Optimized upstream analytical workflow for single-nucleus transcriptomics in main metabolic tissues

References

[1] Silvestri C , Di Marzo V . The endocannabinoid system in energy homeostasis and the etiopathology of metabolic disorders. Cell Metab 2013; 17: 475- 90.

[2] Palmer JA , Rosenthal N , Teichmann SA et al. Revisiting cardiac biology in the era of single cell and spatial omics. Circ Res 2024; 134: 1681- 702.

[3] De Donno C , Hediyeh-Zadeh S , Moinfar AA et al. Population-level integration of single-cell datasets enables multi-scale analysis across samples. Nat Methods 2023; 20: 1683- 92.

[4] Emont MP , Jacobs C , Essene AL et al. A single-cell atlas of human and mouse white adipose tissue. Nature 2022; 603: 926- 33.

[5] Xie L , Hu W , Zhang H et al. Single-nucleus RNA sequencing reveals heterogeneity among multiple white adipose tissue depots. Life Metab. 2023; 2: load045.

[6] Massier L , Jalkanen J , Elmastas M et al. An integrated single cell and spatial transcriptomic map of human white adipose tissue. Nat Commun 2023; 14: 1438.

[7] Scripture-Adams DD , Chesmore KN , Barthélémy F et al. Single nuclei transcriptomics of muscle reveals intra-muscular cell dynamics linked to dystrophin loss and rescue. Commun Biol 2022; 5: 989.

[8] Ramachandran P , Dobie R , Wilson-Kanamori J et al. Resolving the fibrotic niche of human liver cirrhosis at single-cell level. Nature 2019; 575: 512- 8.

[9] Hafemeister C , Satija R . Normalization and variance stabilization of single-cell RNA-seq data using regularized negative binomial regression. Genome Biol 2019; 20: 296.

[10] Heumos L , Schaar AC , Lance C et al. Best practices for single-cell analysis across modalities. Nat Rev Genet 2023; 24: 550- 72.

[11] Fleming SJ , Chaffin MD , Arduini A et al. Unsupervised removal of systematic background noise from droplet-based single-cell experiments using CellBender. Nat Methods 2023; 20: 1323- 35.

[12] Xi NM , Li JJ . Protocol for executing and benchmarking eight computational doublet-detection methods in single-cell RNA sequencing data analysis. STAR Protoc 2021; 2: 100699.

[13] Luecken MD , Büttner M , Chaichoompu K et al. Benchmarking atlas-level data integration in single-cell genomics. Nat Methods 2022; 19: 41- 50.

[14] Yang S , Corbett SE , Koga Y et al. Decontamination of ambient RNA in single-cell RNA-seq with DecontX. Genome Biol 2020; 21: 57.

[15] Young MD , Behjati S . SoupX removes ambient RNA contamination from droplet-based single-cell RNA sequencing data. GigaScience 2020; 9: giaa151.

[16] Aran D , Looney AP , Liu L et al. Reference-based analysis of lung single-cell sequencing reveals a transitional profibrotic macrophage. Nat Immunol 2019; 20: 163- 72.

[17] Hao Y , Hao S , Andersen-Nissen E et al. Integrated analysis of multimodal single-cell data. Cell 2021; 184: 3573- 87.e29.

[18] Huang Y , Wang A , Zhou W et al. Maternal dietary fat during lactation shapes single nucleus transcriptomic profile of postnatal offspring hypothalamus in a sexually dimorphic manner in mice. Nat Commun 2024; 15: 2382.

[19] Steuernagel L , Lam BY , Klemm P et al. HypoMap—a unified single-cell gene expression atlas of the murine hypothalamus. Nat Metab 2022; 4: 1402- 19.

RIGHTS & PERMISSIONS

The Author(s). Published by Oxford University Press on behalf of Higher Education Press.