WO2010138960A3 - Methods and systems for single-molecule rna expression profiling - Google Patents

Methods and systems for single-molecule rna expression profiling Download PDF

Info

Publication number
WO2010138960A3
WO2010138960A3 PCT/US2010/036833 US2010036833W WO2010138960A3 WO 2010138960 A3 WO2010138960 A3 WO 2010138960A3 US 2010036833 W US2010036833 W US 2010036833W WO 2010138960 A3 WO2010138960 A3 WO 2010138960A3
Authority
WO
WIPO (PCT)
Prior art keywords
sample
rna
microreactors
incorporation
expression
Prior art date
Application number
PCT/US2010/036833
Other languages
French (fr)
Other versions
WO2010138960A2 (en
Inventor
Xiaoliang Sunney Xie
Peter A. Sims
William J. Greenleaf
Yuichi Taniguchi
Katsuyuki Shiroguchi
Sangjin Kim
Original Assignee
President And Fellows Of Harvard College
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 President And Fellows Of Harvard College filed Critical President And Fellows Of Harvard College
Publication of WO2010138960A2 publication Critical patent/WO2010138960A2/en
Publication of WO2010138960A3 publication Critical patent/WO2010138960A3/en

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
    • C12Q1/6869—Methods for sequencing

Abstract

In general, the invention features methods and systems for expression profiling of RNA from a sample, e.g., a single cell, based on the simultaneous measurement of continuous incorporation of fluorogenic nucleotides into complementary nucleic acids. Methods for profiling RNA (e.g., of prokaryotic, eukaryotic, or viral origin) expression in a sample may include disposing, in each of a plurality of optionally sealed microreactors, a mixture in solution phase comprising a single copy of a target RNA (or DNA copy thereof) from a sample (e.g., a single cell), a nucleic acid replicating catalyst, and a mixture of nucleotides having a first nucleotide with a first label that is substantially non-fluorescent until after incorporation into a nucleic acid based on complementarity to the target; allowing continuous template-dependent replication of the targets in the microreactors; sequencing the targets in the microreactors by detecting in real time the individual incorporation of the first nucleotide during template-dependent replication by monitoring fluorescence emission resulting from the first label; and determining from the sequencing the level of expression of RNA in the sample.
PCT/US2010/036833 2009-05-29 2010-06-01 Methods and systems for single-molecule rna expression profiling WO2010138960A2 (en)

Applications Claiming Priority (2)

Application Number Priority Date Filing Date Title
US18220809P 2009-05-29 2009-05-29
US61/182,208 2009-05-29

Publications (2)

Publication Number Publication Date
WO2010138960A2 WO2010138960A2 (en) 2010-12-02
WO2010138960A3 true WO2010138960A3 (en) 2011-04-21

Family

ID=43223409

Family Applications (1)

Application Number Title Priority Date Filing Date
PCT/US2010/036833 WO2010138960A2 (en) 2009-05-29 2010-06-01 Methods and systems for single-molecule rna expression profiling

Country Status (1)

Country Link
WO (1) WO2010138960A2 (en)

Families Citing this family (5)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
WO2016191533A1 (en) * 2015-05-26 2016-12-01 The Trustees Of Columbia University In The City Of New York Rna printing and sequencing devices, methods, and systems
EP3717661A1 (en) 2017-11-27 2020-10-07 The Trustees of Columbia University in the City of New York Rna printing and sequencing devices, methods, and systems
CN111836890A (en) * 2018-03-07 2020-10-27 威斯康星校友研究基金会 High throughput nucleic acid profiling of single cells
US20210088422A1 (en) * 2018-03-23 2021-03-25 Dana-Farber Cancer Institute, Inc. Systems and methods for capturing cells
GB2605404A (en) * 2021-03-30 2022-10-05 Sumitomo Chemical Co Sequencing method

Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030104466A1 (en) * 1997-04-04 2003-06-05 Caliper Technologies Corporation Microfluidic sequencing systems
US20050064465A1 (en) * 2003-07-02 2005-03-24 Caliper Life Sciences, Inc. Continuous and non-continuous flow bioreactor
US20060275817A1 (en) * 1999-02-23 2006-12-07 Caliper Life Sciences, Inc.. Sequencing by Incorporation
WO2010017487A1 (en) * 2008-08-08 2010-02-11 President And Fellows Of Harvard College Methods and compositions for continuous single-molecule nucleic acid sequencing by synthesis with fluorogenic nucleotides

Patent Citations (4)

* Cited by examiner, † Cited by third party
Publication number Priority date Publication date Assignee Title
US20030104466A1 (en) * 1997-04-04 2003-06-05 Caliper Technologies Corporation Microfluidic sequencing systems
US20060275817A1 (en) * 1999-02-23 2006-12-07 Caliper Life Sciences, Inc.. Sequencing by Incorporation
US20050064465A1 (en) * 2003-07-02 2005-03-24 Caliper Life Sciences, Inc. Continuous and non-continuous flow bioreactor
WO2010017487A1 (en) * 2008-08-08 2010-02-11 President And Fellows Of Harvard College Methods and compositions for continuous single-molecule nucleic acid sequencing by synthesis with fluorogenic nucleotides

Also Published As

Publication number Publication date
WO2010138960A2 (en) 2010-12-02

Similar Documents

Publication Publication Date Title
Chang et al. TAIL-seq: genome-wide determination of poly (A) tail length and 3′ end modifications
GB2485850B (en) Methods and compositions for detecting copy number and chromosome aneuploidy by ligation probes and partitioning the ligated products prior to amplification
WO2020124050A1 (en) Tiled assays using crispr-cas based detection
RU2017101174A (en) KIT OR DEVICE FOR LIVER CANCER DETECTION AND DETECTION METHOD
WO2007130519A3 (en) Viral nucleic acid microarray and method of use
WO2012162267A3 (en) Nucleic acid encoding reactions
RU2017101353A (en) KIT OR DEVICE FOR DETECTING OESOPHINE CANCER AND DETECTION METHOD
WO2010117420A3 (en) Fret-labeled compounds and uses therefor
RU2017100253A (en) KIT OR DEVICE FOR DETECTING PROSTATE CANCER AND DETECTION METHOD
WO2010026488A3 (en) Methods and kits for nucleic acid sequencing
WO2010111674A3 (en) Methods and apparatus for single molecule sequencing using energy transfer detection
IS8314A (en) Determination of polynucleotide
WO2016154337A3 (en) Method for identification and enumeration of nucleic acid sequences
WO2010138960A3 (en) Methods and systems for single-molecule rna expression profiling
HRP20200321T1 (en) Detection of target nucleic acid and variants
WO2008054830A3 (en) Dna array analysis as a diagnostic for current and emerging strains of influenza
JP2017522015A5 (en)
WO2011156387A3 (en) Enumeration of nucleic acids
Clancy et al. Methods to analyze microRNA‐mediated control of mRNA translation
WO2009057829A3 (en) Nucleic acid primer set for detection of drug-resistant strain of hepatitis b virus, assay kit, and method of detecting drug-resistant strain of hepatitis b virus
RU2016104218A (en) DETERMINATION OF TARGET NUCLEIC ACID SEQUENCES BY SPLITTING A PROBING OLIGONUCLEOTIDE AND HYBRIDIZATION
JP2016537005A5 (en)
US9617606B2 (en) Oligonucleotide for HIV detection, HIV detection kit, and HIV detection method
HRP20150190T1 (en) A method for detection of human papillomavirus (hpv) type
WO2011019533A3 (en) Nucleotide capacitance measurement for low cost dna sequencing

Legal Events

Date Code Title Description
121 Ep: the epo has been informed by wipo that ep was designated in this application

Ref document number: 10781379

Country of ref document: EP

Kind code of ref document: A2

NENP Non-entry into the national phase

Ref country code: DE

122 Ep: pct application non-entry in european phase

Ref document number: 10781379

Country of ref document: EP

Kind code of ref document: A2