cln/J The Jackson Laboratory Strain #:015812 RRID:IMSR_JAX:015812 B6.Cg-Speer6-ps1Tg(Alb-cre)21Mgn/J The Jackson Laboratory Strain #:003574 RRID:IMSR_JAX:003574 C57BL/6JInv The Jackson Laboratory Strain #:000664 RRID:IMSR_JAX:000664 Oligonucleotides Primers for mouse qPCR data This study Table S6 Primers for human qPCR data This study Table S6 shRNA sequences for ADAR1 knock-down This study Table S7 shRNA sequences for Adar knock-down This study Table S7 sgRNA sequences for Adar knock-out This study Table S7 Software and algorithms GraphPad Prism 9 GraphPad https://www.graphpad.com/ scientific-software/prism/ BioRender BioRender BioRender.com R 4.1.2 The R Foundation https://www.r-project.org UMAP Stuart et al.51 https://satijalab.org/seurat/ Seurat Butler et al.52 https://github.com/satijalab/seurat Cellranger 6.1.1 10X Genomics https://www.10xgenomics.com Python 3.6.15 Python Software Foundation https://www.python.org Anaconda 2019.6 Anaconda https://www.anaconda.com Scanpy 1.7.2 PyPI https://pypi.org anndata 0.7.6 PyPI https://pypi.org numpy 1.19.5 PyPI https://pypi.org scipy 1.5.3 PyPI https://pypi.org pandas 1.1.5 PyPI https://pypi.org NicheNet Github https://github.com/saeyslab/nichenetr RNA Velocity velocyto.py GitHub https://github.com/velocyto-team/velocyto.py (Continued on next page) Cell Reports 43, 114400, July 23, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER scVelo 0.2.4 GitHub https://github.com/theislab/scvelo ImageJ 1.53t Schneider et al.53 https://imagej.nih.gov/ij DAVID Bioinformatics Resources Sherman et al., Huang et al.54,55 https://david.ncifcrf.gov/home.jsp Enrichr Chen et al., Kuleshov et al., Xie et al.56–58 https://maayanlab.cloud/Enrichr/ inForm Software 2.6.0 Akoya Biosciences https://www.akoyabio.com/phenoimager/ software/inform-tissue-finder/ Original code for analyses This Study https://zenodo.org/records/11274305 (https://doi.org/10.5281/zenodo.11274305) Others ROCHE Collagenase/Dispase Roche Cat#10269638001 InvitrogenTM eBioscienceTM 1X RBC Lysis Buffer Invitrogen Cat#00-4333-57 RQ1 RNase-Free Dnase Promega Cat#M6101 DirectPCR Lysis Reagent (Ear) Viagen Cat#402-E Recombinant Proteinase K Solution (20 mg/mL) Thermo Fisher Scientific Cat#AM2546 InvitrogenTM PlatinumTM Green Hot Start PCR Master Mix (2X) Thermo Fisher Scientific Cat#13001012 MiniCollect Complete CAT Serum Separator Clot Activator tubes Greiner Cat#450548 SPLInsertTM Hanging SPL Life Sciences Cat#35206 CorningTM FalconTM Cell Culture Inserts Corning Cat#353097 GibcoTM HBSS (10X), no calcium, no magnesium, phenol red Thermo Fisher Scientific Cat#14180046 Collagenase from Clostridium histolyticum, Type IA Sigma-Aldrich Cat#C9891 0.5M EGTA, pH 8.0 1st Base Cat#CUS-1070 GibcoTM ACK Lysing Buffer Thermo Fisher Scientific Cat#A1049201 Percoll Sigma-Aldrich Cat#P1644 Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix Merck Cat#CLS356231 SPRIselect for Size Selection Beckman Coulter Cat#B23317 Qiagen, Inc. RNeasy Mini Kit Qiagen Cat#74106 Advantage RT-for-PCR Kit Takara Cat#639506 GoTaq qPCR Master Mix Promega Cat#A600A cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Roche Cat#11873580001 PhosSTOP Roche Cat#4906845001 LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat#11668019 Clearene Solvent Leica Cat#3803600 CV Ultra Mounting Media Leica Cat#14070936261 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories H-1200-10 Standard Macrophage Depletion Kit (Clodrosome + Encapsome ) Encapsula Nano Sciences SKU# CLD-8901 Paraplast Leica 39603002 CV Ultra Mounting Media Leica cv-ultra-mounting-media Cover glass Size 22 x 22mm Fisher Scientific FIS#12-544-10 Formalin solution, neutral buffered, 10% Sigma-Aldrich HT501128 Clearene Leica 3803600 Target Retrieval Solution, Citrate pH 6.1 (10x) Dako S1699 Peroxidase-Blocking Solution, Dako REAL Dako S2023 (Continued on next page) 22 Cell Reports 43, 114400, July 23, 2024
Real-time Polymerase Chain Reaction:Article Title: Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER AZD5582 Selleck Chemicals Cat#S7362 Emricasan (IDN-6556) Selleck Chemicals Cat#S7775 Critical commercial assays 10x Genomics Chromium Next GEM Single Cell 30 kit v3.1 (Dual index) 10x Genomics Cat#1000268 Visium spatial gene expression slide & reagent kit 10x Genomics Cat#1000184 Deposited data Mouse Bulk RNA sequencing data GEO GEO: GSE225175 Mouse Single-cell RNA sequencing data GEO GEO: GSE227092 Mouse Spatial Transcriptomics data GEO GEO: GSE228195 Human HCC Single-cell RNA sequencing data GEO GEO: GSE223204 Experimental models: Cell lines AML12 - CRL-2254 - ATCC ATCC Cat#ATCC-CRL-2254; RRID:CVCL_0140 SNU449 - ATCC CRL-2234 ATCC Cat#ATCC CRL-2234; RRID:CVCL_0454 RAW 264.7 - TIB-71 - ATCC ATCC Cat#ATCC TIB-71; RRID:CVCL_0493 Hepa 1–6 [Hepa1-6] ATCC Cat#CRL-1830; RRID:CVCL_0327 B16-F10 ATCC Cat#CRL-6475; RRID:CVCL_0159 Experimental models: Organisms/strains B6.129-Adartm1Knk/Mmjax The Jackson Laboratory MMRRC Strain #034619-JAX RRID:MMRRC_034619-JAX B6.Cg-Ifih1tm1.1Cln/J The Jackson Laboratory Strain #:015812 RRID:IMSR_JAX:015812 B6.Cg-Speer6-ps1Tg(Alb-cre)21Mgn/J The Jackson Laboratory Strain #:003574 RRID:IMSR_JAX:003574 C57BL/6JInv The Jackson Laboratory Strain #:000664 RRID:IMSR_JAX:000664 Oligonucleotides Primers for mouse qPCR data This study Table S6 Primers for human qPCR data This study Table S6 shRNA sequences for ADAR1 knock-down This study Table S7 shRNA sequences for Adar knock-down This study Table S7 sgRNA sequences for Adar knock-out This study Table S7 Software and algorithms GraphPad Prism 9 GraphPad https://www.graphpad.com/ scientific-software/prism/ BioRender BioRender BioRender.com R 4.1.2 The R Foundation https://www.r-project.org UMAP Stuart et al.51 https://satijalab.org/seurat/ Seurat Butler et al.52 https://github.com/satijalab/seurat Cellranger 6.1.1 10X Genomics https://www.10xgenomics.com Python 3.6.15 Python Software Foundation https://www.python.org Anaconda 2019.6 Anaconda https://www.anaconda.com Scanpy 1.7.2 PyPI https://pypi.org anndata 0.7.6 PyPI https://pypi.org numpy 1.19.5 PyPI https://pypi.org scipy 1.5.3 PyPI https://pypi.org pandas 1.1.5 PyPI https://pypi.org NicheNet Github https://github.com/saeyslab/nichenetr RNA Velocity velocyto.py GitHub https://github.com/velocyto-team/velocyto.py (Continued on next page) Cell Reports 43, 114400, July 23, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER scVelo 0.2.4 GitHub https://github.com/theislab/scvelo ImageJ 1.53t Schneider et al.53 https://imagej.nih.gov/ij DAVID Bioinformatics Resources Sherman et al., Huang et al.54,55 https://david.ncifcrf.gov/home.jsp Enrichr Chen et al., Kuleshov et al., Xie et al.56–58 https://maayanlab.cloud/Enrichr/ inForm Software 2.6.0 Akoya Biosciences https://www.akoyabio.com/phenoimager/ software/inform-tissue-finder/ Original code for analyses This Study https://zenodo.org/records/11274305 (https://doi.org/10.5281/zenodo.11274305) Others ROCHE Collagenase/Dispase Roche Cat#10269638001 InvitrogenTM eBioscienceTM 1X RBC Lysis Buffer Invitrogen Cat#00-4333-57 RQ1 RNase-Free Dnase Promega Cat#M6101 DirectPCR Lysis Reagent (Ear) Viagen Cat#402-E Recombinant Proteinase K Solution (20 mg/mL) Thermo Fisher Scientific Cat#AM2546 InvitrogenTM PlatinumTM Green Hot Start PCR Master Mix (2X) Thermo Fisher Scientific Cat#13001012 MiniCollect Complete CAT Serum Separator Clot Activator tubes Greiner Cat#450548 SPLInsertTM Hanging SPL Life Sciences Cat#35206 CorningTM FalconTM Cell Culture Inserts Corning Cat#353097 GibcoTM HBSS (10X), no calcium, no magnesium, phenol red Thermo Fisher Scientific Cat#14180046 Collagenase from Clostridium histolyticum, Type IA Sigma-Aldrich Cat#C9891 0.5M EGTA, pH 8.0 1st Base Cat#CUS-1070 GibcoTM ACK Lysing Buffer Thermo Fisher Scientific Cat#A1049201 Percoll Sigma-Aldrich Cat#P1644 Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix Merck Cat#CLS356231 SPRIselect for Size Selection Beckman Coulter Cat#B23317 Qiagen, Inc. RNeasy Mini Kit Qiagen Cat#74106 Advantage RT-for-PCR Kit Takara Cat#639506 GoTaq qPCR Master Mix Promega Cat#A600A cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Roche Cat#11873580001 PhosSTOP Roche Cat#4906845001 LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat#11668019 Clearene Solvent Leica Cat#3803600 CV Ultra Mounting Media Leica Cat#14070936261 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories H-1200-10 Standard Macrophage Depletion Kit (Clodrosome + Encapsome ) Encapsula Nano Sciences SKU# CLD-8901 Paraplast Leica 39603002 CV Ultra Mounting Media Leica cv-ultra-mounting-media Cover glass Size 22 x 22mm Fisher Scientific FIS#12-544-10 Formalin solution, neutral buffered, 10% Sigma-Aldrich HT501128 Clearene Leica 3803600 Target Retrieval Solution, Citrate pH 6.1 (10x) Dako S1699 Peroxidase-Blocking Solution, Dako REAL Dako S2023 (Continued on next page) 22 Cell Reports 43, 114400, July 23, 2024
shRNA:Article Title: Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER AZD5582 Selleck Chemicals Cat#S7362 Emricasan (IDN-6556) Selleck Chemicals Cat#S7775 Critical commercial assays 10x Genomics Chromium Next GEM Single Cell 30 kit v3.1 (Dual index) 10x Genomics Cat#1000268 Visium spatial gene expression slide & reagent kit 10x Genomics Cat#1000184 Deposited data Mouse Bulk RNA sequencing data GEO GEO: GSE225175 Mouse Single-cell RNA sequencing data GEO GEO: GSE227092 Mouse Spatial Transcriptomics data GEO GEO: GSE228195 Human HCC Single-cell RNA sequencing data GEO GEO: GSE223204 Experimental models: Cell lines AML12 - CRL-2254 - ATCC ATCC Cat#ATCC-CRL-2254; RRID:CVCL_0140 SNU449 - ATCC CRL-2234 ATCC Cat#ATCC CRL-2234; RRID:CVCL_0454 RAW 264.7 - TIB-71 - ATCC ATCC Cat#ATCC TIB-71; RRID:CVCL_0493 Hepa 1–6 [Hepa1-6] ATCC Cat#CRL-1830; RRID:CVCL_0327 B16-F10 ATCC Cat#CRL-6475; RRID:CVCL_0159 Experimental models: Organisms/strains B6.129-Adartm1Knk/Mmjax The Jackson Laboratory MMRRC Strain #034619-JAX RRID:MMRRC_034619-JAX B6.Cg-Ifih1tm1.1Cln/J The Jackson Laboratory Strain #:015812 RRID:IMSR_JAX:015812 B6.Cg-Speer6-ps1Tg(Alb-cre)21Mgn/J The Jackson Laboratory Strain #:003574 RRID:IMSR_JAX:003574 C57BL/6JInv The Jackson Laboratory Strain #:000664 RRID:IMSR_JAX:000664 Oligonucleotides Primers for mouse qPCR data This study Table S6 Primers for human qPCR data This study Table S6 shRNA sequences for ADAR1 knock-down This study Table S7 shRNA sequences for Adar knock-down This study Table S7 sgRNA sequences for Adar knock-out This study Table S7 Software and algorithms GraphPad Prism 9 GraphPad https://www.graphpad.com/ scientific-software/prism/ BioRender BioRender BioRender.com R 4.1.2 The R Foundation https://www.r-project.org UMAP Stuart et al.51 https://satijalab.org/seurat/ Seurat Butler et al.52 https://github.com/satijalab/seurat Cellranger 6.1.1 10X Genomics https://www.10xgenomics.com Python 3.6.15 Python Software Foundation https://www.python.org Anaconda 2019.6 Anaconda https://www.anaconda.com Scanpy 1.7.2 PyPI https://pypi.org anndata 0.7.6 PyPI https://pypi.org numpy 1.19.5 PyPI https://pypi.org scipy 1.5.3 PyPI https://pypi.org pandas 1.1.5 PyPI https://pypi.org NicheNet Github https://github.com/saeyslab/nichenetr RNA Velocity velocyto.py GitHub https://github.com/velocyto-team/velocyto.py (Continued on next page) Cell Reports 43, 114400, July 23, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER scVelo 0.2.4 GitHub https://github.com/theislab/scvelo ImageJ 1.53t Schneider et al.53 https://imagej.nih.gov/ij DAVID Bioinformatics Resources Sherman et al., Huang et al.54,55 https://david.ncifcrf.gov/home.jsp Enrichr Chen et al., Kuleshov et al., Xie et al.56–58 https://maayanlab.cloud/Enrichr/ inForm Software 2.6.0 Akoya Biosciences https://www.akoyabio.com/phenoimager/ software/inform-tissue-finder/ Original code for analyses This Study https://zenodo.org/records/11274305 (https://doi.org/10.5281/zenodo.11274305) Others ROCHE Collagenase/Dispase Roche Cat#10269638001 InvitrogenTM eBioscienceTM 1X RBC Lysis Buffer Invitrogen Cat#00-4333-57 RQ1 RNase-Free Dnase Promega Cat#M6101 DirectPCR Lysis Reagent (Ear) Viagen Cat#402-E Recombinant Proteinase K Solution (20 mg/mL) Thermo Fisher Scientific Cat#AM2546 InvitrogenTM PlatinumTM Green Hot Start PCR Master Mix (2X) Thermo Fisher Scientific Cat#13001012 MiniCollect Complete CAT Serum Separator Clot Activator tubes Greiner Cat#450548 SPLInsertTM Hanging SPL Life Sciences Cat#35206 CorningTM FalconTM Cell Culture Inserts Corning Cat#353097 GibcoTM HBSS (10X), no calcium, no magnesium, phenol red Thermo Fisher Scientific Cat#14180046 Collagenase from Clostridium histolyticum, Type IA Sigma-Aldrich Cat#C9891 0.5M EGTA, pH 8.0 1st Base Cat#CUS-1070 GibcoTM ACK Lysing Buffer Thermo Fisher Scientific Cat#A1049201 Percoll Sigma-Aldrich Cat#P1644 Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix Merck Cat#CLS356231 SPRIselect for Size Selection Beckman Coulter Cat#B23317 Qiagen, Inc. RNeasy Mini Kit Qiagen Cat#74106 Advantage RT-for-PCR Kit Takara Cat#639506 GoTaq qPCR Master Mix Promega Cat#A600A cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Roche Cat#11873580001 PhosSTOP Roche Cat#4906845001 LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat#11668019 Clearene Solvent Leica Cat#3803600 CV Ultra Mounting Media Leica Cat#14070936261 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories H-1200-10 Standard Macrophage Depletion Kit (Clodrosome + Encapsome ) Encapsula Nano Sciences SKU# CLD-8901 Paraplast Leica 39603002 CV Ultra Mounting Media Leica cv-ultra-mounting-media Cover glass Size 22 x 22mm Fisher Scientific FIS#12-544-10 Formalin solution, neutral buffered, 10% Sigma-Aldrich HT501128 Clearene Leica 3803600 Target Retrieval Solution, Citrate pH 6.1 (10x) Dako S1699 Peroxidase-Blocking Solution, Dako REAL Dako S2023 (Continued on next page) 22 Cell Reports 43, 114400, July 23, 2024
Knockdown:Article Title: Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER AZD5582 Selleck Chemicals Cat#S7362 Emricasan (IDN-6556) Selleck Chemicals Cat#S7775 Critical commercial assays 10x Genomics Chromium Next GEM Single Cell 30 kit v3.1 (Dual index) 10x Genomics Cat#1000268 Visium spatial gene expression slide & reagent kit 10x Genomics Cat#1000184 Deposited data Mouse Bulk RNA sequencing data GEO GEO: GSE225175 Mouse Single-cell RNA sequencing data GEO GEO: GSE227092 Mouse Spatial Transcriptomics data GEO GEO: GSE228195 Human HCC Single-cell RNA sequencing data GEO GEO: GSE223204 Experimental models: Cell lines AML12 - CRL-2254 - ATCC ATCC Cat#ATCC-CRL-2254; RRID:CVCL_0140 SNU449 - ATCC CRL-2234 ATCC Cat#ATCC CRL-2234; RRID:CVCL_0454 RAW 264.7 - TIB-71 - ATCC ATCC Cat#ATCC TIB-71; RRID:CVCL_0493 Hepa 1–6 [Hepa1-6] ATCC Cat#CRL-1830; RRID:CVCL_0327 B16-F10 ATCC Cat#CRL-6475; RRID:CVCL_0159 Experimental models: Organisms/strains B6.129-Adartm1Knk/Mmjax The Jackson Laboratory MMRRC Strain #034619-JAX RRID:MMRRC_034619-JAX B6.Cg-Ifih1tm1.1Cln/J The Jackson Laboratory Strain #:015812 RRID:IMSR_JAX:015812 B6.Cg-Speer6-ps1Tg(Alb-cre)21Mgn/J The Jackson Laboratory Strain #:003574 RRID:IMSR_JAX:003574 C57BL/6JInv The Jackson Laboratory Strain #:000664 RRID:IMSR_JAX:000664 Oligonucleotides Primers for mouse qPCR data This study Table S6 Primers for human qPCR data This study Table S6 shRNA sequences for ADAR1 knock-down This study Table S7 shRNA sequences for Adar knock-down This study Table S7 sgRNA sequences for Adar knock-out This study Table S7 Software and algorithms GraphPad Prism 9 GraphPad https://www.graphpad.com/ scientific-software/prism/ BioRender BioRender BioRender.com R 4.1.2 The R Foundation https://www.r-project.org UMAP Stuart et al.51 https://satijalab.org/seurat/ Seurat Butler et al.52 https://github.com/satijalab/seurat Cellranger 6.1.1 10X Genomics https://www.10xgenomics.com Python 3.6.15 Python Software Foundation https://www.python.org Anaconda 2019.6 Anaconda https://www.anaconda.com Scanpy 1.7.2 PyPI https://pypi.org anndata 0.7.6 PyPI https://pypi.org numpy 1.19.5 PyPI https://pypi.org scipy 1.5.3 PyPI https://pypi.org pandas 1.1.5 PyPI https://pypi.org NicheNet Github https://github.com/saeyslab/nichenetr RNA Velocity velocyto.py GitHub https://github.com/velocyto-team/velocyto.py (Continued on next page) Cell Reports 43, 114400, July 23, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER scVelo 0.2.4 GitHub https://github.com/theislab/scvelo ImageJ 1.53t Schneider et al.53 https://imagej.nih.gov/ij DAVID Bioinformatics Resources Sherman et al., Huang et al.54,55 https://david.ncifcrf.gov/home.jsp Enrichr Chen et al., Kuleshov et al., Xie et al.56–58 https://maayanlab.cloud/Enrichr/ inForm Software 2.6.0 Akoya Biosciences https://www.akoyabio.com/phenoimager/ software/inform-tissue-finder/ Original code for analyses This Study https://zenodo.org/records/11274305 (https://doi.org/10.5281/zenodo.11274305) Others ROCHE Collagenase/Dispase Roche Cat#10269638001 InvitrogenTM eBioscienceTM 1X RBC Lysis Buffer Invitrogen Cat#00-4333-57 RQ1 RNase-Free Dnase Promega Cat#M6101 DirectPCR Lysis Reagent (Ear) Viagen Cat#402-E Recombinant Proteinase K Solution (20 mg/mL) Thermo Fisher Scientific Cat#AM2546 InvitrogenTM PlatinumTM Green Hot Start PCR Master Mix (2X) Thermo Fisher Scientific Cat#13001012 MiniCollect Complete CAT Serum Separator Clot Activator tubes Greiner Cat#450548 SPLInsertTM Hanging SPL Life Sciences Cat#35206 CorningTM FalconTM Cell Culture Inserts Corning Cat#353097 GibcoTM HBSS (10X), no calcium, no magnesium, phenol red Thermo Fisher Scientific Cat#14180046 Collagenase from Clostridium histolyticum, Type IA Sigma-Aldrich Cat#C9891 0.5M EGTA, pH 8.0 1st Base Cat#CUS-1070 GibcoTM ACK Lysing Buffer Thermo Fisher Scientific Cat#A1049201 Percoll Sigma-Aldrich Cat#P1644 Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix Merck Cat#CLS356231 SPRIselect for Size Selection Beckman Coulter Cat#B23317 Qiagen, Inc. RNeasy Mini Kit Qiagen Cat#74106 Advantage RT-for-PCR Kit Takara Cat#639506 GoTaq qPCR Master Mix Promega Cat#A600A cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Roche Cat#11873580001 PhosSTOP Roche Cat#4906845001 LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat#11668019 Clearene Solvent Leica Cat#3803600 CV Ultra Mounting Media Leica Cat#14070936261 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories H-1200-10 Standard Macrophage Depletion Kit (Clodrosome + Encapsome ) Encapsula Nano Sciences SKU# CLD-8901 Paraplast Leica 39603002 CV Ultra Mounting Media Leica cv-ultra-mounting-media Cover glass Size 22 x 22mm Fisher Scientific FIS#12-544-10 Formalin solution, neutral buffered, 10% Sigma-Aldrich HT501128 Clearene Leica 3803600 Target Retrieval Solution, Citrate pH 6.1 (10x) Dako S1699 Peroxidase-Blocking Solution, Dako REAL Dako S2023 (Continued on next page) 22 Cell Reports 43, 114400, July 23, 2024
Knock-Out:Article Title: Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER AZD5582 Selleck Chemicals Cat#S7362 Emricasan (IDN-6556) Selleck Chemicals Cat#S7775 Critical commercial assays 10x Genomics Chromium Next GEM Single Cell 30 kit v3.1 (Dual index) 10x Genomics Cat#1000268 Visium spatial gene expression slide & reagent kit 10x Genomics Cat#1000184 Deposited data Mouse Bulk RNA sequencing data GEO GEO: GSE225175 Mouse Single-cell RNA sequencing data GEO GEO: GSE227092 Mouse Spatial Transcriptomics data GEO GEO: GSE228195 Human HCC Single-cell RNA sequencing data GEO GEO: GSE223204 Experimental models: Cell lines AML12 - CRL-2254 - ATCC ATCC Cat#ATCC-CRL-2254; RRID:CVCL_0140 SNU449 - ATCC CRL-2234 ATCC Cat#ATCC CRL-2234; RRID:CVCL_0454 RAW 264.7 - TIB-71 - ATCC ATCC Cat#ATCC TIB-71; RRID:CVCL_0493 Hepa 1–6 [Hepa1-6] ATCC Cat#CRL-1830; RRID:CVCL_0327 B16-F10 ATCC Cat#CRL-6475; RRID:CVCL_0159 Experimental models: Organisms/strains B6.129-Adartm1Knk/Mmjax The Jackson Laboratory MMRRC Strain #034619-JAX RRID:MMRRC_034619-JAX B6.Cg-Ifih1tm1.1Cln/J The Jackson Laboratory Strain #:015812 RRID:IMSR_JAX:015812 B6.Cg-Speer6-ps1Tg(Alb-cre)21Mgn/J The Jackson Laboratory Strain #:003574 RRID:IMSR_JAX:003574 C57BL/6JInv The Jackson Laboratory Strain #:000664 RRID:IMSR_JAX:000664 Oligonucleotides Primers for mouse qPCR data This study Table S6 Primers for human qPCR data This study Table S6 shRNA sequences for ADAR1 knock-down This study Table S7 shRNA sequences for Adar knock-down This study Table S7 sgRNA sequences for Adar knock-out This study Table S7 Software and algorithms GraphPad Prism 9 GraphPad https://www.graphpad.com/ scientific-software/prism/ BioRender BioRender BioRender.com R 4.1.2 The R Foundation https://www.r-project.org UMAP Stuart et al.51 https://satijalab.org/seurat/ Seurat Butler et al.52 https://github.com/satijalab/seurat Cellranger 6.1.1 10X Genomics https://www.10xgenomics.com Python 3.6.15 Python Software Foundation https://www.python.org Anaconda 2019.6 Anaconda https://www.anaconda.com Scanpy 1.7.2 PyPI https://pypi.org anndata 0.7.6 PyPI https://pypi.org numpy 1.19.5 PyPI https://pypi.org scipy 1.5.3 PyPI https://pypi.org pandas 1.1.5 PyPI https://pypi.org NicheNet Github https://github.com/saeyslab/nichenetr RNA Velocity velocyto.py GitHub https://github.com/velocyto-team/velocyto.py (Continued on next page) Cell Reports 43, 114400, July 23, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER scVelo 0.2.4 GitHub https://github.com/theislab/scvelo ImageJ 1.53t Schneider et al.53 https://imagej.nih.gov/ij DAVID Bioinformatics Resources Sherman et al., Huang et al.54,55 https://david.ncifcrf.gov/home.jsp Enrichr Chen et al., Kuleshov et al., Xie et al.56–58 https://maayanlab.cloud/Enrichr/ inForm Software 2.6.0 Akoya Biosciences https://www.akoyabio.com/phenoimager/ software/inform-tissue-finder/ Original code for analyses This Study https://zenodo.org/records/11274305 (https://doi.org/10.5281/zenodo.11274305) Others ROCHE Collagenase/Dispase Roche Cat#10269638001 InvitrogenTM eBioscienceTM 1X RBC Lysis Buffer Invitrogen Cat#00-4333-57 RQ1 RNase-Free Dnase Promega Cat#M6101 DirectPCR Lysis Reagent (Ear) Viagen Cat#402-E Recombinant Proteinase K Solution (20 mg/mL) Thermo Fisher Scientific Cat#AM2546 InvitrogenTM PlatinumTM Green Hot Start PCR Master Mix (2X) Thermo Fisher Scientific Cat#13001012 MiniCollect Complete CAT Serum Separator Clot Activator tubes Greiner Cat#450548 SPLInsertTM Hanging SPL Life Sciences Cat#35206 CorningTM FalconTM Cell Culture Inserts Corning Cat#353097 GibcoTM HBSS (10X), no calcium, no magnesium, phenol red Thermo Fisher Scientific Cat#14180046 Collagenase from Clostridium histolyticum, Type IA Sigma-Aldrich Cat#C9891 0.5M EGTA, pH 8.0 1st Base Cat#CUS-1070 GibcoTM ACK Lysing Buffer Thermo Fisher Scientific Cat#A1049201 Percoll Sigma-Aldrich Cat#P1644 Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix Merck Cat#CLS356231 SPRIselect for Size Selection Beckman Coulter Cat#B23317 Qiagen, Inc. RNeasy Mini Kit Qiagen Cat#74106 Advantage RT-for-PCR Kit Takara Cat#639506 GoTaq qPCR Master Mix Promega Cat#A600A cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Roche Cat#11873580001 PhosSTOP Roche Cat#4906845001 LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat#11668019 Clearene Solvent Leica Cat#3803600 CV Ultra Mounting Media Leica Cat#14070936261 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories H-1200-10 Standard Macrophage Depletion Kit (Clodrosome + Encapsome ) Encapsula Nano Sciences SKU# CLD-8901 Paraplast Leica 39603002 CV Ultra Mounting Media Leica cv-ultra-mounting-media Cover glass Size 22 x 22mm Fisher Scientific FIS#12-544-10 Formalin solution, neutral buffered, 10% Sigma-Aldrich HT501128 Clearene Leica 3803600 Target Retrieval Solution, Citrate pH 6.1 (10x) Dako S1699 Peroxidase-Blocking Solution, Dako REAL Dako S2023 (Continued on next page) 22 Cell Reports 43, 114400, July 23, 2024
Software:Article Title: Hepatocyte-macrophage crosstalk via the PGRN-EGFR axis modulates ADAR1-mediated immunity in the liver.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER AZD5582 Selleck Chemicals Cat#S7362 Emricasan (IDN-6556) Selleck Chemicals Cat#S7775 Critical commercial assays 10x Genomics Chromium Next GEM Single Cell 30 kit v3.1 (Dual index) 10x Genomics Cat#1000268 Visium spatial gene expression slide & reagent kit 10x Genomics Cat#1000184 Deposited data Mouse Bulk RNA sequencing data GEO GEO: GSE225175 Mouse Single-cell RNA sequencing data GEO GEO: GSE227092 Mouse Spatial Transcriptomics data GEO GEO: GSE228195 Human HCC Single-cell RNA sequencing data GEO GEO: GSE223204 Experimental models: Cell lines AML12 - CRL-2254 - ATCC ATCC Cat#ATCC-CRL-2254; RRID:CVCL_0140 SNU449 - ATCC CRL-2234 ATCC Cat#ATCC CRL-2234; RRID:CVCL_0454 RAW 264.7 - TIB-71 - ATCC ATCC Cat#ATCC TIB-71; RRID:CVCL_0493 Hepa 1–6 [Hepa1-6] ATCC Cat#CRL-1830; RRID:CVCL_0327 B16-F10 ATCC Cat#CRL-6475; RRID:CVCL_0159 Experimental models: Organisms/strains B6.129-Adartm1Knk/Mmjax The Jackson Laboratory MMRRC Strain #034619-JAX RRID:MMRRC_034619-JAX B6.Cg-Ifih1tm1.1Cln/J The Jackson Laboratory Strain #:015812 RRID:IMSR_JAX:015812 B6.Cg-Speer6-ps1Tg(Alb-cre)21Mgn/J The Jackson Laboratory Strain #:003574 RRID:IMSR_JAX:003574 C57BL/6JInv The Jackson Laboratory Strain #:000664 RRID:IMSR_JAX:000664 Oligonucleotides Primers for mouse qPCR data This study Table S6 Primers for human qPCR data This study Table S6 shRNA sequences for ADAR1 knock-down This study Table S7 shRNA sequences for Adar knock-down This study Table S7 sgRNA sequences for Adar knock-out This study Table S7 Software and algorithms GraphPad Prism 9 GraphPad https://www.graphpad.com/ scientific-software/prism/ BioRender BioRender BioRender.com R 4.1.2 The R Foundation https://www.r-project.org UMAP Stuart et al.51 https://satijalab.org/seurat/ Seurat Butler et al.52 https://github.com/satijalab/seurat Cellranger 6.1.1 10X Genomics https://www.10xgenomics.com Python 3.6.15 Python Software Foundation https://www.python.org Anaconda 2019.6 Anaconda https://www.anaconda.com Scanpy 1.7.2 PyPI https://pypi.org anndata 0.7.6 PyPI https://pypi.org numpy 1.19.5 PyPI https://pypi.org scipy 1.5.3 PyPI https://pypi.org pandas 1.1.5 PyPI https://pypi.org NicheNet Github https://github.com/saeyslab/nichenetr RNA Velocity velocyto.py GitHub https://github.com/velocyto-team/velocyto.py (Continued on next page) Cell Reports 43, 114400, July 23, 2024 21 .. REAGENT or RESOURCE SOURCE IDENTIFIER scVelo 0.2.4 GitHub https://github.com/theislab/scvelo ImageJ 1.53t Schneider et al.53 https://imagej.nih.gov/ij DAVID Bioinformatics Resources Sherman et al., Huang et al.54,55 https://david.ncifcrf.gov/home.jsp Enrichr Chen et al., Kuleshov et al., Xie et al.56–58 https://maayanlab.cloud/Enrichr/ inForm Software 2.6.0 Akoya Biosciences https://www.akoyabio.com/phenoimager/ software/inform-tissue-finder/ Original code for analyses This Study https://zenodo.org/records/11274305 (https://doi.org/10.5281/zenodo.11274305) Others ROCHE Collagenase/Dispase Roche Cat#10269638001 InvitrogenTM eBioscienceTM 1X RBC Lysis Buffer Invitrogen Cat#00-4333-57 RQ1 RNase-Free Dnase Promega Cat#M6101 DirectPCR Lysis Reagent (Ear) Viagen Cat#402-E Recombinant Proteinase K Solution (20 mg/mL) Thermo Fisher Scientific Cat#AM2546 InvitrogenTM PlatinumTM Green Hot Start PCR Master Mix (2X) Thermo Fisher Scientific Cat#13001012 MiniCollect Complete CAT Serum Separator Clot Activator tubes Greiner Cat#450548 SPLInsertTM Hanging SPL Life Sciences Cat#35206 CorningTM FalconTM Cell Culture Inserts Corning Cat#353097 GibcoTM HBSS (10X), no calcium, no magnesium, phenol red Thermo Fisher Scientific Cat#14180046 Collagenase from Clostridium histolyticum, Type IA Sigma-Aldrich Cat#C9891 0.5M EGTA, pH 8.0 1st Base Cat#CUS-1070 GibcoTM ACK Lysing Buffer Thermo Fisher Scientific Cat#A1049201 Percoll Sigma-Aldrich Cat#P1644 Corning Matrigel Growth Factor Reduced (GFR) Basement Membrane Matrix Merck Cat#CLS356231 SPRIselect for Size Selection Beckman Coulter Cat#B23317 Qiagen, Inc. RNeasy Mini Kit Qiagen Cat#74106 Advantage RT-for-PCR Kit Takara Cat#639506 GoTaq qPCR Master Mix Promega Cat#A600A cOmpleteTM, EDTA-free Protease Inhibitor Cocktail Roche Cat#11873580001 PhosSTOP Roche Cat#4906845001 LipofectamineTM 2000 Transfection Reagent Thermo Fisher Scientific Cat#11668019 Clearene Solvent Leica Cat#3803600 CV Ultra Mounting Media Leica Cat#14070936261 VECTASHIELD Antifade Mounting Medium with DAPI Vector Laboratories H-1200-10 Standard Macrophage Depletion Kit (Clodrosome + Encapsome ) Encapsula Nano Sciences SKU# CLD-8901 Paraplast Leica 39603002 CV Ultra Mounting Media Leica cv-ultra-mounting-media Cover glass Size 22 x 22mm Fisher Scientific FIS#12-544-10 Formalin solution, neutral buffered, 10% Sigma-Aldrich HT501128 Clearene Leica 3803600 Target Retrieval Solution, Citrate pH 6.1 (10x) Dako S1699 Peroxidase-Blocking Solution, Dako REAL Dako S2023 (Continued on next page) 22 Cell Reports 43, 114400, July 23, 2024
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