other:
Software:
Article Title: Lysosomal multi-omics reveals altered sphingolipid catabolism associated with lysosomal dysfunction in the aging brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Camk2a-cre mice (B6.Cg-Tg(Camk2a-cre) T29-1Stl/J) Jackson Laboratories 005359 Cx3cr1-creERT2 mice (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) Jackson Laboratories 025524 Software and algorithms ANY-maze software Stoelting Co N/A Prism (v 10–11) GraphPad N/A Elements software (v 5.30.06) Nikon N/A Zen (v 3.9) Zeiss Microimaging N/A Imaris Bitplane software (v 10.2) Oxford Instruments N/A Imspector software Abberior N/A ImageJ/Fiji (v 2.18) Schindellin et al. https://imagej.net/software/fiji/ FCS Express (v 7) De Novo Software N/A org.Mm.e.g.,.db (v 3.18.0) Bioconductor https://bioconductor.org/packages/release/ data/annotation/html/org.Mm.eg.db.html org.Hs.e.g.,.db (v 3.18.0) Bioconductor https://bioconductor.org/packages/release/ data/annotation/html/org.Hs.eg.db.html MOFA2 (v 1.13.0) Bioconductor https://bioconductor.org/packages/release/ bioc/html/MOFA2.html R (v 4.3.1) R Core Team RRID: SCR_001905; https://www.r-project.org/ Custom analysis code for batch correction and feature selection This paper GitHub: https://github.com/cheny36/brain_lyso_ aging_multiomics_code; Zenodo: 10.5281/ zenodo.21251325 randomForest (v 4.7.1.2) CRAN https://cran.r-project.org/package=randomForest DOSE (v 3.30.2) Bioconductor https://github.com/YuLab-SMU/DOSE/tree/ cc64179bccee169a3e102d28036f56e83b490f09 clusterProfiler (v 4.12.6) Bioconductor https://github.com/YuLab-SMU/clusterProfiler/ tree/394892e4ff69fb14fc0d451adfca028fb72a69c3 LION/web (Lipid Ontology enrichment analysis) Molenaar et al. RRID: SCR_017018; http://www.lipidontology.com David Bioinformatics (v 6.0–6.8) NIH https://davidbioinformatics.nih.gov/workspace. .. html?tool=summary_ws Lipid Annotator (v 1.0) Agilent Technologies N/A MassHunter Profinder (v 10.0) Agilent Technologies N/A MetaboAnalyst (v 5.0–6.0) MetaboAnalyst https://www.metaboanalyst.ca/ Proteome Discoverer (v 2.5.0.400) Thermo Fisher N/A Perseus software (v 1.6.14.0) Max Planck Institute https://maxquant.net/perseus/ PRIDE Submission Tool (v 2.11.3–2.11.4) PRIDE website https://www.ebi.ac.uk/pride/ DIA-NN (v 2.2.0) Github https://github.com/vdemichev/DiaNN/releases 24 Cell Reports 45, 118065, October 27, 2026 computational methods for batch correction (described below).
Article Title: Hypothalamic-amygdala gating of caregiving-like prosocial behavior in mice
Article Snippet: .. After confining a naive and a melittin-treated cagemate demonstrators into separate wire cylinders (20 cm high × 8 cm diameter; vertical bars, 0.5 cm apart) in each ending chamber (25 cm × 25 cm × 30 cm), each observer mouse was replaced into the middle (neutral) chamber (13 cm × 25 cm × 30 cm) and subsequent 30-min triadic social interaction was digitally recorded and analyzed by ANYMAZE 10 software (Stoelting). ..
Mouse Assay:
Analysis:Article Title: Lysosomal multi-omics reveals altered sphingolipid catabolism associated with lysosomal dysfunction in the aging brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Camk2a-cre mice (B6.Cg-Tg(Camk2a-cre) T29-1Stl/J) Jackson Laboratories 005359 Cx3cr1-creERT2 mice (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) Jackson Laboratories 025524 Software and algorithms ANY-maze software Stoelting Co N/A Prism (v 10–11) GraphPad N/A Elements software (v 5.30.06) Nikon N/A Zen (v 3.9) Zeiss Microimaging N/A Imaris Bitplane software (v 10.2) Oxford Instruments N/A Imspector software Abberior N/A ImageJ/Fiji (v 2.18) Schindellin et al. https://imagej.net/software/fiji/ FCS Express (v 7) De Novo Software N/A org.Mm.e.g.,.db (v 3.18.0) Bioconductor https://bioconductor.org/packages/release/ data/annotation/html/org.Mm.eg.db.html org.Hs.e.g.,.db (v 3.18.0) Bioconductor https://bioconductor.org/packages/release/ data/annotation/html/org.Hs.eg.db.html MOFA2 (v 1.13.0) Bioconductor https://bioconductor.org/packages/release/ bioc/html/MOFA2.html R (v 4.3.1) R Core Team RRID: SCR_001905; https://www.r-project.org/ Custom analysis code for batch correction and feature selection This paper GitHub: https://github.com/cheny36/brain_lyso_ aging_multiomics_code; Zenodo: 10.5281/ zenodo.21251325 randomForest (v 4.7.1.2) CRAN https://cran.r-project.org/package=randomForest DOSE (v 3.30.2) Bioconductor https://github.com/YuLab-SMU/DOSE/tree/ cc64179bccee169a3e102d28036f56e83b490f09 clusterProfiler (v 4.12.6) Bioconductor https://github.com/YuLab-SMU/clusterProfiler/ tree/394892e4ff69fb14fc0d451adfca028fb72a69c3 LION/web (Lipid Ontology enrichment analysis) Molenaar et al. RRID: SCR_017018; http://www.lipidontology.com David Bioinformatics (v 6.0–6.8) NIH https://davidbioinformatics.nih.gov/workspace. .. html?tool=summary_ws Lipid Annotator (v 1.0) Agilent Technologies N/A MassHunter Profinder (v 10.0) Agilent Technologies N/A MetaboAnalyst (v 5.0–6.0) MetaboAnalyst https://www.metaboanalyst.ca/ Proteome Discoverer (v 2.5.0.400) Thermo Fisher N/A Perseus software (v 1.6.14.0) Max Planck Institute https://maxquant.net/perseus/ PRIDE Submission Tool (v 2.11.3–2.11.4) PRIDE website https://www.ebi.ac.uk/pride/ DIA-NN (v 2.2.0) Github https://github.com/vdemichev/DiaNN/releases 24 Cell Reports 45, 118065, October 27, 2026 computational methods for batch correction (described below).
Selection:Article Title: Lysosomal multi-omics reveals altered sphingolipid catabolism associated with lysosomal dysfunction in the aging brain.
Article Snippet: .. REAGENT or RESOURCE SOURCE IDENTIFIER Camk2a-cre mice (B6.Cg-Tg(Camk2a-cre) T29-1Stl/J) Jackson Laboratories 005359 Cx3cr1-creERT2 mice (B6J.B6N(Cg)Cx3cr1tm1.1(cre)Jung/J) Jackson Laboratories 025524 Software and algorithms ANY-maze software Stoelting Co N/A Prism (v 10–11) GraphPad N/A Elements software (v 5.30.06) Nikon N/A Zen (v 3.9) Zeiss Microimaging N/A Imaris Bitplane software (v 10.2) Oxford Instruments N/A Imspector software Abberior N/A ImageJ/Fiji (v 2.18) Schindellin et al. https://imagej.net/software/fiji/ FCS Express (v 7) De Novo Software N/A org.Mm.e.g.,.db (v 3.18.0) Bioconductor https://bioconductor.org/packages/release/ data/annotation/html/org.Mm.eg.db.html org.Hs.e.g.,.db (v 3.18.0) Bioconductor https://bioconductor.org/packages/release/ data/annotation/html/org.Hs.eg.db.html MOFA2 (v 1.13.0) Bioconductor https://bioconductor.org/packages/release/ bioc/html/MOFA2.html R (v 4.3.1) R Core Team RRID: SCR_001905; https://www.r-project.org/ Custom analysis code for batch correction and feature selection This paper GitHub: https://github.com/cheny36/brain_lyso_ aging_multiomics_code; Zenodo: 10.5281/ zenodo.21251325 randomForest (v 4.7.1.2) CRAN https://cran.r-project.org/package=randomForest DOSE (v 3.30.2) Bioconductor https://github.com/YuLab-SMU/DOSE/tree/ cc64179bccee169a3e102d28036f56e83b490f09 clusterProfiler (v 4.12.6) Bioconductor https://github.com/YuLab-SMU/clusterProfiler/ tree/394892e4ff69fb14fc0d451adfca028fb72a69c3 LION/web (Lipid Ontology enrichment analysis) Molenaar et al. RRID: SCR_017018; http://www.lipidontology.com David Bioinformatics (v 6.0–6.8) NIH https://davidbioinformatics.nih.gov/workspace. .. html?tool=summary_ws Lipid Annotator (v 1.0) Agilent Technologies N/A MassHunter Profinder (v 10.0) Agilent Technologies N/A MetaboAnalyst (v 5.0–6.0) MetaboAnalyst https://www.metaboanalyst.ca/ Proteome Discoverer (v 2.5.0.400) Thermo Fisher N/A Perseus software (v 1.6.14.0) Max Planck Institute https://maxquant.net/perseus/ PRIDE Submission Tool (v 2.11.3–2.11.4) PRIDE website https://www.ebi.ac.uk/pride/ DIA-NN (v 2.2.0) Github https://github.com/vdemichev/DiaNN/releases 24 Cell Reports 45, 118065, October 27, 2026 computational methods for batch correction (described below).
Imaging:
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