Searching journal content for articles similar to Kowalczyk et al. 25 (12): 1860.

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  1. Resource: Common and specific gene regulatory programs in zebrafish caudal fin regeneration at single-cell resolution
    • Yujie Chen,
    • Yiran Hou,
    • Qinglin Zeng,
    • Irene Wang,
    • Meiru Shang,
    • Kwangdeok Shin,
    • Christopher Hemauer,
    • Xiaoyun Xing,
    • Junsu Kang,
    • Guoyan Zhao,
    • and Ting Wang
    Genome Res. January 2025 35: 202-218; Published in Advance January 14, 2025, doi:10.1101/gr.279372.124
    ...of transcriptome and chromatin accessibility at the single-cell level, thus allowing for an in-depth exploration of the cellular dynamics of tissue regeneration.Several studies have utilized single-cell/nucleus RNA sequencing (sc/snRNA-seq) to elucidate cell-type contributions, identify cell...
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  2. Method: A unified analysis of atlas single-cell data
    • Hao Chen,
    • Nam D. Nguyen,
    • Matthew Ruffalo,
    • and Ziv Bar-Joseph
    Genome Res. May 2025 35: 1219-1233; Published in Advance February 18, 2025, doi:10.1101/gr.279631.124
    ...intestine, spleen, and thymus, and three different data modalities, which include single-cell RNA-seq (scRNA-seq), single-cell ATAC-seq (scATAC-seq), and spatial transcriptomics (Slide-seq). Figure 1, A through C, presents an overview of GIANT. We first construct gene graphs for cell clusters from each...
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  3. Method: Single-cell Rapid Capture Hybridization sequencing reliably detects isoform usage and coding mutations in targeted genes
    • Hongke Peng,
    • Jafar S. Jabbari,
    • Luyi Tian,
    • Changqing Wang,
    • Yupei You,
    • Chong Chyn Chua,
    • Natasha S. Anstee,
    • Noorul Amin,
    • Andrew H. Wei,
    • Nadia M. Davidson,
    • Andrew W. Roberts,
    • David C.S. Huang,
    • Matthew E. Ritchie,
    • and Rachel Thijssen
    Genome Res. April 2025 35: 942-955; Published in Advance January 10, 2025, doi:10.1101/gr.279322.124
    ...-read single-cell RNA sequencing (scRNA-seq) data reveals significant gene expression differences in SF3B1-mutated CLL cells, although it does not impact the sensitivity of the anticancer drug venetoclax. scRaCH-seq's capability to study long-read transcripts of multiple genes makes it a powerful tool...
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  4. Research: Single-cell analysis reveals transcriptional dynamics in healthy primary parathyroid tissue
    • Aarthi Venkat,
    • Maximillian J. Carlino,
    • Betty R. Lawton,
    • Manju L. Prasad,
    • Matthew Amodio,
    • Courtney E. Gibson,
    • Caroline J. Zeiss,
    • Scott E. Youlten,
    • Smita Krishnaswamy,
    • and Diane S. Krause
    Genome Res. June 2024 34: 837-850; Published in Advance July 8, 2024, doi:10.1101/gr.278215.123
    ...the glands (Chai et al. 2019; Hu et al. 2021; Mao et al. 2022). To provide cell type–resolved transcriptomic data on PTs, we conducted single-cell RNA sequencing (scRNA-seq) of normal PT glands from adult non-human primates (NHPs) and from hyperfunctioning human PT tissue. By examining the transcriptome...
  5. Research: Long-read single-cell RNA sequencing enables the study of cancer subclone-specific genotypes and phenotypes in chronic lymphocytic leukemia
    • Gage S. Black,
    • Xiaomeng Huang,
    • Yi Qiao,
    • Philip Moos,
    • Deepa Sampath,
    • Deborah M. Stephens,
    • Jennifer A. Woyach,
    • and Gabor T. Marth
    Genome Res. April 2025 35: 686-697; Published in Advance February 18, 2025, doi:10.1101/gr.279049.124
    ...-mutated subclones exhibit distinct transcriptomic behavior when compared to other cancer subclones. To achieve these goals, we use scBayes, which integrates bulk DNA sequencing and single-cell RNA sequencing (scRNA-seq) data to genotype individual cells for subclone-defining mutations. Although the most common...
  6. 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
    ...and environments on the trajectory of aging in individual cells remains unclear. Here, we performed single-cell RNA-seq on >50,000 individual cells across three tissues in young and old mice to allow for direct comparison of aging phenotypes across cell types. We found transcriptional features of aging common...
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  7. 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
    ...environments.DiscussionHere we show that tissue-specific aging programs can be learned from scRNA-seq data and applied to describe aging heterogeneity within single-cell populations. From the Aging Map, a curated database of aging-associated genes, we extended our search for transcriptomic features that could...
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  8. Research: Polycomb misregulation in enterocytes drives tissue decline in the aging Drosophila intestine
    • Sarah M. Leichter,
    • Kami Ahmad,
    • and Steven Henikoff
    Genome Res. January 2026 36: 102-114; Published in Advance November 17, 2025, doi:10.1101/gr.281058.125
    ...to directly profile changes at regulatory elements, which single-cell RNA sequencing (scRNA-seq) does not capture. To identify regulatory elements that exhibit changes in H3K27me3 level with age within each cell type, we identified self-transcribing active regulatory region sequencing (STARR-seq) enhancers...
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  9. Method: Characterizing and inferring quantitative cell cycle phase in single-cell RNA-seq data analysis
    • Chiaowen Joyce Hsiao,
    • PoYuan Tung,
    • John D. Blischak,
    • Jonathan E. Burnett,
    • Kenneth A. Barr,
    • Kushal K. Dey,
    • Matthew Stephens,
    • and Yoav Gilad
    Genome Res. April 2020 30: 611-621; Published in Advance April 20, 2020, doi:10.1101/gr.247759.118
    ..., even in otherwise homogeneous cell populations. Recent advances in single-cell RNA-sequencing (scRNA-seq) facilitate detailed characterization of gene expression heterogeneity and can thus shed new light on the processes driving heterogeneity. Here, we combined fluorescence imaging with scRNA-seq...
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  10. Method: Matching queried single-cell open-chromatin profiles to large pools of single-cell transcriptomes and epigenomes for reference supported analysis
    • Shreya Mishra,
    • Neetesh Pandey,
    • Smriti Chawla,
    • Madhu Sharma,
    • Omkar Chandra,
    • Indra Prakash Jha,
    • Debarka SenGupta,
    • Kedar Nath Natarajan,
    • and Vibhor Kumar
    Genome Res. February 2023 33: 218-231; Published in Advance January 18, 2023, doi:10.1101/gr.277015.122
    ...with mixed-phenotype acute leukaemia (MPAL) (Granja et al. 2019). An initial analysis of MPAL cells and PBMCs from healthy patients in the same study revealed a change in the fraction of cell types. Such that for single-cell epis of PBMCs from healthy individuals, the matching scRNA-seq profiles were from...
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