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METHODS: Fluorescence Polarization in Homogeneous Nucleic Acid Analysis II: 5′-Nuclease Assay
- Sherif Latif,
- Irma Bauer-Sardina,
- Kostubh Ranade,
- Kenneth J. Livak,
- and Pui-Yan Kwok
Genome Res. March 1, 2001 11: 436-440; doi:10.1101/gr.156601
...Fluorescence Polarization in Homogeneous Nucleic Acid Analysis II: 5′-Nuclease Assay Sherif Latif 1 , 4 , Irma Bauer-Sardina 1 , 4 , Kostubh Ranade 2 , Kenneth J. Livak 3 , and Pui-Yan Kwok 1 , 5 1Division of Dermatology...
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METHODS: Homogeneous Assays for Single-Nucleotide Polymorphism Typing Using AlphaScreen
- Lucille Beaudet,
- Julie Bédard,
- Billy Breton,
- Roberto J. Mercuri,
- and Marcia L. Budarf
Genome Res. April 1, 2001 11: 600-608; doi:10.1101/gr.1725501
.... Genome Res. 10 : 549 – 557 . ↵ Chen X. , Levine L. , Kwok P.Y. ( 1999 ) Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res. 9 : 492 – 498 . ↵ Corder E.H. , Saunders A.M. , Strittmatter W.J. , Schmechel D.E. , Gaskell P.C. , Small G.W. , Roses A.D. , Haines J.L. , Pericak-Vance M...
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METHODS: DNA Analysis by Fluorescence Quenching Detection
- Ming Xiao and
- Pui-Yan Kwok
Genome Res. May 1, 2003 13: 932-939; doi:10.1101/gr.987803
..., , 468–470. . ↵ Chen X. , Levine L. , Kwok P.Y. ( 1999 ) Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res. 9 : 492 – 498 . ↵ Germer S. , Holland M.J. , Higuchi R. ( 2000 ) High-throughput SNP allele-frequency determination in pooled DNA samples by kinetic PCR. Genome Res. 10...
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Research: Cell-type- and chromosome-specific chromatin landscapes and DNA replication programs of Drosophila testis tumor stem cell–like cells
- Jennifer A. Urban,
- Daniel Ringwalt,
- John M. Urban,
- Wingel Xue,
- Ryan Gleason,
- Keji Zhao,
- and Xin Chen
Genome Res. January 2026 36: 83-101; Published in Advance December 10, 2025, doi:10.1101/gr.280809.125
...ligand unpaired (Upd) (Fig. 1B; Supplemental Fig. S1B). Hyperactivation of the JAK-STAT pathway in the testis results in overproliferation of both stem-cell types (Kiger et al. 2001; Tulina and Matunis 2001; Leatherman and DiNardo 2010), resulting in a more homogenous tissue composition for genomic...
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Research: Combinatorial microRNA activity is essential for the transition of pluripotent cells from proliferation into dormancy
- Dhanur P. Iyer,
- Lambert Moyon,
- Lars Wittler,
- Chieh-Yu Cheng,
- Francisca R. Ringeling,
- Stefan Canzar,
- Annalisa Marsico,
- and Aydan Bulut-Karslioğlu
Genome Res. April 2024 34: 572-589; Published in Advance May 6, 2024, doi:10.1101/gr.278662.123
...and survival; therefore, miRNA expression profiles may show inter-embryo variation. For this reason, we profiled individual embryos in proliferative (E4.5) and dormant states (in vivo and in vitro; see Methods). During in vivo diapause, dormancy progresses from the mural end of the embryo to the polar end over...
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Resource: An organism-wide ATAC-seq peak catalog for the bovine and its use to identify regulatory variants
- Can Yuan,
- Lijing Tang,
- Thomas Lopdell,
- Vyacheslav A. Petrov,
- Claire Oget-Ebrad,
- Gabriel Costa Monteiro Moreira,
- José Luis Gualdrón Duarte,
- Arnaud Sartelet,
- Zhangrui Cheng,
- Mazdak Salavati,
- D. Claire Wathes,
- Mark A. Crowe,
- GplusE Consortium,
- Wouter Coppieters,
- Mathew Littlejohn,
- Carole Charlier,
- Tom Druet,
- Michel Georges,
- and Haruko Takeda
Genome Res. October 2023 33: 1848-1864; Published in Advance September 26, 2023, doi:10.1101/gr.277947.123
...-seq library constructionATAC-seq libraries were constructed following the Omni ATAC-seq protocol (Corces et al. 2017) with some modifications.Tissue homogenizationA cryopreserved tissue in a vial was quickly thawed in a water bath and transferred to an excess amount of ice-cold Dulbecco's phosphate buffered...
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Research: Trajectory mapping of the early Drosophila germline reveals controls of zygotic activation and sex differentiation
- Yi-Ru Li,
- Hsiao Wen Lai,
- Hsiao Han Huang,
- Hsing-Chun Chen,
- Sebastian D. Fugmann,
- and Shu Yuan Yang
Genome Res. June 2021 31: 1011-1023; Published in Advance April 15, 2021, doi:10.1101/gr.271148.120
...(Supplemental Fig. S2A).View larger version: In this window In a new window Figure 1. Clustering and pseudotime analysis of single-cell germline transcriptomes. (A) FACS plot for sorting germ cells from embryonic homogenates of 0- to 8-h embryos with the GFP+ germ cells highlighted by a dotted circle. x...
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Research: Spatial organization of chromosomes leads to heterogeneous chromatin motion and drives the liquid- or gel-like dynamical behavior of chromatin
- Hossein Salari,
- Marco Di Stefano,
- and Daniel Jost
Genome Res. January 2022 32: 28-43; Published in Advance December 28, 2021, doi:10.1101/gr.275827.121
...as a function of time. Experimentally, this is typically performed either by tracking single fluorescently labeled loci (Cabal et al. 2006) or by monitoring the dynamics of the nuclear local densities of stained histones (Zidovska et al. 2013) during ∼10–30 sec. From these experiments, trajectories...
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Research: Exome sequencing and CRISPR/Cas genome editing identify mutations of ZAK as a cause of limb defects in humans and mice
- Malte Spielmann,
- Naseebullah Kakar,
- Naeimeh Tayebi,
- Catherine Leettola,
- Gudrun Nürnberg,
- Nadine Sowada,
- Darío G. Lupiáñez,
- Izabela Harabula,
- Ricarda Flöttmann,
- Denise Horn,
- Wing Lee Chan,
- Lars Wittler,
- Rüstem Yilmaz,
- Janine Altmüller,
- Holger Thiele,
- Hans van Bokhoven,
- Charles E. Schwartz,
- Peter Nürnberg,
- James U. Bowie,
- Jamil Ahmad,
- Christian Kubisch,
- Stefan Mundlos,
- and Guntram Borck
Genome Res. February 2016 26: 183-191; Published in Advance January 11, 2016, doi:10.1101/gr.199430.115
...complex hindlimb duplication phenotypes with low penetrance (four out of 64 animals) (Fig. 4A–D). In one mouse at E18.5, one supernumerary hindlimbwith normal polarity was connected to an imperfectly duplicated pelvic girdle (Fig. 4A). The duplicated hindlimb showed a shortened femur, fibula, and tibia...
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Research: Yeast genetic interaction screen of human genes associated with amyotrophic lateral sclerosis: identification of MAP2K5 kinase as a potential drug target
- Myungjin Jo,
- Ah Young Chung,
- Nozomu Yachie,
- Minchul Seo,
- Hyejin Jeon,
- Youngpyo Nam,
- Yeojin Seo,
- Eunmi Kim,
- Quan Zhong,
- Marc Vidal,
- Hae Chul Park,
- Frederick P. Roth,
- and Kyoungho Suk
Genome Res. September 2017 27: 1487-1500; Published in Advance June 8, 2017, doi:10.1101/gr.211649.116
...expressed in yeast as GFP-fused proteins, which were then visualized under a fluorescence microscope. Of the 20 human genes, 16 genes induced the formation of protein aggregates when expressed in yeast. Protein aggregation was not observed for four genes: sodium channel epithelial 1 beta subunit; bone...
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