Searching journal content for articles similar to Subramanian et al. 1 (3): 187.

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  1. Method: Tn5 tagments and transposes oligos to single-stranded DNA for strand-specific RNA sequencing
    • Yanjun Zhang,
    • Yin Tang,
    • Zhongxing Sun,
    • Junqi Jia,
    • Yuan Fang,
    • Xinyi Wan,
    • and Dong Fang
    Genome Res. March 2023 33: 412-426; Published in Advance March 23, 2023, doi:10.1101/gr.277213.122
    ...McClintock, can “jump” from one location to another within a (McClintock 1950). The Tn5 transposons, which are found in Escherichia coli, consist of two inverted IS50 sequences. These sequences contain two pairs of 19-bp outside ends (OEs) and inside ends (IEs) (Berg et al. 1975; York and Reznikoff...
  2. 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
    ...in insufficient read coverage, thereby limiting our ability to perform mutation calling for specific genes. Here, we developed a single-cell Rapid Capture Hybridization sequencing (scRaCH-seq) method that demonstrates high specificity and efficiency in capturing targeted transcripts using long-read sequencing...
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  3. Method: Tissular chromatin-state cartography based on double-barcoded DNA arrays that capture unloaded PA-Tn5 transposase
    • Maria Grazia Mendoza-Ferri,
    • Gwendoline Lozachmeur,
    • Maximilien Duvina,
    • Laetitia Perret,
    • Didier Merciris,
    • Anne Gigout,
    • and Marco Antonio Mendoza-Parra
    Genome Res. July 2025 35: 1633-1645; Published in Advance May 13, 2025, doi:10.1101/gr.280305.124
    ...(G) primer presenting a known adapter sequence at its 5′-extremity (Adpt1), followed by Klenow polymerase extension (Fig. 1E). Finally, DNA arrays are exposed again to alkaline conditions for releasing the elongated complementary DNA sequence and are collected in a tube for performing two rounds of PCR...
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  4. Method: Seamless, rapid, and accurate analyses of outbreak genomic data using split k-mer analysis
    • Romain Derelle,
    • Johanna von Wachsmann,
    • Tommi Mäklin,
    • Joel Hellewell,
    • Timothy Russell,
    • Ajit Lalvani,
    • Leonid Chindelevitch,
    • Nicholas J. Croucher,
    • Simon R. Harris,
    • and John A. Lees
    Genome Res. October 2024 34: 1661-1673; Published in Advance October 15, 2024, doi:10.1101/gr.279449.124
    ...internet tools, file sizes ≲10 MB are desirable. To efficiently store large amounts of data, we propose reducing the size of SKFs by filtering split k-mers using the ska weed function. Here, we tested the power lost using an online approach by using iterative analyses of 288 Escherichia coli assemblies...
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  5. Method: Rapid and accurate demultiplexing of direct RNA nanopore sequencing data with SeqTagger
    • Leszek P. Pryszcz,
    • Gregor Diensthuber,
    • Laia Llovera,
    • Rebeca Medina,
    • Anna Delgado-Tejedor,
    • Luca Cozzuto,
    • Julia Ponomarenko,
    • and Eva Maria Novoa
    Genome Res. April 2025 35: 956-966; Published in Advance January 29, 2025, doi:10.1101/gr.279290.124
    ...performance on in vivo data using two runs of poly(A)-tailed, total RNA from Escherichia coli (Delgado-Tejedor et al. 2024). Both runs contained two (out of the four possible) barcodes used in our b04 models, thus allowing us to determine the false positive rate per barcode. This showed that between 0...
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  6. Research: The rate and spectrum of new mutations in mice inferred by long-read sequencing
    • Eugenio López-Cortegano,
    • Jobran Chebib,
    • Anika Jonas,
    • Anastasia Vock,
    • Sven Künzel,
    • Peter D. Keightley,
    • and Diethard Tautz
    Genome Res. January 2025 35: 43-54; Published in Advance December 2, 2024, doi:10.1101/gr.279982.124
    ...of read and assembly-based methods to call the complete spectrum of new mutations. On average, there are about 45 mutations per haploid per generation, about half of which (54%) are insertions and deletions shorter than 50 bp (indels). The remainder are single-nucleotide mutations (SNMs; 44%) and large...
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  7. Research: Long-read transcriptome sequencing of CLL and MDS patients uncovers molecular effects of SF3B1 mutations
    • Alicja Pacholewska,
    • Matthias Lienhard,
    • Mirko Brüggemann,
    • Heike Hänel,
    • Lorina Bilalli,
    • Anja Königs,
    • Felix Heß,
    • Kerstin Becker,
    • Karl Köhrer,
    • Jesko Kaiser,
    • Holger Gohlke,
    • Norbert Gattermann,
    • Michael Hallek,
    • Carmen D. Herling,
    • Julian König,
    • Christina Grimm,
    • Ralf Herwig,
    • Kathi Zarnack,
    • and Michal R. Schweiger
    Genome Res. November 2024 34: 1832-1848; Published in Advance September 13, 2024, doi:10.1101/gr.279327.124
    ...(PSI) among groups with or without SF3B1 mutation. (E) Validation of the differential splicing associated with SF3B1 mutation with RT-PCR experiments in isogenic K562 and Nalm6 cell lines. (F) Minigene assays workflow. HEK293T cells were cotransfected with minigenes and either SF3B1wt or SF3B1K700E...
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  8. Research: Extensive variation in germline de novo mutations in Poecilia reticulata
    • Yuying Lin,
    • Iulia Darolti,
    • Wouter van der Bijl,
    • Jake Morris,
    • and Judith E. Mank
    Genome Res. August 2023 33: 1317-1324; Published in Advance July 13, 2023, doi:10.1101/gr.277936.123
    ..., is a model of rapid adaptation, however the relative contribution of standing genetic variation versus de novo mutation (DNM) to evolution in this species remains unclear. Here, we use pedigree-based approaches to quantify and characterize germline DNMs in three large guppy families. Our results suggest...
  9. Method: Tn5 transposase and tagmentation procedures for massively scaled sequencing projects
    • Simone Picelli,
    • Åsa K. Björklund,
    • Björn Reinius,
    • Sven Sagasser,
    • Gösta Winberg,
    • and Rickard Sandberg
    Genome Res. December 2014 24: 2033-2040; Published in Advance July 30, 2014, doi:10.1101/gr.177881.114
    ...after tagmentation and proceeding directly with the PCR, indicating that the subsequent incubation at 72°C (gap filling) probably suffices to release the transposase from the DNA. Conversely, our in-house Tn5 necessitates a stripping buffer with at least 0.1% SDS. Finetuning the concentration of SDS, we...
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  10. Research: Alu insertion variants alter gene transcript levels
    • Lindsay M. Payer,
    • Jared P. Steranka,
    • Maria S. Kryatova,
    • Giacomo Grillo,
    • Mathieu Lupien,
    • Pedro P. Rocha,
    • and Kathleen H. Burns
    Genome Res. December 2021 31: 2236-2248; Published in Advance November 19, 2021, doi:10.1101/gr.261305.120
    ...that the Alu reduces expression of a nearby gene, potentially PTHLH, which in turn leads to cancer risk. We measured expression of the genes near the Alu insertion site in the CRISPR-edited 293T cell lines by qRT-PCR. The presence of the Alu results in a 0.49-fold change in PTHLH expression relative to when...
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