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    Proteome Software Inc products scaffold dia dia nn v1 8 1 github
    Products Scaffold Dia Dia Nn V1 8 1 Github, supplied by Proteome Software Inc, used in various techniques. Bioz Stars score: 86/100, based on 1 PubMed citations. ZERO BIAS - scores, article reviews, protocol conditions and more
    https://www.bioz.com/product/github/dia+scaffold/pm42234563-385-169-166
    Average 86 stars, based on 1 article reviews
    products scaffold dia dia nn v1 8 1 github - by Bioz Stars, 2026-09
    86/100 stars

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    Related Articles

    Data-independent acquisition:

    Article Title: The Pseudogymnoascus destructans Proteome Under Copper Stress Conditions
    Article Snippet: .. Scaffold DIA (v3.4.1; Proteome Software) was used for all DIA-MS data processing: fixed modification, cysteine carbamidomethylation; proteolytic enzyme, trypsin with one missed cleavage allowed; peptide mass tolerance, ±10.0 ppm; fragment mass tolerance, ±10.0 ppm; charge states, 2+ and 3+; peptide length, 6–30. ..

    Article Title: The Pseudogymnoascus destructans Proteome Under Copper Stress Conditions
    Article Snippet: .. Scaffold DIA (v3.4.1; Proteome Software, Portland, OR, USA) was used for all DIA-MS data processing: fixed modification, cysteine carbamidomethylation; proteolytic enzyme, trypsin with one missed cleavage allowed; peptide mass tolerance, ±10.0 ppm; fragment mass tolerance, ±10.0 ppm; charge states, 2+ and 3+; peptide length, 6–30. ..

    Article Title: Proteomic Profiling Reveals HECTD4-dependent Regulation of Protein Ubiquitination and Signaling Pathways in Prostate Cancer
    Article Snippet: .. LC-MS/MS raw files were searched against human spectral libraries generated by Prosit (Max Planck Institute of Biochemistry, Martinsried, Germany) using Scaffold DIA (Proteome Software, Portland, OR, USA). ..

    Article Title: Hepatocyte growth factor in biosheets promotes autonomous regeneration of cutaneous tissue after transplantation onto a full-thickness skin defect
    Article Snippet: .. The isolation width for MS2 was set to 4 Da, and overlapping window patterns at m / z 500–740 were used for window placements optimized via Scaffold DIA v3.2.1 (Proteome Software, Portland, OR, USA). ..

    Article Title: CIDEB and CGI-58 differentially regulate liver lipid-droplet cholesterol to modulate metabolic dysfunction-associated steatohepatitis severity.
    Article Snippet: .. The isolation width for MS2 was set to 4 Th, window patterns at m/z 500–740 were used for window placements optimized via Scaffold DIA v3.0.1 (Proteome Software, Portland, OR, USA). ..

    Article Title: The Pseudogymnoascus destructans Proteome Under Copper Stress Conditions
    Article Snippet: The Zeiss Zen software (version 3.8) package was used for image processing. .. Scaffold DIA (v3.4.1; Proteome Software; Portland, OR, USA) was used to generate pairwise comparison tables using a pairwise t -test versus control samples with a significance threshold value of 0.05. ..

    Article Title: The Pseudogymnoascus destructans Proteome Under Copper Stress Conditions
    Article Snippet: The Zeiss Zen software (version 3.8) package was used for image processing. .. Scaffold DIA (v3.4.1; Proteome Software; Portland, OR, USA) was used to generate pairwise comparison tables using a pairwise t-test versus control samples with a significance threshold value of 0.05. ..

    Article Title: CIDEB and CGI-58 differentially regulate liver lipid-droplet cholesterol to modulate metabolic dysfunction-associated steatohepatitis severity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CD68 Boster Biological Technology Cat #: BA3638; RRID: AB_2813855 Chemicals, peptides, and recombinant proteins Bempedoic Acid Cayman Cat #: 26409 BODIPY 493/503 Invitrogen Cat #: D3922 Filipin III from Streptomyces filipinensis Sigma Cat #: F4767 Critical commercial assays Total Cholesterol Assay Kits Cell Biolabs Cat #: STA-384 Triglycerides-SL Sekisui Diagnostics Part #: 239-99 RNeasy Mini Kit Qiagen Cat #: 74104 Deposited data Proteomics ProteomeXchange PXD075672 Raw RNA-seq data DDBJ PRJDB40719; DRR932858–DRR932893 RNA-seq raw count data DDBJ E-GEAD-1232 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory Strain #: 000664 Oligonucleotides GalNAc cEt control ASO: CGCCGATAAGGTACAC Ionis Pharmaceuticals ISIS-1287694 GalNAc cEt Cd36 ASO: TCAGTAAATCAGAACC Ionis Pharmaceuticals ISIS-1073763 GalNAc MOE Atgl ASO: AGGACAACTTGGAGCTTGGC Ionis Pharmaceuticals ISIS- 1843565 GalNAc MOE Soat2 ASO: TCATCATATCGAGACAGATG Ionis Pharmaceuticals ISIS- 1895903 MOE control ASO: CCTTCCCTGAAGGTTCCTCC Ionis Pharmaceuticals ISIS-141923 MOE CGI-58 ASO: TAGGTACACTGGCATATGGA Ionis Pharmaceuticals ISIS-421294 MOE Cideb ASO: ACCTAGATGAAGCAGCGATT Ionis Pharmaceuticals ISIS-455087 MOE Gpam ASO: AGAGCTTTAGTAACACCCAG Ionis Pharmaceuticals ISIS-322308 Software and algorithms RNAseqChef RNAseqChef https://imeg-ku.shinyapps.io/ RNAseqChef/ Scaffold DIA v3.0.1 Proteome Software https://www.proteomesoftware.com/ products/scaffold-dia DIA-NN v1.8.1 GitHub https://github.com/vdemichev/DiaNN/ releases/tag/1.8.1 GraphPad Prism 10.0 GraphPad Software https://www.graphpad.com/scientific- software/prism/ Fiji ImageJ Fiji https://imagej.net/software/fiji/ Other Regular Chow Diet Envigo Cat #: 2018S L-Amino Acid Diet With 60 kcal% Fat With 0.1% Methionine and No Added Choline Research Diets Cat #: A06071302 (Continued on next page) 12 Cell Reports 45, 117369, June 23, 2026 ..

    Modification:

    Article Title: The Pseudogymnoascus destructans Proteome Under Copper Stress Conditions
    Article Snippet: .. Scaffold DIA (v3.4.1; Proteome Software) was used for all DIA-MS data processing: fixed modification, cysteine carbamidomethylation; proteolytic enzyme, trypsin with one missed cleavage allowed; peptide mass tolerance, ±10.0 ppm; fragment mass tolerance, ±10.0 ppm; charge states, 2+ and 3+; peptide length, 6–30. ..

    Article Title: The Pseudogymnoascus destructans Proteome Under Copper Stress Conditions
    Article Snippet: .. Scaffold DIA (v3.4.1; Proteome Software, Portland, OR, USA) was used for all DIA-MS data processing: fixed modification, cysteine carbamidomethylation; proteolytic enzyme, trypsin with one missed cleavage allowed; peptide mass tolerance, ±10.0 ppm; fragment mass tolerance, ±10.0 ppm; charge states, 2+ and 3+; peptide length, 6–30. ..

    Generated:

    Article Title: Proteomic Profiling Reveals HECTD4-dependent Regulation of Protein Ubiquitination and Signaling Pathways in Prostate Cancer
    Article Snippet: .. LC-MS/MS raw files were searched against human spectral libraries generated by Prosit (Max Planck Institute of Biochemistry, Martinsried, Germany) using Scaffold DIA (Proteome Software, Portland, OR, USA). ..

    Isolation:

    Article Title: Hepatocyte growth factor in biosheets promotes autonomous regeneration of cutaneous tissue after transplantation onto a full-thickness skin defect
    Article Snippet: .. The isolation width for MS2 was set to 4 Da, and overlapping window patterns at m / z 500–740 were used for window placements optimized via Scaffold DIA v3.2.1 (Proteome Software, Portland, OR, USA). ..

    Article Title: CIDEB and CGI-58 differentially regulate liver lipid-droplet cholesterol to modulate metabolic dysfunction-associated steatohepatitis severity.
    Article Snippet: .. The isolation width for MS2 was set to 4 Th, window patterns at m/z 500–740 were used for window placements optimized via Scaffold DIA v3.0.1 (Proteome Software, Portland, OR, USA). ..

    Comparison:

    Article Title: The Pseudogymnoascus destructans Proteome Under Copper Stress Conditions
    Article Snippet: The Zeiss Zen software (version 3.8) package was used for image processing. .. Scaffold DIA (v3.4.1; Proteome Software; Portland, OR, USA) was used to generate pairwise comparison tables using a pairwise t -test versus control samples with a significance threshold value of 0.05. ..

    Article Title: The Pseudogymnoascus destructans Proteome Under Copper Stress Conditions
    Article Snippet: The Zeiss Zen software (version 3.8) package was used for image processing. .. Scaffold DIA (v3.4.1; Proteome Software; Portland, OR, USA) was used to generate pairwise comparison tables using a pairwise t-test versus control samples with a significance threshold value of 0.05. ..

    Control:

    Article Title: The Pseudogymnoascus destructans Proteome Under Copper Stress Conditions
    Article Snippet: The Zeiss Zen software (version 3.8) package was used for image processing. .. Scaffold DIA (v3.4.1; Proteome Software; Portland, OR, USA) was used to generate pairwise comparison tables using a pairwise t -test versus control samples with a significance threshold value of 0.05. ..

    Article Title: The Pseudogymnoascus destructans Proteome Under Copper Stress Conditions
    Article Snippet: The Zeiss Zen software (version 3.8) package was used for image processing. .. Scaffold DIA (v3.4.1; Proteome Software; Portland, OR, USA) was used to generate pairwise comparison tables using a pairwise t-test versus control samples with a significance threshold value of 0.05. ..

    Article Title: CIDEB and CGI-58 differentially regulate liver lipid-droplet cholesterol to modulate metabolic dysfunction-associated steatohepatitis severity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CD68 Boster Biological Technology Cat #: BA3638; RRID: AB_2813855 Chemicals, peptides, and recombinant proteins Bempedoic Acid Cayman Cat #: 26409 BODIPY 493/503 Invitrogen Cat #: D3922 Filipin III from Streptomyces filipinensis Sigma Cat #: F4767 Critical commercial assays Total Cholesterol Assay Kits Cell Biolabs Cat #: STA-384 Triglycerides-SL Sekisui Diagnostics Part #: 239-99 RNeasy Mini Kit Qiagen Cat #: 74104 Deposited data Proteomics ProteomeXchange PXD075672 Raw RNA-seq data DDBJ PRJDB40719; DRR932858–DRR932893 RNA-seq raw count data DDBJ E-GEAD-1232 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory Strain #: 000664 Oligonucleotides GalNAc cEt control ASO: CGCCGATAAGGTACAC Ionis Pharmaceuticals ISIS-1287694 GalNAc cEt Cd36 ASO: TCAGTAAATCAGAACC Ionis Pharmaceuticals ISIS-1073763 GalNAc MOE Atgl ASO: AGGACAACTTGGAGCTTGGC Ionis Pharmaceuticals ISIS- 1843565 GalNAc MOE Soat2 ASO: TCATCATATCGAGACAGATG Ionis Pharmaceuticals ISIS- 1895903 MOE control ASO: CCTTCCCTGAAGGTTCCTCC Ionis Pharmaceuticals ISIS-141923 MOE CGI-58 ASO: TAGGTACACTGGCATATGGA Ionis Pharmaceuticals ISIS-421294 MOE Cideb ASO: ACCTAGATGAAGCAGCGATT Ionis Pharmaceuticals ISIS-455087 MOE Gpam ASO: AGAGCTTTAGTAACACCCAG Ionis Pharmaceuticals ISIS-322308 Software and algorithms RNAseqChef RNAseqChef https://imeg-ku.shinyapps.io/ RNAseqChef/ Scaffold DIA v3.0.1 Proteome Software https://www.proteomesoftware.com/ products/scaffold-dia DIA-NN v1.8.1 GitHub https://github.com/vdemichev/DiaNN/ releases/tag/1.8.1 GraphPad Prism 10.0 GraphPad Software https://www.graphpad.com/scientific- software/prism/ Fiji ImageJ Fiji https://imagej.net/software/fiji/ Other Regular Chow Diet Envigo Cat #: 2018S L-Amino Acid Diet With 60 kcal% Fat With 0.1% Methionine and No Added Choline Research Diets Cat #: A06071302 (Continued on next page) 12 Cell Reports 45, 117369, June 23, 2026 ..

    Recombinant:

    Article Title: CIDEB and CGI-58 differentially regulate liver lipid-droplet cholesterol to modulate metabolic dysfunction-associated steatohepatitis severity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CD68 Boster Biological Technology Cat #: BA3638; RRID: AB_2813855 Chemicals, peptides, and recombinant proteins Bempedoic Acid Cayman Cat #: 26409 BODIPY 493/503 Invitrogen Cat #: D3922 Filipin III from Streptomyces filipinensis Sigma Cat #: F4767 Critical commercial assays Total Cholesterol Assay Kits Cell Biolabs Cat #: STA-384 Triglycerides-SL Sekisui Diagnostics Part #: 239-99 RNeasy Mini Kit Qiagen Cat #: 74104 Deposited data Proteomics ProteomeXchange PXD075672 Raw RNA-seq data DDBJ PRJDB40719; DRR932858–DRR932893 RNA-seq raw count data DDBJ E-GEAD-1232 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory Strain #: 000664 Oligonucleotides GalNAc cEt control ASO: CGCCGATAAGGTACAC Ionis Pharmaceuticals ISIS-1287694 GalNAc cEt Cd36 ASO: TCAGTAAATCAGAACC Ionis Pharmaceuticals ISIS-1073763 GalNAc MOE Atgl ASO: AGGACAACTTGGAGCTTGGC Ionis Pharmaceuticals ISIS- 1843565 GalNAc MOE Soat2 ASO: TCATCATATCGAGACAGATG Ionis Pharmaceuticals ISIS- 1895903 MOE control ASO: CCTTCCCTGAAGGTTCCTCC Ionis Pharmaceuticals ISIS-141923 MOE CGI-58 ASO: TAGGTACACTGGCATATGGA Ionis Pharmaceuticals ISIS-421294 MOE Cideb ASO: ACCTAGATGAAGCAGCGATT Ionis Pharmaceuticals ISIS-455087 MOE Gpam ASO: AGAGCTTTAGTAACACCCAG Ionis Pharmaceuticals ISIS-322308 Software and algorithms RNAseqChef RNAseqChef https://imeg-ku.shinyapps.io/ RNAseqChef/ Scaffold DIA v3.0.1 Proteome Software https://www.proteomesoftware.com/ products/scaffold-dia DIA-NN v1.8.1 GitHub https://github.com/vdemichev/DiaNN/ releases/tag/1.8.1 GraphPad Prism 10.0 GraphPad Software https://www.graphpad.com/scientific- software/prism/ Fiji ImageJ Fiji https://imagej.net/software/fiji/ Other Regular Chow Diet Envigo Cat #: 2018S L-Amino Acid Diet With 60 kcal% Fat With 0.1% Methionine and No Added Choline Research Diets Cat #: A06071302 (Continued on next page) 12 Cell Reports 45, 117369, June 23, 2026 ..

    Cholesterol Assay:

    Article Title: CIDEB and CGI-58 differentially regulate liver lipid-droplet cholesterol to modulate metabolic dysfunction-associated steatohepatitis severity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CD68 Boster Biological Technology Cat #: BA3638; RRID: AB_2813855 Chemicals, peptides, and recombinant proteins Bempedoic Acid Cayman Cat #: 26409 BODIPY 493/503 Invitrogen Cat #: D3922 Filipin III from Streptomyces filipinensis Sigma Cat #: F4767 Critical commercial assays Total Cholesterol Assay Kits Cell Biolabs Cat #: STA-384 Triglycerides-SL Sekisui Diagnostics Part #: 239-99 RNeasy Mini Kit Qiagen Cat #: 74104 Deposited data Proteomics ProteomeXchange PXD075672 Raw RNA-seq data DDBJ PRJDB40719; DRR932858–DRR932893 RNA-seq raw count data DDBJ E-GEAD-1232 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory Strain #: 000664 Oligonucleotides GalNAc cEt control ASO: CGCCGATAAGGTACAC Ionis Pharmaceuticals ISIS-1287694 GalNAc cEt Cd36 ASO: TCAGTAAATCAGAACC Ionis Pharmaceuticals ISIS-1073763 GalNAc MOE Atgl ASO: AGGACAACTTGGAGCTTGGC Ionis Pharmaceuticals ISIS- 1843565 GalNAc MOE Soat2 ASO: TCATCATATCGAGACAGATG Ionis Pharmaceuticals ISIS- 1895903 MOE control ASO: CCTTCCCTGAAGGTTCCTCC Ionis Pharmaceuticals ISIS-141923 MOE CGI-58 ASO: TAGGTACACTGGCATATGGA Ionis Pharmaceuticals ISIS-421294 MOE Cideb ASO: ACCTAGATGAAGCAGCGATT Ionis Pharmaceuticals ISIS-455087 MOE Gpam ASO: AGAGCTTTAGTAACACCCAG Ionis Pharmaceuticals ISIS-322308 Software and algorithms RNAseqChef RNAseqChef https://imeg-ku.shinyapps.io/ RNAseqChef/ Scaffold DIA v3.0.1 Proteome Software https://www.proteomesoftware.com/ products/scaffold-dia DIA-NN v1.8.1 GitHub https://github.com/vdemichev/DiaNN/ releases/tag/1.8.1 GraphPad Prism 10.0 GraphPad Software https://www.graphpad.com/scientific- software/prism/ Fiji ImageJ Fiji https://imagej.net/software/fiji/ Other Regular Chow Diet Envigo Cat #: 2018S L-Amino Acid Diet With 60 kcal% Fat With 0.1% Methionine and No Added Choline Research Diets Cat #: A06071302 (Continued on next page) 12 Cell Reports 45, 117369, June 23, 2026 ..

    RNA Sequencing:

    Article Title: CIDEB and CGI-58 differentially regulate liver lipid-droplet cholesterol to modulate metabolic dysfunction-associated steatohepatitis severity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CD68 Boster Biological Technology Cat #: BA3638; RRID: AB_2813855 Chemicals, peptides, and recombinant proteins Bempedoic Acid Cayman Cat #: 26409 BODIPY 493/503 Invitrogen Cat #: D3922 Filipin III from Streptomyces filipinensis Sigma Cat #: F4767 Critical commercial assays Total Cholesterol Assay Kits Cell Biolabs Cat #: STA-384 Triglycerides-SL Sekisui Diagnostics Part #: 239-99 RNeasy Mini Kit Qiagen Cat #: 74104 Deposited data Proteomics ProteomeXchange PXD075672 Raw RNA-seq data DDBJ PRJDB40719; DRR932858–DRR932893 RNA-seq raw count data DDBJ E-GEAD-1232 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory Strain #: 000664 Oligonucleotides GalNAc cEt control ASO: CGCCGATAAGGTACAC Ionis Pharmaceuticals ISIS-1287694 GalNAc cEt Cd36 ASO: TCAGTAAATCAGAACC Ionis Pharmaceuticals ISIS-1073763 GalNAc MOE Atgl ASO: AGGACAACTTGGAGCTTGGC Ionis Pharmaceuticals ISIS- 1843565 GalNAc MOE Soat2 ASO: TCATCATATCGAGACAGATG Ionis Pharmaceuticals ISIS- 1895903 MOE control ASO: CCTTCCCTGAAGGTTCCTCC Ionis Pharmaceuticals ISIS-141923 MOE CGI-58 ASO: TAGGTACACTGGCATATGGA Ionis Pharmaceuticals ISIS-421294 MOE Cideb ASO: ACCTAGATGAAGCAGCGATT Ionis Pharmaceuticals ISIS-455087 MOE Gpam ASO: AGAGCTTTAGTAACACCCAG Ionis Pharmaceuticals ISIS-322308 Software and algorithms RNAseqChef RNAseqChef https://imeg-ku.shinyapps.io/ RNAseqChef/ Scaffold DIA v3.0.1 Proteome Software https://www.proteomesoftware.com/ products/scaffold-dia DIA-NN v1.8.1 GitHub https://github.com/vdemichev/DiaNN/ releases/tag/1.8.1 GraphPad Prism 10.0 GraphPad Software https://www.graphpad.com/scientific- software/prism/ Fiji ImageJ Fiji https://imagej.net/software/fiji/ Other Regular Chow Diet Envigo Cat #: 2018S L-Amino Acid Diet With 60 kcal% Fat With 0.1% Methionine and No Added Choline Research Diets Cat #: A06071302 (Continued on next page) 12 Cell Reports 45, 117369, June 23, 2026 ..

    Allele-specific Oligonucleotide:

    Article Title: CIDEB and CGI-58 differentially regulate liver lipid-droplet cholesterol to modulate metabolic dysfunction-associated steatohepatitis severity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CD68 Boster Biological Technology Cat #: BA3638; RRID: AB_2813855 Chemicals, peptides, and recombinant proteins Bempedoic Acid Cayman Cat #: 26409 BODIPY 493/503 Invitrogen Cat #: D3922 Filipin III from Streptomyces filipinensis Sigma Cat #: F4767 Critical commercial assays Total Cholesterol Assay Kits Cell Biolabs Cat #: STA-384 Triglycerides-SL Sekisui Diagnostics Part #: 239-99 RNeasy Mini Kit Qiagen Cat #: 74104 Deposited data Proteomics ProteomeXchange PXD075672 Raw RNA-seq data DDBJ PRJDB40719; DRR932858–DRR932893 RNA-seq raw count data DDBJ E-GEAD-1232 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory Strain #: 000664 Oligonucleotides GalNAc cEt control ASO: CGCCGATAAGGTACAC Ionis Pharmaceuticals ISIS-1287694 GalNAc cEt Cd36 ASO: TCAGTAAATCAGAACC Ionis Pharmaceuticals ISIS-1073763 GalNAc MOE Atgl ASO: AGGACAACTTGGAGCTTGGC Ionis Pharmaceuticals ISIS- 1843565 GalNAc MOE Soat2 ASO: TCATCATATCGAGACAGATG Ionis Pharmaceuticals ISIS- 1895903 MOE control ASO: CCTTCCCTGAAGGTTCCTCC Ionis Pharmaceuticals ISIS-141923 MOE CGI-58 ASO: TAGGTACACTGGCATATGGA Ionis Pharmaceuticals ISIS-421294 MOE Cideb ASO: ACCTAGATGAAGCAGCGATT Ionis Pharmaceuticals ISIS-455087 MOE Gpam ASO: AGAGCTTTAGTAACACCCAG Ionis Pharmaceuticals ISIS-322308 Software and algorithms RNAseqChef RNAseqChef https://imeg-ku.shinyapps.io/ RNAseqChef/ Scaffold DIA v3.0.1 Proteome Software https://www.proteomesoftware.com/ products/scaffold-dia DIA-NN v1.8.1 GitHub https://github.com/vdemichev/DiaNN/ releases/tag/1.8.1 GraphPad Prism 10.0 GraphPad Software https://www.graphpad.com/scientific- software/prism/ Fiji ImageJ Fiji https://imagej.net/software/fiji/ Other Regular Chow Diet Envigo Cat #: 2018S L-Amino Acid Diet With 60 kcal% Fat With 0.1% Methionine and No Added Choline Research Diets Cat #: A06071302 (Continued on next page) 12 Cell Reports 45, 117369, June 23, 2026 ..

    Software:

    Article Title: CIDEB and CGI-58 differentially regulate liver lipid-droplet cholesterol to modulate metabolic dysfunction-associated steatohepatitis severity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CD68 Boster Biological Technology Cat #: BA3638; RRID: AB_2813855 Chemicals, peptides, and recombinant proteins Bempedoic Acid Cayman Cat #: 26409 BODIPY 493/503 Invitrogen Cat #: D3922 Filipin III from Streptomyces filipinensis Sigma Cat #: F4767 Critical commercial assays Total Cholesterol Assay Kits Cell Biolabs Cat #: STA-384 Triglycerides-SL Sekisui Diagnostics Part #: 239-99 RNeasy Mini Kit Qiagen Cat #: 74104 Deposited data Proteomics ProteomeXchange PXD075672 Raw RNA-seq data DDBJ PRJDB40719; DRR932858–DRR932893 RNA-seq raw count data DDBJ E-GEAD-1232 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory Strain #: 000664 Oligonucleotides GalNAc cEt control ASO: CGCCGATAAGGTACAC Ionis Pharmaceuticals ISIS-1287694 GalNAc cEt Cd36 ASO: TCAGTAAATCAGAACC Ionis Pharmaceuticals ISIS-1073763 GalNAc MOE Atgl ASO: AGGACAACTTGGAGCTTGGC Ionis Pharmaceuticals ISIS- 1843565 GalNAc MOE Soat2 ASO: TCATCATATCGAGACAGATG Ionis Pharmaceuticals ISIS- 1895903 MOE control ASO: CCTTCCCTGAAGGTTCCTCC Ionis Pharmaceuticals ISIS-141923 MOE CGI-58 ASO: TAGGTACACTGGCATATGGA Ionis Pharmaceuticals ISIS-421294 MOE Cideb ASO: ACCTAGATGAAGCAGCGATT Ionis Pharmaceuticals ISIS-455087 MOE Gpam ASO: AGAGCTTTAGTAACACCCAG Ionis Pharmaceuticals ISIS-322308 Software and algorithms RNAseqChef RNAseqChef https://imeg-ku.shinyapps.io/ RNAseqChef/ Scaffold DIA v3.0.1 Proteome Software https://www.proteomesoftware.com/ products/scaffold-dia DIA-NN v1.8.1 GitHub https://github.com/vdemichev/DiaNN/ releases/tag/1.8.1 GraphPad Prism 10.0 GraphPad Software https://www.graphpad.com/scientific- software/prism/ Fiji ImageJ Fiji https://imagej.net/software/fiji/ Other Regular Chow Diet Envigo Cat #: 2018S L-Amino Acid Diet With 60 kcal% Fat With 0.1% Methionine and No Added Choline Research Diets Cat #: A06071302 (Continued on next page) 12 Cell Reports 45, 117369, June 23, 2026 ..

    Fat:

    Article Title: CIDEB and CGI-58 differentially regulate liver lipid-droplet cholesterol to modulate metabolic dysfunction-associated steatohepatitis severity.
    Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Antibodies Anti-CD68 Boster Biological Technology Cat #: BA3638; RRID: AB_2813855 Chemicals, peptides, and recombinant proteins Bempedoic Acid Cayman Cat #: 26409 BODIPY 493/503 Invitrogen Cat #: D3922 Filipin III from Streptomyces filipinensis Sigma Cat #: F4767 Critical commercial assays Total Cholesterol Assay Kits Cell Biolabs Cat #: STA-384 Triglycerides-SL Sekisui Diagnostics Part #: 239-99 RNeasy Mini Kit Qiagen Cat #: 74104 Deposited data Proteomics ProteomeXchange PXD075672 Raw RNA-seq data DDBJ PRJDB40719; DRR932858–DRR932893 RNA-seq raw count data DDBJ E-GEAD-1232 Experimental models: Organisms/strains C57BL/6J The Jackson Laboratory Strain #: 000664 Oligonucleotides GalNAc cEt control ASO: CGCCGATAAGGTACAC Ionis Pharmaceuticals ISIS-1287694 GalNAc cEt Cd36 ASO: TCAGTAAATCAGAACC Ionis Pharmaceuticals ISIS-1073763 GalNAc MOE Atgl ASO: AGGACAACTTGGAGCTTGGC Ionis Pharmaceuticals ISIS- 1843565 GalNAc MOE Soat2 ASO: TCATCATATCGAGACAGATG Ionis Pharmaceuticals ISIS- 1895903 MOE control ASO: CCTTCCCTGAAGGTTCCTCC Ionis Pharmaceuticals ISIS-141923 MOE CGI-58 ASO: TAGGTACACTGGCATATGGA Ionis Pharmaceuticals ISIS-421294 MOE Cideb ASO: ACCTAGATGAAGCAGCGATT Ionis Pharmaceuticals ISIS-455087 MOE Gpam ASO: AGAGCTTTAGTAACACCCAG Ionis Pharmaceuticals ISIS-322308 Software and algorithms RNAseqChef RNAseqChef https://imeg-ku.shinyapps.io/ RNAseqChef/ Scaffold DIA v3.0.1 Proteome Software https://www.proteomesoftware.com/ products/scaffold-dia DIA-NN v1.8.1 GitHub https://github.com/vdemichev/DiaNN/ releases/tag/1.8.1 GraphPad Prism 10.0 GraphPad Software https://www.graphpad.com/scientific- software/prism/ Fiji ImageJ Fiji https://imagej.net/software/fiji/ Other Regular Chow Diet Envigo Cat #: 2018S L-Amino Acid Diet With 60 kcal% Fat With 0.1% Methionine and No Added Choline Research Diets Cat #: A06071302 (Continued on next page) 12 Cell Reports 45, 117369, June 23, 2026 ..



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