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Corrigendum: Corrigendum: 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. January 2020 30: 153_1; doi:10.1101/gr.259820.119
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Method: Semisupervised adversarial neural networks for single-cell classification
- Jacob C. Kimmel and
- David R. Kelley
Genome Res. October 2021 31: 1781-1793; Published in Advance February 24, 2021, doi:10.1101/gr.268581.120
...methods where appropriate (Platt 1999). We performed quality-control filtering and preprocessing on each data set before training (Supplemental Methods).For the Rat Aging Cell Atlas (Ma et al. 2020) benchmark, we trained scNym models on single-cell RNA-seq from young, ad libitum fed rats (5 mo old...
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Research: Loss of epigenetic suppression of retrotransposons with oncogenic potential in aging mammary luminal epithelial cells
- Parijat Senapati,
- Masaru Miyano,
- Rosalyn W. Sayaman,
- Mudaser Basam,
- Amy Leung,
- Mark A. LaBarge,
- and Dustin E. Schones
Genome Res. August 2023 33: 1229-1241; Published in Advance July 18, 2023, doi:10.1101/gr.277511.122
...that is established in early development and maintained through successive cycles of cell division to preserve cell identity (Bird 2002). DNA methylation patterns, however, are known to change with age (Maegawa et al. 2010; Rakyan et al. 2010; Heyn et al. 2012; Horvath 2013). DNA methylation levels of specific Cp...
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Research: Cellular age explains variation in age-related cell-to-cell transcriptome variability
- Ming Yang,
- Benjamin R. Harrison,
- and Daniel E.L. Promislow
Genome Res. November 2023 33: 1906-1916; Published in Advance November 16, 2023, doi:10.1101/gr.278144.123
...why the transcriptome shows signs of aging in some cell types but not others. Through analysis of mouse single-cell transcriptome data across diverse tissues and ages, we find that cellular age explains a large proportion of the variation in the age-related increase in transcriptome variance. We...
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Resource: Zebrafish transposable elements show extensive diversification in age, genomic distribution, and developmental expression
- Ni-Chen Chang,
- Quirze Rovira,
- Jonathan Wells,
- Cédric Feschotte,
- and Juan M. Vaquerizas
Genome Res. July 2022 32: 1408-1423; Published in Advance January 5, 2022, doi:10.1101/gr.275655.121
..., including a pronounced activation of LTR retroelements shortly after ZGA, when early cell fate decisions are made.Single-cell RNA-seq resolves somatic TE expression during early embryogenesisOur analysis of whole-embryo RNA-seq data suggests that many zebrafish TE families display stage-specific expression...
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Perspective: Notable challenges posed by long-read sequencing for the study of transcriptional diversity and genome annotation
- Carolina Monzó,
- Adam Frankish,
- and Ana Conesa
Genome Res. April 2025 35: 583-592; Published in Advance March 3, 2025, doi:10.1101/gr.279865.124
...reveals cell-identity- and tissue-specific trajectories of aging. Genome Res 29: 2088–2103. doi:10.1101/gr.253880.119 ↵Kovaka S, Zimin AV, Pertea GM, Razaghi R, Salzberg SL, Pertea M. 2019. Transcriptome assembly from long-read RNA-seq alignments with StringTie2. Genome Biol 20: 278. doi:10.1186/s13059...
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