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Method: High-resolution spatial transcriptomics in fixed tissue using a cost-effective PCL-seq workflow
- Xue Dong,
- Mengzhu Hu,
- Xiaonan Cui,
- Wenjian Zhou,
- Jingtao Cai,
- Guangyao Mao,
- and Weiyang Shi
Genome Res. September 2025 35: 2052-2063; Published in Advance August 5, 2025, doi:10.1101/gr.279906.124
..., detecting approximately 170,000 unique molecular identifiers (UMIs) and 8600 genes (illumination diameter = 100 µm). Moreover, PCL-seq is compatible with formalin-fixed paraffin-embedded (FFPE) tissues, successfully identifying thousands of differentially enriched transcripts in the digits and vertebrae...
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Method: Profiling chromatin accessibility in formalin-fixed paraffin-embedded samples
- Hua Zhang,
- Vamsi Krishna Polavarapu,
- Pengwei Xing,
- Miao Zhao,
- Lucy Mathot,
- Linxuan Zhao,
- Gabriela Rosen,
- Fredrik J. Swartling,
- Tobias Sjöblom,
- and Xingqi Chen
Genome Res. January 2022 32: 150-161; Published in Advance July 14, 2021, doi:10.1101/gr.275269.121
...by sequencing (ATAC-seq) (Buenrostro et al. 2013) and DNase I hypersensitivity sequencing (DNase-seq) (Jin et al. 2015), allow profiling of chromatin accessibility in cells and frozen tissues. Archived formalin-fixed paraffin-embedded (FFPE) tissues are the global standard format for preservation...
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Method: High-resolution genotype-free mapping of genetic variation with CRI-SPA-Map
- Sheila Lutz,
- Megan Lawler,
- Samuel Amidon,
- and Frank W Albert
Genome Res. March 23, 2026 gr.281514.125; Published in Advance March 23, 2026, doi:10.1101/gr.281514.125
...High-resolution, genotype-free mapping of genetic 1 variation with CRI-SPA-Map 2 3 Sheila Lutz*, Megan Lawler†, Samuel Amidon†, Frank W. Albert* 4 Department of Genetics, Cell Biology, & Development, 5 University of Minnesota, 6 6-160 Jackson Hall, 321 Church St SE 7 Minneapolis, MN 55455, USA 8...
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Method: Early feature extraction drives model performance in high-resolution chromatin accessibility prediction
- Aayush Grover,
- Till Muser,
- Liine Kasak,
- Lin Zhang,
- Ekaterina Krymova,
- and Valentina Boeva
Genome Res. March 2026 36: 619-629; Published in Advance January 12, 2026, doi:10.1101/gr.281042.125
...by the Genome Data Commons (GDC) Data Portal (Grossman et al. 2016). The choice of these patients was made due to the availability of the data on their somatic mutations and single-nucleotide polymorphisms (SNPs) in the International Cancer Genome Consortium (ICGC) and GDC data portals, respectively (Grossman...
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Method: FFPEcap-seq: a method for sequencing capped RNAs in formalin-fixed paraffin-embedded samples
- Jeffery M. Vahrenkamp,
- Kathryn Szczotka,
- Mark K. Dodson,
- Elke A. Jarboe,
- Andrew P. Soisson,
- and Jason Gertz
Genome Res. November 2019 29: 1826-1835; Published in Advance October 24, 2019, doi:10.1101/gr.249656.119
..., University of Utah, Salt Lake City, Utah 84112, USA; 3Department of Pathology, Huntsman Cancer Institute, University of Utah, Salt Lake City, Utah 84112, USA Corresponding author: jay.gertz@hci.utah.eduAbstractThe majority of clinical cancer specimens are preserved as formalin-fixed paraffin-embedded (FFPE...
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Method: Parallel analysis of replication timing, gene expression, and copy number with PARTAGE
- Lakshana Sruthi Sadu Murari,
- Quinn Dickinson,
- Silvia Meyer-Nava,
- and Juan Carlos Rivera-Mulia
Genome Res. March 19, 2026 ; Published in Advance March 19, 2026, doi:10.1101/gr.281532.125
...of RT and transcriptomes from independent batches of samples, which obscures the complex coregulation between the epi and transcriptome. Here, we present PARTAGE, a multiomics approach that enables joint profiling of copy number variation (CNV), RT, and gene expression from the same sample, providing...
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Research: High resolution genomes of multiple Xiphophorus species provide new insights into microevolution, hybrid incompatibility, and epistasis
- Yuan Lu,
- Edward Rice,
- Kang Du,
- Susanne Kneitz,
- Magali Naville,
- Corentin Dechaud,
- Jean-Nicolas Volff,
- Mikki Boswell,
- William Boswell,
- LaDeana Hillier,
- Chad Tomlinson,
- Kremitzki Milin,
- Ronald B. Walter,
- Manfred Schartl,
- and Wesley C. Warren
Genome Res. April 2023 33: 557-571; Published in Advance May 5, 2023, doi:10.1101/gr.277434.122
...-colony bred X. hellerii. Per fish type, we investigated polymorphisms (SNP and short indels) and structural variations (SVs). Nucleotide diversity (π) estimates showed X. hellerii had the highest π (0.0078), followed in order by the wild-caught X. maculatus, the X. maculatus Jp163B inbred strain (6.11 × 10...
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Research: Long-read RNA sequencing of archival tissues reveals novel genes and transcripts associated with clear cell renal cell carcinoma recurrence and immune evasion
- Joshua Lee,
- Elizabeth A. Snell,
- Joanne Brown,
- Charlotte E. Booth,
- Rosamonde E. Banks,
- Daniel J. Turner,
- Naveen S. Vasudev,
- and Dimitris Lagos
Genome Res. November 2024 34: 1849-1864; Published in Advance September 16, 2024, doi:10.1101/gr.278801.123
...meaning all sequenced transcripts are polyadenylated. Some read-through events were observed but we did not analyze them systematically as we were mindful of the relatively low percentage of full-length reads in our analyses of archival tissue. Despite using total RNA as input for PCS and DRS library...
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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
..., the Polycomb landscape of differentiated cell types remains unexplored. Differentiated cells comprise the majority of the gut epithelium and directly impact both tissue and whole organismal aging. Using single-cell chromatin profiling of the Drosophila intestine, we identify cell type–specific chromatin...
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Method: Gene expression profiling of single cells from archival tissue with laser-capture microdissection and Smart-3SEQ
- Joseph W. Foley,
- Chunfang Zhu,
- Philippe Jolivet,
- Shirley X. Zhu,
- Peipei Lu,
- Michael J. Meaney,
- and Robert B. West
Genome Res. November 2019 29: 1816-1825; Published in Advance September 13, 2019, doi:10.1101/gr.234807.118
...and the hg38 reference sequence, masked for SNPs according to dbSNP version 150 (obtained from the UCSC Genome Browser) (Sherry et al. 2001), and the GENCODE version 27 gene annotations (Harrow et al. 2012) were provided as the reference transcriptome. Reads from the experiments with human tissue were...
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