Transcriptional profiling of cells sorted by RNA abundance

Sandy Klemm; Stefan Semrau; Kay Wiebrands; Dylan Mooijman; Dina A Faddah; Rudolf Jaenisch; Alexander van Oudenaarden

doi:10.1038/nmeth.2910

Transcriptional profiling of cells sorted by RNA abundance

Sandy Klemm, Stefan Semrau, Kay Wiebrands, Dylan Mooijman, Dina A Faddah, Rudolf Jaenisch, Alexander van Oudenaarden

Hubrecht Institute

Research output: Contribution to journal/periodical › Article › Scientific › peer-review

28 Citations (Scopus)

Abstract

We have developed a quantitative technique for sorting cells on the basis of endogenous RNA abundance, with a molecular resolution of 10-20 transcripts. We demonstrate efficient and unbiased RNA extraction from transcriptionally sorted cells and report a high-fidelity transcriptome measurement of mouse induced pluripotent stem cells (iPSCs) isolated from a heterogeneous reprogramming culture. This method is broadly applicable to profiling transcriptionally distinct cellular states without requiring antibodies or transgenic fluorescent proteins.

Original language	English
Pages (from-to)	549-51
Number of pages	3
Journal	Nature Methods
Volume	11
Issue number	5
DOIs	https://doi.org/10.1038/nmeth.2910
Publication status	Published - May 2014

Keywords

Alleles
Animals
Cell Culture Techniques
Cellular Reprogramming
Doxycycline
Embryonic Stem Cells
Fibroblasts
Flow Cytometry
Gene Expression Profiling
Genome-Wide Association Study
Green Fluorescent Proteins
In Situ Hybridization, Fluorescence
Induced Pluripotent Stem Cells
Mice
NIH 3T3 Cells
Oligonucleotide Array Sequence Analysis
Polymerase Chain Reaction
RNA
RNA, Messenger
Transcription, Genetic
Transgenes

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10.1038/nmeth.2910

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title = "Transcriptional profiling of cells sorted by RNA abundance",

abstract = "We have developed a quantitative technique for sorting cells on the basis of endogenous RNA abundance, with a molecular resolution of 10-20 transcripts. We demonstrate efficient and unbiased RNA extraction from transcriptionally sorted cells and report a high-fidelity transcriptome measurement of mouse induced pluripotent stem cells (iPSCs) isolated from a heterogeneous reprogramming culture. This method is broadly applicable to profiling transcriptionally distinct cellular states without requiring antibodies or transgenic fluorescent proteins.",

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author = "Sandy Klemm and Stefan Semrau and Kay Wiebrands and Dylan Mooijman and Faddah, {Dina A} and Rudolf Jaenisch and {van Oudenaarden}, Alexander",

year = "2014",

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doi = "10.1038/nmeth.2910",

language = "English",

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journal = "Nature Methods",

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T1 - Transcriptional profiling of cells sorted by RNA abundance

AU - Klemm, Sandy

AU - Semrau, Stefan

AU - Wiebrands, Kay

AU - Mooijman, Dylan

AU - Faddah, Dina A

AU - Jaenisch, Rudolf

AU - van Oudenaarden, Alexander

PY - 2014/5

Y1 - 2014/5

N2 - We have developed a quantitative technique for sorting cells on the basis of endogenous RNA abundance, with a molecular resolution of 10-20 transcripts. We demonstrate efficient and unbiased RNA extraction from transcriptionally sorted cells and report a high-fidelity transcriptome measurement of mouse induced pluripotent stem cells (iPSCs) isolated from a heterogeneous reprogramming culture. This method is broadly applicable to profiling transcriptionally distinct cellular states without requiring antibodies or transgenic fluorescent proteins.

AB - We have developed a quantitative technique for sorting cells on the basis of endogenous RNA abundance, with a molecular resolution of 10-20 transcripts. We demonstrate efficient and unbiased RNA extraction from transcriptionally sorted cells and report a high-fidelity transcriptome measurement of mouse induced pluripotent stem cells (iPSCs) isolated from a heterogeneous reprogramming culture. This method is broadly applicable to profiling transcriptionally distinct cellular states without requiring antibodies or transgenic fluorescent proteins.

KW - Alleles

KW - Animals

KW - Cell Culture Techniques

KW - Cellular Reprogramming

KW - Doxycycline

KW - Embryonic Stem Cells

KW - Fibroblasts

KW - Flow Cytometry

KW - Gene Expression Profiling

KW - Genome-Wide Association Study

KW - Green Fluorescent Proteins

KW - In Situ Hybridization, Fluorescence

KW - Induced Pluripotent Stem Cells

KW - Mice

KW - NIH 3T3 Cells

KW - Oligonucleotide Array Sequence Analysis

KW - Polymerase Chain Reaction

KW - RNA

KW - RNA, Messenger

KW - Transcription, Genetic

KW - Transgenes

U2 - 10.1038/nmeth.2910

DO - 10.1038/nmeth.2910

M3 - Article

C2 - 24681693

SN - 1548-7091

VL - 11

SP - 549

EP - 551

JO - Nature Methods

JF - Nature Methods

IS - 5

ER -

Transcriptional profiling of cells sorted by RNA abundance

Abstract

Keywords

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