ATE503843T1 - Gesamt-chromosom analyse von protein-dns wechselwirkungen - Google Patents

Gesamt-chromosom analyse von protein-dns wechselwirkungen

Info

Publication number
ATE503843T1
ATE503843T1 AT00959909T AT00959909T ATE503843T1 AT E503843 T1 ATE503843 T1 AT E503843T1 AT 00959909 T AT00959909 T AT 00959909T AT 00959909 T AT00959909 T AT 00959909T AT E503843 T1 ATE503843 T1 AT E503843T1
Authority
AT
Austria
Prior art keywords
protein
cell
genomic dna
dna
region
Prior art date
Application number
AT00959909T
Other languages
English (en)
Inventor
John Wyrick
Richard Young
Francois Robert
Original Assignee
Whitehead Biomedical Inst
Priority date (The priority date is an assumption and is not a legal conclusion. Google has not performed a legal analysis and makes no representation as to the accuracy of the date listed.)
Filing date
Publication date
Application filed by Whitehead Biomedical Inst filed Critical Whitehead Biomedical Inst
Application granted granted Critical
Publication of ATE503843T1 publication Critical patent/ATE503843T1/de

Links

Classifications

    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6809—Methods for determination or identification of nucleic acids involving differential detection
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6804—Nucleic acid analysis using immunogens
    • C—CHEMISTRY; METALLURGY
    • C12—BIOCHEMISTRY; BEER; SPIRITS; WINE; VINEGAR; MICROBIOLOGY; ENZYMOLOGY; MUTATION OR GENETIC ENGINEERING
    • C12Q—MEASURING OR TESTING PROCESSES INVOLVING ENZYMES, NUCLEIC ACIDS OR MICROORGANISMS; COMPOSITIONS OR TEST PAPERS THEREFOR; PROCESSES OF PREPARING SUCH COMPOSITIONS; CONDITION-RESPONSIVE CONTROL IN MICROBIOLOGICAL OR ENZYMOLOGICAL PROCESSES
    • C12Q1/00—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions
    • C12Q1/68—Measuring or testing processes involving enzymes, nucleic acids or microorganisms; Compositions therefor; Processes of preparing such compositions involving nucleic acids
    • C12Q1/6844—Nucleic acid amplification reactions
    • C12Q1/6853—Nucleic acid amplification reactions using modified primers or templates
    • C12Q1/6855—Ligating adaptors
    • G—PHYSICS
    • G01—MEASURING; TESTING
    • G01N—INVESTIGATING OR ANALYSING MATERIALS BY DETERMINING THEIR CHEMICAL OR PHYSICAL PROPERTIES
    • G01N33/00—Investigating or analysing materials by specific methods not covered by groups G01N1/00 - G01N31/00
    • G01N33/48—Biological material, e.g. blood, urine; Haemocytometers
    • G01N33/50—Chemical analysis of biological material, e.g. blood, urine; Testing involving biospecific ligand binding methods; Immunological testing
    • G01N33/53—Immunoassay; Biospecific binding assay; Materials therefor
    • G01N33/5308—Immunoassay; Biospecific binding assay; Materials therefor for analytes not provided for elsewhere, e.g. nucleic acids, uric acid, worms, mites

Landscapes

  • Chemical & Material Sciences (AREA)
  • Life Sciences & Earth Sciences (AREA)
  • Health & Medical Sciences (AREA)
  • Engineering & Computer Science (AREA)
  • Organic Chemistry (AREA)
  • Immunology (AREA)
  • Molecular Biology (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Wood Science & Technology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Biochemistry (AREA)
  • Biotechnology (AREA)
  • Physics & Mathematics (AREA)
  • Microbiology (AREA)
  • General Health & Medical Sciences (AREA)
  • Genetics & Genomics (AREA)
  • Biophysics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biomedical Technology (AREA)
  • Pathology (AREA)
  • Hematology (AREA)
  • Urology & Nephrology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • Cell Biology (AREA)
  • Food Science & Technology (AREA)
  • Medicinal Chemistry (AREA)
  • General Physics & Mathematics (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Peptides Or Proteins (AREA)
AT00959909T 1999-09-01 2000-09-01 Gesamt-chromosom analyse von protein-dns wechselwirkungen ATE503843T1 (de)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US15197299P 1999-09-01 1999-09-01
PCT/US2000/024358 WO2001016378A2 (en) 1999-09-01 2000-09-01 Chromosome-wide analysis of protein-dna interactions

Publications (1)

Publication Number Publication Date
ATE503843T1 true ATE503843T1 (de) 2011-04-15

Family

ID=22541045

Family Applications (1)

Application Number Title Priority Date Filing Date
AT00959909T ATE503843T1 (de) 1999-09-01 2000-09-01 Gesamt-chromosom analyse von protein-dns wechselwirkungen

Country Status (7)

Country Link
US (1) US6410243B1 (de)
EP (1) EP1220949B1 (de)
JP (1) JP2003508066A (de)
AT (1) ATE503843T1 (de)
CA (1) CA2383928A1 (de)
DE (2) DE00959909T1 (de)
WO (1) WO2001016378A2 (de)

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US7470507B2 (en) * 1999-09-01 2008-12-30 Whitehead Institute For Biomedical Research Genome-wide location and function of DNA binding proteins
US20030087231A1 (en) * 2000-05-19 2003-05-08 Albertson Donna G. Methods and compositions for preparation of a polynucleotide array
WO2002022884A2 (en) * 2000-09-12 2002-03-21 Transgenetics Incorporated Microarrayed organization of transcription factor target genes
DE10056899A1 (de) * 2000-11-16 2002-05-29 Aventis Pharma Gmbh Promotor zur funktionellen Charakterisierung von G-Protein gekoppelten Rezeptoren in der Hefe Saccharomyces cerevisiae
EP1381692A2 (de) * 2000-12-21 2004-01-21 Whitehead Institute For Biomedical Research Genom-breite position und funktion der dna-verbindlichen proteine
US20040058356A1 (en) * 2001-03-01 2004-03-25 Warren Mary E. Methods for global profiling gene regulatory element activity
AU2003270582A1 (en) * 2002-09-12 2004-04-30 Massachusetts Institute Of Technology Rb pahtway and chromatin remodeling genes that antagonize let-60 ras signaling
US20060099713A1 (en) * 2002-10-01 2006-05-11 Buck Institute Targeted-assisted iterative screening (tais):a novel screening format for large molecular repertoires
US20040161779A1 (en) * 2002-11-12 2004-08-19 Affymetrix, Inc. Methods, compositions and computer software products for interrogating sequence variations in functional genomic regions
US20040115794A1 (en) * 2002-12-12 2004-06-17 Affymetrix, Inc. Methods for detecting transcriptional factor binding sites
US7750908B2 (en) * 2003-04-04 2010-07-06 Agilent Technologies, Inc. Focus plus context viewing and manipulation of large collections of graphs
JP2007524399A (ja) 2003-07-03 2007-08-30 ザ・レジェンツ・オブ・ザ・ユニバーシティ・オブ・カリフォルニア 機能性ｄｎａエレメントおよび細胞性タンパク質のゲノムマッピング
US8222005B2 (en) * 2003-09-17 2012-07-17 Agency For Science, Technology And Research Method for gene identification signature (GIS) analysis
DE112004002318T5 (de) * 2003-11-26 2007-01-18 Whitehead Institute For Biomedical Research, Cambridge Transkriptionsregulatoren und Verfahren dazu
US8321138B2 (en) * 2005-07-29 2012-11-27 Agilent Technologies, Inc. Method of characterizing quality of hybridized CGH arrays
WO2005088306A2 (en) * 2004-03-04 2005-09-22 Whitehead Institute For Biomedical Research Biologically-active dna-binding sites and related methods
US20070031883A1 (en) * 2004-03-04 2007-02-08 Kincaid Robert H Analyzing CGH data to identify aberrations
US20050282193A1 (en) * 2004-04-23 2005-12-22 Bulyk Martha L Space efficient polymer sets
WO2006028565A2 (en) * 2004-06-30 2006-03-16 Whitehead Institute For Biomedical Research Novel methods for high-throughput genome-wide location analysis
JP2006078313A (ja) * 2004-09-09 2006-03-23 Hitachi Software Eng Co Ltd タンパク質の結合位置同定方法
US20070099227A1 (en) * 2004-10-12 2007-05-03 Curry Bo U Significance analysis using data smoothing with shaped response functions
US20090011955A1 (en) * 2005-07-06 2009-01-08 Forskarpatent L Uppsala Ab Method for Localization of Nucleic Acid Associated Molecules and Modifications
WO2007030678A2 (en) * 2005-09-07 2007-03-15 Whitehead Institute For Biomedical Research Methods of genome-wide location analysis in stem cells
US20070190542A1 (en) * 2005-10-03 2007-08-16 Ling Xinsheng S Hybridization assisted nanopore sequencing
WO2007064898A2 (en) * 2005-12-02 2007-06-07 Whitehead Institute For Biomedical Research Methods for mapping signal transduction pathways to gene expression programs
US7297477B2 (en) * 2006-02-13 2007-11-20 Agilent Technologies, Inc. Methods and compositions for detecting viral nucleic acid in a cell
US8071296B2 (en) 2006-03-13 2011-12-06 Agency For Science, Technology And Research Nucleic acid interaction analysis
US8058055B2 (en) 2006-04-07 2011-11-15 Agilent Technologies, Inc. High resolution chromosomal mapping
US20070238104A1 (en) * 2006-04-07 2007-10-11 Agilent Technologies, Inc. Competitive oligonucleotides
US20080124707A1 (en) * 2006-06-09 2008-05-29 Agency For Science, Technology And Research Nucleic acid concatenation
US7437249B2 (en) * 2006-06-30 2008-10-14 Agilent Technologies, Inc. Methods and systems for detrending signal intensity data from chemical arrays
US7881876B2 (en) * 2006-10-12 2011-02-01 Agilent Technologies, Inc. Methods and systems for removing offset bias in chemical array data
US8077951B2 (en) 2006-10-12 2011-12-13 Agilent Technologies, Inc. Method and system for dynamic, automated detection of outlying feature and feature background regions during processing of data scanned from a chemical array
US20080090236A1 (en) * 2006-10-13 2008-04-17 Yakhini Zohar H Methods and systems for identifying tumor progression in comparative genomic hybridization data
US20080102453A1 (en) * 2006-10-31 2008-05-01 Jayati Ghosh Methods and systems and analysis of CGH data
US20090215029A1 (en) * 2007-01-16 2009-08-27 Cytocure, Inc. Methods of isolating and purifying nucleic acid-binding biomolecules and compositions including same
WO2009046094A1 (en) 2007-10-01 2009-04-09 Nabsys, Inc. Biopolymer sequencing by hybridization of probes to form ternary complexes and variable range alignment
US8263367B2 (en) * 2008-01-25 2012-09-11 Agency For Science, Technology And Research Nucleic acid interaction analysis
JP5717634B2 (ja) * 2008-09-03 2015-05-13 ナブシス， インコーポレイテッド 流体チャネル内の生体分子および他の分析物の電圧感知のための、長手方向に変位されるナノスケールの電極の使用
US8262879B2 (en) 2008-09-03 2012-09-11 Nabsys, Inc. Devices and methods for determining the length of biopolymers and distances between probes bound thereto
US9650668B2 (en) 2008-09-03 2017-05-16 Nabsys 2.0 Llc Use of longitudinally displaced nanoscale electrodes for voltage sensing of biomolecules and other analytes in fluidic channels
US8583380B2 (en) 2008-09-05 2013-11-12 Aueon, Inc. Methods for stratifying and annotating cancer drug treatment options
RU2565550C2 (ru) 2010-09-24 2015-10-20 Те Борд Оф Трастиз Оф Те Лилэнд Стэнфорд Джуниор Юниверсити Прямой захват, амплификация и секвенирование днк-мишени с использованием иммобилизированных праймеров
US8715933B2 (en) 2010-09-27 2014-05-06 Nabsys, Inc. Assay methods using nicking endonucleases
US20120115132A1 (en) 2010-11-05 2012-05-10 Chromatin, Inc. Identification of centromere sequences using centromere associated proteins and uses thereof
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US11274341B2 (en) 2011-02-11 2022-03-15 NABsys, 2.0 LLC Assay methods using DNA binding proteins
AU2013274036B2 (en) * 2012-06-14 2017-08-17 Dana-Farber Cancer Institute, Inc. Genome-wide method of assessing interactions between chemical entities and their target molecules
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US6046165A (en) * 1997-06-23 2000-04-04 Ophidian Pharmaceuticals, Inc. Compositions and methods for identifying and testing TGF-β pathway agonists and antagonists
US6066452A (en) * 1997-08-06 2000-05-23 Yale University Multiplex selection technique for identifying protein-binding sites and DNA-binding proteins
US6109776A (en) * 1998-04-21 2000-08-29 Gene Logic, Inc. Method and system for computationally identifying clusters within a set of sequences

Also Published As

Publication number Publication date
JP2003508066A (ja) 2003-03-04
DE00959909T1 (de) 2005-11-10
DE60045796D1 (de) 2011-05-12
WO2001016378A2 (en) 2001-03-08
WO2001016378A3 (en) 2002-05-02
CA2383928A1 (en) 2001-03-08
EP1220949B1 (de) 2011-03-30
US6410243B1 (en) 2002-06-25
EP1220949A2 (de) 2002-07-10
WO2001016378A9 (en) 2002-11-28

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