Searching journal content for articles similar to Mullikin and Ning 13 (1): 81.

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  1. Method: Mapping and quantifying nascent transcript start sites using TT-TSS-seq
    • Eleanor Elgood Hunt,
    • Claudia Vivori,
    • Richard Mitter,
    • Vedis Agnadottir,
    • and Folkert J. van Werven
    Genome Res. March 2026 36: 600-610; Published in Advance February 17, 2026, doi:10.1101/gr.280726.125
    ...added to the reverse transcription reaction and incubated for 5 min. Beads were washed twice with 85% ethanol, dried, and eluted twice in nuclease-free water. cDNA preamplification was performed with i5_s and i7_s (300 nM each) primers and Phusion HF PCR Mastermix (Thermo Fisher Scientific). Six PCR...
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  2. Review: k-mer approaches for biodiversity genomics
    • Katharine M. Jenike,
    • Lucía Campos-Domínguez,
    • Marilou Boddé,
    • José Cerca,
    • Christina N. Hodson,
    • Michael C. Schatz,
    • and Kamil S. Jaron
    Genome Res. February 2025 35: 219-230; Published in Advance January 31, 2025, doi:10.1101/gr.279452.124
    ...a comprehensive review to the theoretical properties and practical applications of k-mers in biodiversity genomics with a special focus on modeling.The genomics field has come a long way in the past quarter century. Sequencing and assembling even a partial was once a multibillion dollar accomplishment. Now...
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  3. Research: Characterization of the role of spatial proximity of DNA double-strand breaks in the formation of CRISPR-Cas9-induced large structural variations
    • Mikkel Dahl-Jessen,
    • Thorkild Terkelsen,
    • Rasmus O. Bak,
    • and Uffe Birk Jensen
    Genome Res. February 2025 35: 231-241; Published in Advance January 13, 2025, doi:10.1101/gr.278575.123
    ...to transfect cells with individual sgRNA pairs (Laustsen and Bak 2019). To assemble RNPs with the sgRNA pairs, 6 µg Cas9 enzyme (0.6 µL of 10 µg/µL) was mixed with 1.6 µg (0.5 µL of 3.2 µg/µL) of each of the two sgRNAs in PCR tubes in no predefined order. RNPs were then stored at −20°C or used immediately...
  4. Research: Cohesin organizes 3D DNA contacts surrounding active enhancers in C. elegans
    • Jun Kim,
    • Haoyu Wang,
    • and Sevinç Ercan
    Genome Res. May 2025 35: 1108-1123; Published in Advance April 10, 2025, doi:10.1101/gr.279365.124
  5. Research: Genomic context sensitivity of insulator function
    • André M. Ribeiro-dos-Santos,
    • Megan S. Hogan,
    • Raven D. Luther,
    • Ran Brosh,
    • and Matthew T. Maurano
    Genome Res. March 2022 32: 425-436; Published in Advance January 26, 2022, doi:10.1101/gr.276449.121
    ...(525 ± 50 nm).Generation of barcoded reporter plasmidsSleeping Beauty reporter constructs used in this study were barcoded using a Gibson Assembly approach before introduction into K562 cells (Supplemental Fig. S3). The plasmid backbone to be barcoded was PCR amplified using pTR-GibsonBC-FW and p...
  6. 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
    ...). The latter were located closest to 3′ splice sites (Fig. 6L), suggesting that multiple SF3B1 binding sites assemble into complex binding patterns at 3′ splice sites. We then investigated the differences in binding between K562-SF3B1K700E/wt and K562-SF3B1wt/wt solely in the C3 cluster. We noticed that K562...
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  7. Method: HD-Marker: a highly multiplexed and flexible approach for targeted genotyping of more than 10,000 genes in a single-tube assay
    • Jia Lv,
    • Wenqian Jiao,
    • Haobing Guo,
    • Pingping Liu,
    • Ruijia Wang,
    • Lingling Zhang,
    • Qifan Zeng,
    • Xiaoli Hu,
    • Zhenmin Bao,
    • and Shi Wang
    Genome Res. December 2018 28: 1919-1930; Published in Advance November 8, 2018, doi:10.1101/gr.235820.118
    ...multiplex SNP genotyping, has been widely adopted in numerous and diverse applications. The BeadArray platform enables the production of randomly assembled universal arrays and the analysis of any custom-built panel of SNPs, thus providing more flexibility than conventional microarrays (Oliphant et al. 2002...
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  8. Research: Complex mosaic structural variations in human fetal brains
    • Shobana Sekar,
    • Livia Tomasini,
    • Christos Proukakis,
    • Taejeong Bae,
    • Logan Manlove,
    • Yeongjun Jang,
    • Soraya Scuderi,
    • Bo Zhou,
    • Maria Kalyva,
    • Anahita Amiri,
    • Jessica Mariani,
    • Fritz J. Sedlazeck,
    • Alexander E. Urban,
    • Flora M. Vaccarino,
    • and Alexej Abyzov
    Genome Res. December 2020 30: 1695-1704; Published in Advance October 29, 2020, doi:10.1101/gr.262667.120
    ...that includes SV discovery, local assembly of the allele with an SV, and SV genotyping across multiple samples (Fig. 1A). SVs were called in fetal brain clones (N = 3 brains and 41 clones) using Manta (Chen et al. 2016), and somatic events were selected based on clone-to-clone comparisons (Methods). Briefly...
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  9. Research: tRNA-derived small RNAs are embedded in the gene regulatory network instructing Drosophila metamorphosis
    • Junling Shi,
    • Jiaqi Xu,
    • Jun Ma,
    • and Feng He
    Genome Res. December 2023 33: 2119-2132; Published in Advance November 16, 2023, doi:10.1101/gr.278128.123
    ...mRNAs for binding with YBX1 and suppress their stability (Goodarzi et al. 2015). Moreover, tsRNAs can frequently associate with translation machinery and related factors to participate in multiple layers of translation control, such as rRNA biogenesis, ribosome assembly, translation initiation...
  10. Resource: An 11-point time course midgut transcriptome across 72 h after bloodfeeding provides detailed temporal resolution of transcript expression in the arbovirus vector, Aedes aegypti
    • Hitoshi Tsujimoto and
    • Zach N. Adelman
    Genome Res. September 2023 33: 1638-1648; Published in Advance October 6, 2023, doi:10.1101/gr.277808.123
    ...) and 105,509,782 fragments per time point. We mapped these fragments using HISAT2 (ver. 2.1.0) (Pertea et al. 2016) onto the AaegL5 AGWG assembly (obtained from VectorBase) (Giraldo-Calderón et al. 2015; Matthews et al. 2018; https://vectorbase.org/vectorbase/app) with a 78.48% average mapping rate...
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