Searching journal content for articles similar to Sullivan et al. 2 (1): 34.

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  1. 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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  2. Research: Analysis of a cell-free DNA–based cancer screening cohort links fragmentomic profiles, nuclease levels, and plasma DNA concentrations
    • Yasine Malki,
    • Guannan Kang,
    • W.K. Jacky Lam,
    • Qing Zhou,
    • Suk Hang Cheng,
    • Peter P.H. Cheung,
    • Jinyue Bai,
    • Ming Lok Chan,
    • Chui Ting Lee,
    • Wenlei Peng,
    • Yiqiong Zhang,
    • Wanxia Gai,
    • Winsome W.S. Wong,
    • Mary-Jane L. Ma,
    • Wenshuo Li,
    • Xinzhou Xu,
    • Zhuoran Gao,
    • Irene O.L. Tse,
    • Huimin Shang,
    • L.Y. Lois Choy,
    • Peiyong Jiang,
    • K.C. Allen Chan,
    • and Y.M. Dennis Lo
    Genome Res. January 2025 35: 31-42; Published in Advance November 27, 2024, doi:10.1101/gr.279667.124
    ...for probes (Bio-Rad), final concentration of 900 μmol/L of each primer, and 250 nmol/L of the DNA probe. The ddPCR thermal profile consisted of an initial incubation for 30 min at 37°C followed by the denaturation step for 10 min at 95°C . It was further followed by 45 cycles of amplification, with each...
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  3. Review: Artificial intelligence and machine learning in cell-free-DNA-based diagnostics
    • W.H. Adrian Tsui,
    • Spencer C. Ding,
    • Peiyong Jiang,
    • and Y.M. Dennis Lo
    Genome Res. January 2025 35: 1-19; doi:10.1101/gr.278413.123
    ...labels (Alloghani et al. 2020). Classification models return categorical variables as the final output (e.g., a pregnancy involving a normal or trisomic fetus), whereas regression models return continuous variables (e.g., fetal DNA fraction in maternal plasma). On the other hand, unsupervised learning...
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  4. Method: Spatially resolved whole transcriptome profiling in human and mouse tissue using Digital Spatial Profiling
    • Stephanie M. Zimmerman,
    • Robin Fropf,
    • Bridget R. Kulasekara,
    • Maddy Griswold,
    • Oliver Appelbe,
    • Arya Bahrami,
    • Rich Boykin,
    • Derek L. Buhr,
    • Kit Fuhrman,
    • Margaret L. Hoang,
    • Quoc Huynh,
    • Lesley Isgur,
    • Andrew Klock,
    • Alecksandr Kutchma,
    • Alexa E. Lasley,
    • Yan Liang,
    • Jill McKay-Fleisch,
    • Jeffrey S. Nelson,
    • Karen Nguyen,
    • Erin Piazza,
    • Aric Rininger,
    • Daniel R. Zollinger,
    • Michael Rhodes,
    • and Joseph M. Beechem
    Genome Res. October 2022 32: 1892-1905; Published in Advance September 13, 2022, doi:10.1101/gr.276206.121
    ...of the kidney; therefore, we used WTA to spatially profile the transcriptomes of three nephron substructures: the glomeruli, the proximal convoluted tubules, and the distal convoluted tubules.We profiled three normal and four DKD FFPE human kidney samples labeled with fluorescent antibodies targeting epithelia...
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  5. Method: Phenotypic profiling of the human genome reveals gene products involved in plasma membrane targeting of SRC kinases
    • Julia Ritzerfeld,
    • Steffen Remmele,
    • Tao Wang,
    • Koen Temmerman,
    • Britta Brügger,
    • Sabine Wegehingel,
    • Stella Tournaviti,
    • Jeroen R.P.M. Strating,
    • Felix T. Wieland,
    • Beate Neumann,
    • Jan Ellenberg,
    • Chris Lawerenz,
    • Jürgen Hesser,
    • Holger Erfle,
    • Rainer Pepperkok,
    • and Walter Nickel
    Genome Res. November 2011 21: 1955-1968; Published in Advance July 27, 2011, doi:10.1101/gr.116087.110
    ...Phenotypic profiling of the human genome reveals gene products involved in plasma membrane targeting of SRC kinases Julia Ritzerfeld 1 , Steffen Remmele 2 , Tao Wang 1 , Koen Temmerman 1 , Britta Brügger 1 , Sabine Wegehingel 1...
  6. ARTICLE: An infrared fluorescent dATP for labeling DNA.
    • D L Steffens,
    • G Y Jang,
    • S L Sutter,
    • J A Brumbaugh,
    • L R Middendorf,
    • K Mühlegger,
    • E R Mardis,
    • L A Weinstock,
    • and R K Wilson
    Genome Res. November 1995 5: 393-399; doi:10.1101/gr.5.4.393
    ...can be uti- lized as a versatile mechanism for enzy- matically labeling various types of DNA molecules. Sequencing fragments can be labeled internally, thus obviating the need for fluorescent primers. PCR prod- ucts, such as short tandem repeat poly- morphisms (STRPs), and restriction frag- ments can...
  7. Method: Single-cell mutational profiling and clonal phylogeny in cancer
    • Nicola E. Potter,
    • Luca Ermini,
    • Elli Papaemmanuil,
    • Giovanni Cazzaniga,
    • Gowri Vijayaraghavan,
    • Ian Titley,
    • Anthony Ford,
    • Peter Campbell,
    • Lyndal Kearney,
    • and Mel Greaves
    Genome Res. December 2013 23: 2115-2125; Published in Advance September 20, 2013, doi:10.1101/gr.159913.113
    ...at 95°C, followed by 24 cycles of amplification for 15 sec at 95°C and for 4 min at 60°C. The STA product was then diluted 1:6 using DNA suspension buffer (Teknova). Finally, 2.7 mL of the single-cell target amplified DNA was interrogated by Q-PCR for each DNA target of interest using the 96.96 dynamic...
  8. Research: Bacterial infection remodels the DNA methylation landscape of human dendritic cells
    • Alain Pacis,
    • Ludovic Tailleux,
    • Alexander M. Morin,
    • John Lambourne,
    • Julia L. MacIsaac,
    • Vania Yotova,
    • Anne Dumaine,
    • Anne Danckaert,
    • Francesca Luca,
    • Jean-Christophe Grenier,
    • Kasper D. Hansen,
    • Brigitte Gicquel,
    • Miao Yu,
    • Athma Pai,
    • Chuan He,
    • Jenny Tung,
    • Tomi Pastinen,
    • Michael S. Kobor,
    • Roger Pique-Regi,
    • Yoav Gilad,
    • and Luis B. Barreiro
    Genome Res. December 2015 25: 1801-1811; Published in Advance September 21, 2015, doi:10.1101/gr.192005.115
    ...or the Illumina Total Stranded RNA Library kit, as per the manufacturer’s instructions. MethylCseq libraries were generated by ligation of methylated sequencing adapters to fragmented genomic DNA, followed by gel purification, sodium bisulfite conversion, and six cycles of PCR amplification. TAB-seq libraries...
  9. Methods: High-throughput DNA methylation profiling using universal bead arrays
    • Marina Bibikova,
    • Zhenwu Lin,
    • Lixin Zhou,
    • Eugene Chudin,
    • Eliza Wickham Garcia,
    • Bonnie Wu,
    • Dennis Doucet,
    • Neal J. Thomas,
    • Yunhua Wang,
    • Ekkehard Vollmer,
    • Torsten Goldmann,
    • Carola Seifart,
    • Wei Jiang,
    • David L. Barker,
    • Mark S. Chee,
    • Joanna Floros,
    • and Jian-Bing Fan
    Genome Res. March 2006 16: 383-393; Published in Advance January 31, 2006, doi:10.1101/gr.4410706
    .... After PCR, a thermal melt profile was performed to examine the homogeneity of PCR amplicons. Each DNA sample was analyzed in duplicate, and the mean was used for further analysis. The difference of the threshold cycle number (the C t -values) between the methylated and unmethylated alleles, Δ C t = C t...
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  10. Methods: DNA Mapping Using Microfluidic Stretching and Single-Molecule Detection of Fluorescent Site-Specific Tags
    • Eugene Y. Chan,
    • Nuno M. Goncalves,
    • Rebecca A. Haeusler,
    • Amie J. Hatch,
    • Jonathan W. Larson,
    • Anthony M. Maletta,
    • Gregory R. Yantz,
    • Eugene D. Carstea,
    • Martin Fuchs,
    • Gordon G. Wong,
    • Steven R. Gullans,
    • and Rudolf Gilmanshin
    Genome Res. June 2004 14: 1137-1146; doi:10.1101/gr.1635204
    ...DNA Mapping Using Microfluidic Stretching and Single-Molecule Detection of Fluorescent Site-Specific Tags Eugene Y. Chan 1 , 4 , Nuno M. Goncalves 1 , Rebecca A. Haeusler 1 , Amie J. Hatch 1 , Jonathan W. Larson 1 , Anthony M. Maletta...
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