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REVIEW: Microfabrication technologies for integrated nucleic acid analysis.
- D T Burke,
- M A Burns,
- and C Mastrangelo
Genome Res. March 1997 7: 189-197; doi:10.1101/gr.7.3.189
...increase to hundreds of millions of indi- vidual reactions per year. Nucleic Acid Analysis is Consistent and Amenable to Automation The biochemistries for extracting nucleic acid infor- mation are relatively uniform. Samples are aqueous and within a defined range of volume (1 ml-0.1 lJl), temperature (0°C...
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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
...that is coupled to a multicolor detection system capable of single-fluorophore sensitivity. Double-stranded DNA molecules were tagged at sequence-specific motif sites with fluorescent bisPNA (Peptide Nucleic Acid) tags. The DNA molecules were then stretched in the microfluidic device and driven in a flow stream...
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Method: A plug and play microfluidic platform for standardized sensitive low-input chromatin immunoprecipitation
- René A.M. Dirks,
- Peter C. Thomas,
- Haoyu Wu,
- Robert C. Jones,
- Hendrik G. Stunnenberg,
- and Hendrik Marks
Genome Res. May 2021 31: 919-933; Published in Advance March 11, 2021, doi:10.1101/gr.260745.120
...as they require sophisticated custom-made equipment and in-depth microfluidic and ChIP expertise, while lacking parallelization. To enable standardized, automated ChIP-seq profiling of low-input samples, we constructed microfluidic PDMS-based plates capable of performing 24 sensitive ChIP reactions within 30 min...
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Research: EHMT2 directs DNA methylation for efficient gene silencing in mouse embryos
- Ghislain Auclair,
- Julie Borgel,
- Lionel A. Sanz,
- Judith Vallet,
- Sylvain Guibert,
- Michael Dumas,
- Patricia Cavelier,
- Michael Girardot,
- Thierry Forné,
- Robert Feil,
- and Michael Weber
Genome Res. February 2016 26: 192-202; Published in Advance November 17, 2015, doi:10.1101/gr.198291.115
.... The embryos were dissociated and cross-linked as described above, and ChIP was performed with the true MicroChIP kit (Diagenode). Primer sequences for qPCR are provided in the Supplemental Table S3. H3K9me2 ChIP-seq ChIPwas performed as described above on three pools of eight embryos collected at E8.5. Ch...
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RESOURCE: GeneDesign: Rapid, automated design of multikilobase synthetic genes
- Sarah M. Richardson,
- Sarah J. Wheelan,
- Robert M. Yarrington,
- and Jef D. Boeke
Genome Res. April 2006 16: 550-556; Published in Advance February 15, 2006, doi:10.1101/gr.4431306
.... 32 : W176 – W180 . ↵ Rychlik W. , Spencer W.J. , Rhoads R.E. ( 1990 ) Optimization of the annealing temperature for DNA amplification in vitro. Nucleic Acids Res. 18 : 6409 – 6412 . ↵ Sharp P.M. , Cowe E. , Higgins D.G. , Shields D.C. , Wolfe K.H. , Wright F. ( 1988 ) Codon usage patterns...
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PERSPECTIVE: Emerging technologies in DNA sequencing
- Michael L. Metzker
Genome Res. December 2005 15: 1767-1776; doi:10.1101/gr.3770505
.... Caged RNA: Photo-control of a ribozyme reaction. Nucleic Acids Res. 26 : 3173 -3178. ↵ Collins, F. and Galas, D. 1993 . A new five-year plan for the U.S. Human Genome Project. Science 262 : 43 -46. ↵ Collins, F.S., Guyer, M.S., and Chakravarti, A. 1997 . Variations on a theme: Cataloging human DNA...
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METHODS: Determination of Single-Nucleotide Polymorphisms by Real-time Pyrophosphate DNA Sequencing
- Anders Alderborn,
- Anna Kristofferson,
- and Ulf Hammerling
Genome Res. August 1, 2000 10: 1249-1258; doi:10.1101/gr.10.8.1249
.... Biol. Chem. 265 : 7576 – 7582 . ↵ Gilles P.N. , Wu D.J. , Foster C.B. , Dillon P.J. , Chanock S.J. ( 1999 ) Single nucleotide polymorphic discrimination by an electronic dot blot assay on semiconductor microchips. Nature Biotechnol. 17 : 365 – 370 . ↵ Goodfriend T.L. , Elliott M.E. , Catt K.J. ( 1995...
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METHODS: Genotyping on a Thermal Gradient DNA Chip
- Tomoharu Kajiyama,
- Yuji Miyahara,
- Larry J. Kricka,
- Peter Wilding,
- David J. Graves,
- Saul Surrey,
- and Paolo Fortina
Genome Res. March 1, 2003 13: 467-475; doi:10.1101/gr.790603
.... ↵ Yuen P.-K. , Kricka L.J. , Fortina P. , Panaro N.J. , Sakazume T. , Wilding P. ( 2002 ) Microchip module for blood sample preparation and nucleic acid amplification reactions. Genome Res. 11 : 405 – 412 . ↵ Zarrinkar P.P. , Mainquist J.K. , Zamora M. , Stern D. , Welsh J.B. , Sapinoso L.M. , Hampton G...
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Methods: MicroRNA expression detected by oligonucleotide microarrays: System establishment and expression profiling in human tissues
- Omer Barad,
- Eti Meiri,
- Amir Avniel,
- Ranit Aharonov,
- Adi Barzilai,
- Isaac Bentwich,
- Uri Einav,
- Shlomit Gilad,
- Patrick Hurban,
- Yael Karov,
- Edward K. Lobenhofer,
- Eilon Sharon,
- Yoel M. Shiboleth,
- Marat Shtutman,
- Zvi Bentwich,
- and Paz Einat
Genome Res. December 2004 14: 2486-2494; doi:10.1101/gr.2845604
...capture-oligo for each targeted MIR that is covalently coupled onto color-coded microspheres (beads), and a detection-oligo that is labeled with biotin ( Fig. 4 ). Both capture and detection oligos are spiked with Locked Nucleic Acid (LNA) nucleotides to increase specificity and sensitivity ( Petersen...
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LETTER: E2F in vivo binding specificity: Comparison of consensus versus nonconsensus binding sites
- Alina Rabinovich,
- Victor X. Jin,
- Roman Rabinovich,
- Xiaoqin Xu,
- and Peggy J. Farnham
Genome Res. November 2008 18: 1763-1777; Published in Advance October 3, 2008, doi:10.1101/gr.080622.108
...performed ChIP assays using antibodies to E2F4, H3me3K27, H3me3K9, and 5-MeC (two independent ChIP assays were performed for each antibody), prepared amplicons, and analyzed the samples using ENCODE arrays that represent 44 regions (∼1% of the human ) ranging from 500 kb to 2 Mb. We first identified 116 E2F...

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