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Evaluation of TRAP-sequencing technology with a versatile conditional mouse model

Hupe, Mike ; Li, Minerva Xueting LU ; Gertow Gillner, Karin ; Adams, Ralf H and Stenman, Jan M LU (2013) In Nucleic Acids Research 42(2).
Abstract

Gene expression profiling of various cell lineages has provided invaluable insights into the molecular mechanisms regulating cellular development and differentiation. However, in vivo molecular profiling of rare and interspersed cell populations, such as endothelial cells, has remained challenging. We have generated a versatile floxed translating ribosome affinity purification (TRAP) mouse model, mCherryTRAP, for Cre-dependent translational profiling of distinct cell lineages from intact tissues. To identify cell type-specific transcripts using TRAP, the data have to be filtered to remove both background transcripts not expressed in the profiled cell type and transcripts expressed in all cell populations of the tissue/organ. Filtering... (More)

Gene expression profiling of various cell lineages has provided invaluable insights into the molecular mechanisms regulating cellular development and differentiation. However, in vivo molecular profiling of rare and interspersed cell populations, such as endothelial cells, has remained challenging. We have generated a versatile floxed translating ribosome affinity purification (TRAP) mouse model, mCherryTRAP, for Cre-dependent translational profiling of distinct cell lineages from intact tissues. To identify cell type-specific transcripts using TRAP, the data have to be filtered to remove both background transcripts not expressed in the profiled cell type and transcripts expressed in all cell populations of the tissue/organ. Filtering has previously been achieved using transcribed RNA from the tissue/organ. Using the mCherryTRAP model, we demonstrate extensive differential expression of RNAs between the translatome and transcriptome of embryonic brains and kidneys. We evaluate the implications of these data for TRAP studies of abundant and rare cell populations. Finally, we demonstrate the applicability of the technology to study organ-specific endothelial cell differentiation.

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author
; ; ; and
publishing date
type
Contribution to journal
publication status
published
subject
keywords
Animals, Brain/embryology, Cell Differentiation, Endothelial Cells/cytology, Gene Expression Profiling, Luminescent Proteins/genetics, Mice/genetics, Models, Animal, Protein Biosynthesis, Recombinant Fusion Proteins/analysis, Sequence Analysis, RNA
in
Nucleic Acids Research
volume
42
issue
2
article number
e14
publisher
Oxford University Press
external identifiers
  • pmid:24165879
  • scopus:84892695635
ISSN
1362-4962
DOI
10.1093/nar/gkt995
language
English
LU publication?
no
id
f2b0bc24-f976-434f-9623-abfaafcb8aa6
date added to LUP
2021-08-09 12:47:14
date last changed
2024-05-18 13:28:39
@article{f2b0bc24-f976-434f-9623-abfaafcb8aa6,
  abstract     = {{<p>Gene expression profiling of various cell lineages has provided invaluable insights into the molecular mechanisms regulating cellular development and differentiation. However, in vivo molecular profiling of rare and interspersed cell populations, such as endothelial cells, has remained challenging. We have generated a versatile floxed translating ribosome affinity purification (TRAP) mouse model, mCherryTRAP, for Cre-dependent translational profiling of distinct cell lineages from intact tissues. To identify cell type-specific transcripts using TRAP, the data have to be filtered to remove both background transcripts not expressed in the profiled cell type and transcripts expressed in all cell populations of the tissue/organ. Filtering has previously been achieved using transcribed RNA from the tissue/organ. Using the mCherryTRAP model, we demonstrate extensive differential expression of RNAs between the translatome and transcriptome of embryonic brains and kidneys. We evaluate the implications of these data for TRAP studies of abundant and rare cell populations. Finally, we demonstrate the applicability of the technology to study organ-specific endothelial cell differentiation. </p>}},
  author       = {{Hupe, Mike and Li, Minerva Xueting and Gertow Gillner, Karin and Adams, Ralf H and Stenman, Jan M}},
  issn         = {{1362-4962}},
  keywords     = {{Animals; Brain/embryology; Cell Differentiation; Endothelial Cells/cytology; Gene Expression Profiling; Luminescent Proteins/genetics; Mice/genetics; Models, Animal; Protein Biosynthesis; Recombinant Fusion Proteins/analysis; Sequence Analysis, RNA}},
  language     = {{eng}},
  month        = {{10}},
  number       = {{2}},
  publisher    = {{Oxford University Press}},
  series       = {{Nucleic Acids Research}},
  title        = {{Evaluation of TRAP-sequencing technology with a versatile conditional mouse model}},
  url          = {{http://dx.doi.org/10.1093/nar/gkt995}},
  doi          = {{10.1093/nar/gkt995}},
  volume       = {{42}},
  year         = {{2013}},
}