Warning: Undefined array key "mm" in /www/wwwroot/www.ai-bt.com/si.php on line 10 Deprecated: trim(): Passing null to parameter #1 ($string) of type string is deprecated in /www/wwwroot/www.ai-bt.com/si.php on line 10 A versatile genome-scale PCR-based pipeline for high-definition DNA FISH.

Literature DB >> 23263692

A versatile genome-scale PCR-based pipeline for high-definition DNA FISH.

Magda Bienko¹, Nicola Crosetto¹, Leonid Teytelman¹, Sandy Klemm², Shalev Itzkovitz¹, Alexander van Oudenaarden^1,3.

Abstract

We developed a cost-effective genome-scale PCR-based method for high-definition DNA FISH (HD-FISH). We visualized gene loci with diffraction-limited resolution, chromosomes as spot clusters and single genes together with transcripts by combining HD-FISH with single-molecule RNA FISH. We provide a database of over 4.3 million primer pairs targeting the human and mouse genomes that is readily usable for rapid and flexible generation of probes.

Entities: Chemical Disease Gene Species

Mesh：

Substances：
DNA Primers

Year: 2012 PMID： 23263692 PMCID： PMC3735345 DOI： 10.1038/nmeth.2306

Source DB: PubMed Journal: Nat Methods ISSN： 1548-7091 Impact factor: 28.547

11 in total

1. ULS: a versatile method of labeling nucleic acids for FISH based on a monofunctional reaction of cisplatin derivatives with guanine moieties.

Authors: J C Wiegant; R P van Gijlswijk; R J Heetebrij; V Bezrookove; A K Raap; H J Tanke
Journal: Cytogenet Cell Genet Date: 1999

2. BLAT--the BLAST-like alignment tool.

Authors: W James Kent
Journal: Genome Res Date: 2002-04 Impact factor: 9.043

3. 3D-FISH on cultured cells combined with immunostaining.

Authors: Irina Solovei; Marion Cremer
Journal: Methods Mol Biol Date: 2010

4. Single-molecule transcript counting of stem-cell markers in the mouse intestine.

Authors: Shalev Itzkovitz; Anna Lyubimova; Irene C Blat; Mindy Maynard; Johan van Es; Jacqueline Lees; Tyler Jacks; Hans Clevers; Alexander van Oudenaarden
Journal: Nat Cell Biol Date: 2011-11-27 Impact factor: 28.824

5. Visualization of fine-scale genomic structure by oligonucleotide-based high-resolution FISH.

Authors: N A Yamada; L S Rector; P Tsang; E Carr; A Scheffer; M C Sederberg; M E Aston; R A Ach; A Tsalenko; N Sampas; B Peter; L Bruhn; A R Brothman
Journal: Cytogenet Genome Res Date: 2010-12-18 Impact factor: 1.636

6. Relationship of gene expression and chromosomal abnormalities in colorectal cancer.

Authors: Dafna Tsafrir; Manny Bacolod; Zachariah Selvanayagam; Ilan Tsafrir; Jinru Shia; Zhaoshi Zeng; Hao Liu; Curtis Krier; Robert F Stengel; Francis Barany; William L Gerald; Philip B Paty; Eytan Domany; Daniel A Notterman
Journal: Cancer Res Date: 2006-02-15 Impact factor: 12.701

7. Database resources of the National Center for Biotechnology.

Authors: David L Wheeler; Deanna M Church; Scott Federhen; Alex E Lash; Thomas L Madden; Joan U Pontius; Gregory D Schuler; Lynn M Schriml; Edwin Sequeira; Tatiana A Tatusova; Lukas Wagner
Journal: Nucleic Acids Res Date: 2003-01-01 Impact factor: 16.971

8. Primer3--new capabilities and interfaces.

Authors: Andreas Untergasser; Ioana Cutcutache; Triinu Koressaar; Jian Ye; Brant C Faircloth; Maido Remm; Steven G Rozen
Journal: Nucleic Acids Res Date: 2012-06-22 Impact factor: 16.971

9. Imaging individual mRNA molecules using multiple singly labeled probes.

Authors: Arjun Raj; Patrick van den Bogaard; Scott A Rifkin; Alexander van Oudenaarden; Sanjay Tyagi
Journal: Nat Methods Date: 2008-09-21 Impact factor: 28.547

10. Fluorescence in situ hybridization with high-complexity repeat-free oligonucleotide probes generated by massively parallel synthesis.

Authors: Shelagh Boyle; Matthew J Rodesch; Heather A Halvensleben; Jeffrey A Jeddeloh; Wendy A Bickmore
Journal: Chromosome Res Date: 2011-10-18 Impact factor: 5.239

24 in total

Review 1. Spatially resolved transcriptomics and beyond.

Authors: Nicola Crosetto; Magda Bienko; Alexander van Oudenaarden
Journal: Nat Rev Genet Date: 2014-12-02 Impact factor: 53.242

2. Direct visualization of cardiac transcription factories reveals regulatory principles of nuclear architecture during pathological remodeling.

Authors: Elaheh Karbassi; Manuel Rosa-Garrido; Douglas J Chapski; Yong Wu; Shuxun Ren; Yibin Wang; Enrico Stefani; Thomas M Vondriska
Journal: J Mol Cell Cardiol Date: 2019-02-08 Impact factor: 5.000

3. Cell lineage analysis in human brain using endogenous retroelements.

Authors: Gilad D Evrony; Eunjung Lee; Bhaven K Mehta; Yuval Benjamini; Robert M Johnson; Xuyu Cai; Lixing Yang; Psalm Haseley; Hillel S Lehmann; Peter J Park; Christopher A Walsh
Journal: Neuron Date: 2015-01-07 Impact factor: 17.173

4. Versatile design and synthesis platform for visualizing genomes with Oligopaint FISH probes.

Authors: Brian J Beliveau; Eric F Joyce; Nicholas Apostolopoulos; Feyza Yilmaz; Chamith Y Fonseka; Ruth B McCole; Yiming Chang; Jin Billy Li; Tharanga Niroshini Senaratne; Benjamin R Williams; Jean-Marie Rouillard; Chao-ting Wu
Journal: Proc Natl Acad Sci U S A Date: 2012-12-11 Impact factor: 11.205