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ARTICLE: In situ PCR: protocols and applications.
- G J Nuovo
Genome Res. February 1995 4: S151-S167
..., State University of New York at Stony Brook 11794, USA. Abstract Many groups have now published data based on the in situ detection of PCR-amplified DNA and cDNA. As with standard in situ hybridization or PCR, variables that can affect in situ PCR results include type of fixative and time of fixation...
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ARTICLES: Analysis of nonspecific DNA synthesis during in situ PCR and solution-phase PCR.
- G J Nuovo,
- P MacConnell,
- and F Gallery
Genome Res. October 1994 4: 89-96
...of different variables for optimizing in situ detection of PCR-amplified DNA. PCR Methods Applic. 2 : 305 – 312 . 7.. Nuovo, G.J., , Becker, J. , MacConnell, P. , Margiotta, M. , Comite, S. , Hochman. H. Nuovo, G.J., Becker, J. MacConnell, P. Margiotta, M. Comite, S. and Hochman. H. 1992 . Histological...
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Methods: Genome-wide detection and analysis of hippocampus core promoters using DeepCAGE
- Eivind Valen,
- Giovanni Pascarella,
- Alistair Chalk,
- Norihiro Maeda,
- Miki Kojima,
- Chika Kawazu,
- Mitsuyoshi Murata,
- Hiromi Nishiyori,
- Dejan Lazarevic,
- Dario Motti,
- Troels Torben Marstrand,
- Man-Hung Eric Tang,
- Xiaobei Zhao,
- Anders Krogh,
- Ole Winther,
- Takahiro Arakawa,
- Jun Kawai,
- Christine Wells,
- Carsten Daub,
- Matthias Harbers,
- Yoshihide Hayashizaki,
- Stefano Gustincich,
- Albin Sandelin,
- and Piero Carninci
Genome Res. February 2009 19: 255-265; Published in Advance December 11, 2008, doi:10.1101/gr.084541.108
...previously believed, and deeper sequencing is necessary to detect all active promoters in a given tissue. Here, we present a new method for high-throughput sequencing of 5′ cDNA tags—DeepCAGE: merging the Cap Analysis of Gene Expression method with ultra-high-throughput sequence technology. We apply Deep...
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Research: Comprehensive functional annotation of ESR1-driven enhancers in breast cancer reveals hierarchical activity independent of genomic and epigenomic contexts
- Yanis Zekri,
- Sebastian Gregoricchio,
- Elif Yapıcı,
- Chia-Chi Flora Huang,
- Tunç Morova,
- Umut Berkay Altıntaş,
- Gozde Korkmaz,
- Nathan A. Lack,
- and Wilbert Zwart
Genome Res. July 2025 35: 1530-1543; Published in Advance June 10, 2025, doi:10.1101/gr.280320.124
...). Briefly, a custom oligonucleotide probe pool was designed to capture ESR1 binding regions from both clinical breast tumors and T-47D cell line ESR1 ChIP-seq. Pooled human genomic DNA was sheared, captured, PCR-amplified, and cloned into the hSTARR-ORI plasmid (Addgene, plasmid 99296). The ESR1-focused...
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Research: Alternative splicing generates HER2 isoform diversity underlying antibody–drug conjugate resistance in breast cancer
- Gabriela D.A. Guardia,
- Carlos H. dos Anjos,
- Aline Rangel-Pozzo,
- Filipe F. dos Santos,
- Alexander Birbrair,
- Paula F. Asprino,
- Anamaria A. Camargo,
- and Pedro A.F. Galante
Genome Res. September 2025 35: 1942-1958; Published in Advance July 15, 2025, doi:10.1101/gr.280304.124
...(c.1181G>C, p.R394T), previously identified as a potential mechanism of resistance to T-DXd, because SLX4 encodes a DNA repair protein that regulates structure-specific endonucleases and seems to play a role in resistance to TOP1 inhibition. Among HER2- cell lines, MCF-7 and ZR-75-1 (HR+) and MDA...
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Methods: High definition profiling of mammalian DNA methylation by array capture and single molecule bisulfite sequencing
- Emily Hodges,
- Andrew D. Smith,
- Jude Kendall,
- Zhenyu Xuan,
- Kandasamy Ravi,
- Michelle Rooks,
- Michael Q. Zhang,
- Kenny Ye,
- Arindam Bhattacharjee,
- Leonardo Brizuela,
- W. Richard McCombie,
- Michael Wigler,
- Gregory J. Hannon,
- and James B. Hicks
Genome Res. September 2009 19: 1593-1605; Published in Advance July 6, 2009, doi:10.1101/gr.095190.109
...selection and massively parallel bisulfite sequencing to profile DNA methylation in genomic regions spanning hundreds of thousands of bases. This single molecule strategy enables methylation variable positions to be quantitatively examined with high sampling precision. Using bisulfite capture, we assessed...
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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
...the Smart-seq2) to add a PCR sequence at the cDNA 3′ end, after which the cDNA was PCR-amplified and fragmented with Tn5A transposase. The fragmented cDNAs were then amplified to generate the sequencing library (as shown in Fig. 2A; Supplemental Fig. 2).View larger version: In this window In a new window...
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Method: Sequencing Illumina libraries at high accuracy on the ONT MinION using R2C2
- Alexander Zee,
- Dori Z.Q. Deng,
- Matthew Adams,
- Kayla D. Schimke,
- Russell Corbett-Detig,
- Shelbi L. Russell,
- Xuan Zhang,
- Robert J. Schmitz,
- and Christopher Vollmers
Genome Res. November/December 2022 32: 2092-2106; Published in Advance November 9, 2022, doi:10.1101/gr.277031.122
...levels of read numbers and accuracy, and many, like standard RNA-seq, ChIP-seq, or targeted sequencing of PCR amplified genomic DNA, are unlikely to ever take advantage of the raw read length ONT and PacBio sequencers provide. However, there have been several studies to take advantage of long...
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Research: Diversification and collapse of a telomere elongation mechanism
- Bastien Saint-Leandre,
- Son C. Nguyen,
- and Mia T. Levine
Genome Res. June 2019 29: 920-931; Published in Advance May 28, 2019, doi:10.1101/gr.245001.118
...-restricted satellite DNA and DNA transposon fragments occupy its terminal ends. We infer that D. biarmipes relies instead on a recombination-based mechanism conserved from yeast to flies to humans. Telomeric retrotransposon diversification and disappearance suggest that persistently “selfish” machinery shapes telomere...
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Resource: The accessible chromatin landscape of the murine hippocampus at single-cell resolution
- John R. Sinnamon,
- Kristof A. Torkenczy,
- Michael W. Linhoff,
- Sarah A. Vitak,
- Ryan M. Mulqueen,
- Hannah A. Pliner,
- Cole Trapnell,
- Frank J. Steemers,
- Gail Mandel,
- and Andrew C. Adey
Genome Res. May 2019 29: 857-869; Published in Advance April 1, 2019, doi:10.1101/gr.243725.118
...coaccessibility framework, Cicero, which identified 146,818 links between promoters and putative distal regulatory DNA. Identified coaccessibility networks showed cell-type specificity, shedding light on key dynamic loci that reconfigure to specify hippocampal cell lineages. Lastly, we performed an additional sci...

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