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Method: A transcriptome-based single-cell biological age model and resource for tissue-specific aging measures
- Shulin Mao,
- Jiayu Su,
- Longteng Wang,
- Xiaochen Bo,
- Cheng Li,
- and Hebing Chen
Genome Res. August 2023 33: 1381-1394; Published in Advance July 31, 2023, doi:10.1101/gr.277491.122
...literature. By encouraging the inclusion of well-recognized and experimentally confirmed aging genes (Fig. 3B), SCALE is more explainable and robust to spurious correlation and technical variability, as shown in the external validation in aging-related diseases and rejuvenating interventions data (Fig. 4...
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Research: Genome-wide transcript and protein analysis highlights the role of protein homeostasis in the aging mouse heart
- Isabela Gerdes Gyuricza,
- Joel M. Chick,
- Gregory R. Keele,
- Andrew G. Deighan,
- Steven C. Munger,
- Ron Korstanje,
- Steven P. Gygi,
- and Gary A. Churchill
Genome Res. May 2022 32: 838-852; Published in Advance March 11, 2022, doi:10.1101/gr.275672.121
...malleable and could contribute to individual variability in heart aging.DiscussionIn this study, we examine the changes that occur with aging in the transcriptome and proteome of heart tissue from 185 genetically diverse mice. Most mice in this study are still healthy at 18 mo of age, and thus the age-related...
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Research: Single-cell RNA-seq reveals changes in cell cycle and differentiation programs upon aging of hematopoietic stem cells
- Monika S. Kowalczyk,
- Itay Tirosh,
- Dirk Heckl,
- Tata Nageswara Rao,
- Atray Dixit,
- Brian J. Haas,
- Rebekka K. Schneider,
- Amy J. Wagers,
- Benjamin L. Ebert,
- and Aviv Regev
Genome Res. December 2015 25: 1860-1872; Published in Advance October 1, 2015, doi:10.1101/gr.192237.115
...to a joint PCA for all cells and ages in Fig. 3) showed that aging dominates the cell-to-cell variability within both of these cell types, and we could not find additional major independent sources of variability, such as additional subsets of cells. This suggests that most variations discernible within LT...
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Research: Genome-wide gene expression regulation as a function of genotype and age in C. elegans
- Ana Viñuela,
- L. Basten Snoek,
- Joost A.G. Riksen,
- and Jan E. Kammenga
Genome Res. July 2010 20: 929-937; Published in Advance May 20, 2010, doi:10.1101/gr.102160.109
...that variation in -wide gene expression increases in aging worms. This agrees with findings by Bahar et al. (2006), who reported increased cell-to-cell variation in gene expression in agingmouse heart. Somel et al. (2006) used a number of microarray gene expression tissue data sets from humans and rats and found...
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Research: Suv39h-catalyzed H3K9me3 is critical for euchromatic genome organization and the maintenance of gene transcription
- Christine R. Keenan,
- Hannah D. Coughlan,
- Nadia Iannarella,
- Andres Tapia del Fierro,
- Andrew Keniry,
- Timothy M. Johanson,
- Wing Fuk Chan,
- Alexandra L. Garnham,
- Lachlan W. Whitehead,
- Marnie E. Blewitt,
- Gordon K. Smyth,
- and Rhys S. Allan
Genome Res. April 2024 34: 556-571; Published in Advance May 6, 2024, doi:10.1101/gr.279119.124
.... (B) Barcode enrichment plot showing ranking of aging-related genes from the GenAge database (de Magalhaes et al. 2009) among the DE genes. Genes are ranked right to left from most up-regulated to most down-regulated in DKO cells. The rank of genes associated with increased lifespan is marked by red...
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Resource: Murine single-cell RNA-seq reveals cell-identity- and tissue-specific trajectories of aging
- Jacob C. Kimmel,
- Lolita Penland,
- Nimrod D. Rubinstein,
- David G. Hendrickson,
- David R. Kelley,
- and Adam Z. Rosenthal
Genome Res. December 2019 29: 2088-2103; Published in Advance November 21, 2019, doi:10.1101/gr.253880.119
...an integrated read-out, allowing us to estimate the magnitude of age-related transcriptional change across cell identities. Using this approach, cell identities showed multifold differences in aging magnitude, and cell identity again explained the majority of variation. Our results are conceptually consistent...
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