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DE60045796D1 - Gesamt-chromosom analyse von protein-dns wechselwirkungen - Google Patents

Gesamt-chromosom analyse von protein-dns wechselwirkungen

Info

Publication number
DE60045796D1
DE60045796D1 DE60045796T DE60045796T DE60045796D1 DE 60045796 D1 DE60045796 D1 DE 60045796D1 DE 60045796 T DE60045796 T DE 60045796T DE 60045796 T DE60045796 T DE 60045796T DE 60045796 D1 DE60045796 D1 DE 60045796D1
Authority
DE
Germany
Prior art keywords
protein
cell
genomic dna
dns
interactions
Prior art date
Legal status (The legal status 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 status listed.)
Expired - Lifetime
Application number
DE60045796T
Other languages
English (en)
Inventor
John Wyrick
Richard A Young
Francois Robert
Current Assignee (The listed assignees may be inaccurate. Google has not performed a legal analysis and makes no representation or warranty as to the accuracy of the list.)
Whitehead Institute for Biomedical Research
Original Assignee
Whitehead Institute for Biomedical Research
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 Institute for Biomedical Research filed Critical Whitehead Institute for Biomedical Research
Application granted granted Critical
Publication of DE60045796D1 publication Critical patent/DE60045796D1/de
Anticipated expiration legal-status Critical
Expired - Lifetime legal-status Critical Current

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)
  • Organic Chemistry (AREA)
  • Engineering & Computer Science (AREA)
  • Immunology (AREA)
  • Wood Science & Technology (AREA)
  • Analytical Chemistry (AREA)
  • Zoology (AREA)
  • Proteomics, Peptides & Aminoacids (AREA)
  • Molecular Biology (AREA)
  • Microbiology (AREA)
  • General Health & Medical Sciences (AREA)
  • Biotechnology (AREA)
  • Biochemistry (AREA)
  • Physics & Mathematics (AREA)
  • Bioinformatics & Cheminformatics (AREA)
  • General Engineering & Computer Science (AREA)
  • Biophysics (AREA)
  • Genetics & Genomics (AREA)
  • Biomedical Technology (AREA)
  • Urology & Nephrology (AREA)
  • Pathology (AREA)
  • Hematology (AREA)
  • Food Science & Technology (AREA)
  • Tropical Medicine & Parasitology (AREA)
  • General Physics & Mathematics (AREA)
  • Medicinal Chemistry (AREA)
  • Cell Biology (AREA)
  • Chemical Kinetics & Catalysis (AREA)
  • Measuring Or Testing Involving Enzymes Or Micro-Organisms (AREA)
  • Investigating Or Analysing Biological Materials (AREA)
  • Peptides Or Proteins (AREA)
DE60045796T 1999-09-01 2000-09-01 Gesamt-chromosom analyse von protein-dns wechselwirkungen Expired - Lifetime DE60045796D1 (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
DE60045796D1 true DE60045796D1 (de) 2011-05-12

Family

ID=22541045

Family Applications (2)

Application Number Title Priority Date Filing Date
DE60045796T Expired - Lifetime DE60045796D1 (de) 1999-09-01 2000-09-01 Gesamt-chromosom analyse von protein-dns wechselwirkungen
DE2000959909 Pending DE00959909T1 (de) 1999-09-01 2000-09-01 Gesamt-chromosom analyse von protein-dns wechselwirkungen

Family Applications After (1)

Application Number Title Priority Date Filing Date
DE2000959909 Pending DE00959909T1 (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) DE60045796D1 (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
US20050079492A1 (en) * 2000-09-12 2005-04-14 Burgess Jr. Robert M. Micro-arrayed 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
WO2005007814A2 (en) * 2003-07-03 2005-01-27 The Regents Of The University Of California Genome mapping of functional dna elements and cellular proteins
US8222005B2 (en) * 2003-09-17 2012-07-17 Agency For Science, Technology And Research Method for gene identification signature (GIS) analysis
US20050239106A1 (en) * 2003-11-26 2005-10-27 Whitehead Institute For Biomedical Research Transcriptional regulators and methods thereof
US8321138B2 (en) * 2005-07-29 2012-11-27 Agilent Technologies, Inc. Method of characterizing quality of hybridized CGH arrays
US20070031883A1 (en) * 2004-03-04 2007-02-08 Kincaid Robert H Analyzing CGH data to identify aberrations
EP1721012A2 (de) * 2004-03-04 2006-11-15 Whitehead Institute For Biomedical Research Biologisch aktive dna-bindungsstellen und verfahren in verbindung damit
US20050282193A1 (en) * 2004-04-23 2005-12-22 Bulyk Martha L Space efficient polymer sets
US20060035251A1 (en) * 2004-06-30 2006-02-16 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
JP2009500033A (ja) * 2005-07-06 2009-01-08 フォルスカルパテント・アイ・ウプサラ・エービー 核酸付随分子及び修飾の局在化方法
US20090221428A1 (en) * 2005-09-07 2009-09-03 Young Richard A Methods of Genome-Wide Location Analysis in Stem Cells
WO2007041621A2 (en) * 2005-10-03 2007-04-12 Xingsheng Sean Ling Hybridization assisted nanopore sequencing
US7556921B2 (en) * 2005-12-02 2009-07-07 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
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
US7881876B2 (en) * 2006-10-12 2011-02-01 Agilent Technologies, Inc. Methods and systems for removing offset bias in chemical array data
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
EP2126075A2 (de) * 2007-01-16 2009-12-02 Cytocure, Inc. Verfahren zur isolierung und reinigung nukleinsäurebindender biomoleküle und zusammensetzungen damit
US8278047B2 (en) 2007-10-01 2012-10-02 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
EP2342362B1 (de) * 2008-09-03 2017-03-01 Nabsys 2.0 LLC Verwendung von längseits versetzten nanogrossen elektroden zur spannungsmessung von biomolekülen und anderen analyten in fluidischen kanälen
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
EP3216874A1 (de) 2008-09-05 2017-09-13 TOMA Biosciences, Inc. Verfahren zum stratifizieren und annotieren der behandlungsoptionen eines krebsmedikaments
US9309556B2 (en) 2010-09-24 2016-04-12 The Board Of Trustees Of The Leland Stanford Junior University Direct capture, amplification and sequencing of target DNA using immobilized primers
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
WO2012067911A1 (en) 2010-11-16 2012-05-24 Nabsys, Inc. Methods for sequencing a biomolecule by detecting relative positions of hybridized probes
US11274341B2 (en) 2011-02-11 2022-03-15 NABsys, 2.0 LLC Assay methods using DNA binding proteins
EP2861988B1 (de) 2012-06-14 2019-05-22 The Whitehead Institute for Biomedical Research Genomweites verfahren zur bestimmung der interaktion von chemischen entitäten und deren zielmolekülen
US20140087390A1 (en) 2012-09-26 2014-03-27 Nabsys, Inc. Method and system for analysis of protein and other modifications on dna and rna
US9914966B1 (en) 2012-12-20 2018-03-13 Nabsys 2.0 Llc Apparatus and methods for analysis of biomolecules using high frequency alternating current excitation
WO2014113557A1 (en) 2013-01-18 2014-07-24 Nabsys, Inc. Enhanced probe binding

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US4882269A (en) * 1985-12-13 1989-11-21 Princeton University Amplified hybridization assay
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
EP1220949B1 (de) 2011-03-30
CA2383928A1 (en) 2001-03-08
JP2003508066A (ja) 2003-03-04
WO2001016378A2 (en) 2001-03-08
WO2001016378A3 (en) 2002-05-02
EP1220949A2 (de) 2002-07-10
ATE503843T1 (de) 2011-04-15
US6410243B1 (en) 2002-06-25
DE00959909T1 (de) 2005-11-10
WO2001016378A9 (en) 2002-11-28

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