Searching journal content for articles similar to Aslanidis et al. 4 (3): 172.

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  1. Method: KAS-ATAC reveals the genome-wide single-stranded accessible chromatin landscape of the human genome
    • Samuel H. Kim,
    • Georgi K. Marinov,
    • and William J. Greenleaf
    Genome Res. January 2025 35: 124-134; Published in Advance November 21, 2024, doi:10.1101/gr.279621.124
    ...with 300 μL TWB for 2 min at 55°C, 1000 rpm in a ThermoMixer. After separation on a magnetic stand, beads were washed in 100 μL 0.1× TE buffer, resuspended in 15 μL 0.1× TE buffer, and heated for 10 min at 98°C.For PCR, 5 μL of each of the i5 and i7 NEB Next sequencing adapters were added together with 25...
  2. 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
    ...by asymmetric PCR and then subjected this ssDNA to ExoI and Tn5 treatment (Fig. 1E). The synthesized ssDNA was fully digested by ExoI, confirming that the DNA was single-stranded. In addition, ≥160-nt ssDNA was tagmented by Tn5, whereas 130-nt and 110-nt ssDNA were not tagmented, indicating that a length >130...
  3. Research: Chromosome-specific telomere lengths and the minimal functional telomere revealed by nanopore sequencing
    • Samantha L. Sholes,
    • Kayarash Karimian,
    • Ariel Gershman,
    • Thomas J. Kelly,
    • Winston Timp,
    • and Carol W. Greider
    Genome Res. April 2022 32: 616-628; Published in Advance October 26, 2021, doi:10.1101/gr.275868.121
    ...(Corning; at 200 µg/mL). Integration at the TEL1 locus was confirmed by junction polymerase chain reaction (PCR). A list of primers and plasmids used in this study is presented in Supplemental Tables S5 and S6, respectively.To perform the W303-0,1,2,3 experiment, CVy61 was streaked to single colony on YPD...
  4. Method: Determining the impact of uncharacterized inversions in the human genome by droplet digital PCR
    • Marta Puig,
    • Jon Lerga-Jaso,
    • Carla Giner-Delgado,
    • Sarai Pacheco,
    • David Izquierdo,
    • Alejandra Delprat,
    • Magdalena Gayà-Vidal,
    • Jack F. Regan,
    • George Karlin-Neumann,
    • and Mario Cáceres
    Genome Res. May 2020 30: 724-735; Published in Advance May 18, 2020, doi:10.1101/gr.255273.119
    ...genotyping methods did not exist (the well-known 17q21 inversion [or HsInv0573], HsInv0390, HsInv0290, and HsInv0786) and two control inversions already genotyped by iPCR-based assays (HsInv0241 and HsInv0389) (Supplemental Table S1). Minimal inversion sizes range from 3.1 to 741.7 kb and IRs at breakpoints...
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  5. Method: Quantitative mitochondrial DNA copy number determination using droplet digital PCR with single-cell resolution
    • Ryan O'Hara,
    • Enzo Tedone,
    • Andrew Ludlow,
    • Ejun Huang,
    • Beatrice Arosio,
    • Daniela Mari,
    • and Jerry W. Shay
    Genome Res. November 2019 29: 1878-1888; Published in Advance September 23, 2019, doi:10.1101/gr.250480.119
    ...of mtDNA as a biomarker highlights the need for a more high-throughput method of mtDNA quantification. The current standard employed in the measurement of mtDNA copy number is quantitative PCR (qPCR). Measurements by qPCR require the use of a reference gene and are often displayed as a ratio...
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  6. ARTICLE: Rapid and reliable cloning of PCR products.
    • J B Lorens
    Genome Res. November 1991 1: 140-141; doi:10.1101/gr.1.2.140
    ...- zymes, t]) The concurrent incubation of Klenow, T4 polynucleotide kinase, and T4 DNA ligase employed here effective- ly creates concatemeric DNA substrates by polishing, phosphorylating, and ligating PCR termini in a single step (Fig. 1). A variation for linker and adaptor cloning requiring minimal...
  7. Method: Quantification of in vivo progenitor mutation accrual with ultra-low error rate and minimal input DNA using SIP-HAVA-seq
    • Pete H. Taylor,
    • Amanda Cinquin,
    • and Olivier Cinquin
    Genome Res. November 2016 26: 1600-1611; Published in Advance October 19, 2016, doi:10.1101/gr.200501.115
    ...to hairpin adapters comprising a variable barcode. After linearization using NEB’s “USER” enzyme, a first PCR is performed to amplify the material, and a second to add Illumina sequencing adapters. Illumina reads that correspond to the same “duplex” are grouped using the custom program “Mutinack” that relies...
  8. Research: SARS-CoV-2 genomic diversity and the implications for qRT-PCR diagnostics and transmission
    • Nicolae Sapoval,
    • Medhat Mahmoud,
    • Michael D. Jochum,
    • Yunxi Liu,
    • R.A. Leo Elworth,
    • Qi Wang,
    • Dreycey Albin,
    • Huw A. Ogilvie,
    • Michael D. Lee,
    • Sonia Villapol,
    • Kyle M. Hernandez,
    • Irina Maljkovic Berry,
    • Jonathan Foox,
    • Afshin Beheshti,
    • Krista Ternus,
    • Kjersti M. Aagaard,
    • David Posada,
    • Christopher E. Mason,
    • Fritz J. Sedlazeck,
    • and Todd J. Treangen
    Genome Res. April 2021 31: 635-644; Published in Advance February 18, 2021, doi:10.1101/gr.268961.120
    ...-CoV-2. In this setting, sensitivity determines how well the detection tests can capture the diversity of all SARS-CoV-2 variants. Lack of sensitivity leads to an increase in false-negative qRT-PCR results, because two or more mismatches can result in increases in CT values and degradation in accuracy...
    OPEN ACCESS ARTICLE
  9. Method: Minimal positional substring cover is a haplotype threading alternative to Li and Stephens model
    • Ahsan Sanaullah,
    • Degui Zhi,
    • and Shaojie Zhang
    Genome Res. July 2023 33: 1007-1014; Published in Advance June 14, 2023, doi:10.1101/gr.277673.123
    ...) to the LS HMM. Previously, we introduced the minimal positional substring cover (MPSC) problem as an alternative formulation of LS whose objective is to cover a query haplotype by a minimum number of segments from haplotypes in a reference panel. The MPSC formulation allows the generation of a haplotype...
  10. Resource: A platform for curated products from novel open reading frames prompts reinterpretation of disease variants
    • Matthew D.C. Neville,
    • Robin Kohze,
    • Chaitanya Erady,
    • Narendra Meena,
    • Matthew Hayden,
    • David N. Cooper,
    • Matthew Mort,
    • and Sudhakaran Prabakaran
    Genome Res. February 2021 31: 327-336; Published in Advance January 19, 2021, doi:10.1101/gr.263202.120
    ...that some nORFs are becoming canonical CDS, and plan to regularly update our GENCODE reference in future iterations of the nORFs database.Database and web platformTo reduce the threshold of accessibility, databases need to be accessible with minimal requirements of tools or prior knowledge. We therefore...
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