The DOI matches its Crossref record; 33 of the 33 references it cites were found in a registry or an index; 5 of the 34 sources its claims cite were checked for support.
Quantifying E. coli Proteome and Transcriptome with Single-Molecule Sensitivity in Single Cells
Open accessAbstract
Devil in the Detail: Genetically identical cells in the same environment can show variation in gene expression that may cause phenotypic variation at the single-cell level. But how noisy are most genes? Taniguchi et al. (p. 533 ; see the Perspective by Tyagi ) now report single-cell global profiling of both messenger RNA (mRNA) and proteins in Escherichia coli using a yellow fluorescent protein fusion library. As well as a common extrinsic noise in high-abundance proteins, large fluctuations were observed in low-abundance proteins. Remarkably, in single-cell experiments, mRNA and protein levels for the same gene were uncorrelated.
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Claims the paper makes
13 No full text of the sources · 10 Own result · 7 Own interpretation · 3 Own method · 1 Supported so far · 1 Partly supported · 1 Couldn’t confirm · 1 Not checked yet · 1 No basis given · accuracy not yet measured
The cited sources support only part of this claim — read each source’s verdict below.
In the paper
“Such stochasticity is manifested in fluctuations of mRNA and protein copy numbers within a cell lineage over time, and in variations of mRNA and protein copy numbers among a population of genetically identical cells at a particular time (1, 2, 3, 4).”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Abstract
What the sources say
- Not checked — no full text of the sourcecites [1] source
- Partly supportedcites [2] sourceExperimental — accuracy not yet measured
The Abstract says stochastic gene expression can produce variation among identical cells, and its model predicts cell-to-cell variability in mRNA levels for both eukaryotic and prokaryotic promoters. However, the paper's single-cell protein-reporter measurements were made in yeast, not bacteria; it does not establish that both protein and mRNA copy numbers differ among individual bacterial cells. (LLM, conf=0.83)
- Not checked — no full text of the sourcecites [3] source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
The cited sources that could be checked couldn’t confirm or dispute this claim.
In the paper
“Single molecule sensitivity was confirmed by abrupt photobleaching of membrane-bound YFPs expressed at low level (Fig. S14) (8, 18, 23).”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Single-molecule imaging of a YFP reporter library
What the sources say
- Not checked — no full text of the sourcecites [8] source
- Not checked — no full text of the sourcecites [18] source
- Could not verifycites [23] sourceExperimental — accuracy not yet measured
The Results and discussion passage on deletion-mutant verification describes PCR checks, while Materials and methods > Growth tests describes absorbance measurements; neither addresses single-molecule imaging. Searches for photobleaching, membrane-bound YFP, and fluorescence imaging found no passage confirming the claimed sensitivity test. Page numbers were not available in our copy. (LLM, conf=0.78)
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
In the paper
“We found that E. coli proteins generally had larger noise and Fano factors than yeast proteins, even for those present at similar copy numbers (Fig. S6) (18).”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Comparison between E. coli and yeast
What the sources say
- Not checked — no full text of the sourcecites [18] source
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Furthermore, we found that in a single cell mRNA and protein levels for the same gene are completely uncorrelated.”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Conclusion
plain- Asserted: passes — The authors put it forward as true.
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In the paper
“The distributions for 1,009 out of the 1,018 strains can be well fit by the gamma distribution, Eq. 2 (Fig. S20) (18).”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Analysis of protein distributions
What the sources say
- Not checked — no full text of the sourcecites [18] source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Below ten molecules per cell, ηp2 is inversely proportional to protein abundance, indicative of intrinsic noise.”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Global scaling of intrinsic and extrinsic protein noise
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“mRNA and protein copy numbers in a single cell are not correlated (r = 0.01 ± 0.03, SEM, N = 5,447).”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Simultaneous RNA and protein measurements in single cells
plainn = 5,447- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The protein noise (ηp2 ≡ σp2/μp2) exhibits two distinct scaling properties (Fig. 2B).”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Global scaling of intrinsic and extrinsic protein noise
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The average protein abundances of essential genes are higher than those for all genes.”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Single-molecule imaging of a YFP reporter library
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Average protein abundances span five orders of magnitude, ranging from 10-1 to 104 molecules per cell (Fig 2A).”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Single-molecule imaging of a YFP reporter library
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
- It may state two separate claims as one. 13
- Probably not a substantial claim. 3
The sources with a verdict support this claim; the rest weren’t checked yet, have no full text we could read, or their verdicts aren’t rated yet.
In the paper
“In recent years, single-molecule fluorescence microscopy has been used to count mRNA (12-16) or protein (8, 17) molecules in individual cells, especially in bacteria. However, these methods have only been applied to limited number of specific genes.”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Abstract
What the sources say
- Not checked — no full text of the sourcecites [12] source
- Supportedcites [13] source
The Results section (page not available) describes fluorescence microscopy used to count individual mRNA molecules from a specific reporter gene in mammalian cells. This paper supports the mRNA-counting citation as an example; the sentence’s broader reference to bacteria does not describe this study. (LLM, conf=0.88)
- Not checked — no full text of the sourcecites [14] source
- Supportedcites [15] source
The passage labeled Abstract describes using fluorescence in situ hybridization and microscopy to count individual comK mRNA molecules in single Bacillus subtilis cells. It also describes counting an engineered comK transcript, making this paper an example of the gene-specific, single-cell mRNA measurements for which it is cited. (LLM, conf=0.91)
- Supportedcites [16] source
The Abstract reports counting individual mRNAs in single yeast cells for different genes. The Discussion describes extending the method to analyze multiple genes simultaneously as future work. This paper supports the mRNA-counting example for which it is cited; the sentence assigns protein counting to other citations. (LLM, conf=0.91)
- Not checked — no full text of the sourcecites [8] source
- Not checked — no full text of the sourcecites [17] source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“In contrast, at higher expression levels (>10 molecules per cell), the noise reaches a plateau of ∼0.1 and does not decrease further, suggesting that each protein has at least 30% variation in its expression level.”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Global scaling of intrinsic and extrinsic protein noise
hedgedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“We found that the noise floor does not result from cell size effects, nor did it arise from measurement noise (18).”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Global scaling of intrinsic and extrinsic protein noise
What the sources say
- Not checked — no full text of the sourcecites [18] source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We discovered large fluctuations in low abundance proteins as well as a common extrinsic noise in high abundance proteins.”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Conclusion
plaincorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- The authors state this as an assumption: The transcription and translation rates a and b have static or slowly varying heterogeneous distributions f(a) and g(b) across cells.
A result the paper reports from its own data — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“We further demonstrate that the extrinsic noise is global to all high expression genes by analyzing the correlations between expression levels of 13 pairs of randomly selected genes.”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Global scaling of intrinsic and extrinsic protein noise
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- The authors state this as an assumption: The transcription and translation rates a and b have static or slowly varying heterogeneous distributions f(a) and g(b) across cells.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“The prevalence of proteins with very low copy number suggests that single-molecule experiments are necessary for bacteriology.”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Single-molecule imaging of a YFP reporter library
hedgeddirect- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“This striking result highlights the disconnect between proteome and transcriptome analyses of a single cell, as well as the need for single cell proteome analysis.”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Conclusion
boostedcorrelational- Asserted: passes — The authors put it forward as true.
- Checkable: unclear — It is unclear whether it could be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A claim is checked only against the cited paper’s full text, never its abstract, and none is available for its sources.
In the paper
“A fluorescent protein reporter library of Saccharomyces cerevisiae (9) has proven to be extremely useful in protein profiling (10, 11).”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Abstract
What the sources say
boosted- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: fails — The paper’s conclusions may not depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. The paper’s conclusions may not depend on it.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“However, our result offers a cautionary note in interpreting single-cell transcriptome analysis and argues for the necessity for single cell proteome analysis.”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Simultaneous RNA and protein measurements in single cells
plain- Asserted: passes — The authors put it forward as true.
- Checkable: fails — It may be too vague to check against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
Probably not a substantial claim. It may be too vague to check against evidence. It may state two separate claims as one.
In the paper
“We attribute the additional noise to extrinsic noise (3), that is the slow variation of the values of a and b, which we confirm with real time observation of protein levels for four randomly selected high copy library strains.”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Global scaling of intrinsic and extrinsic protein noise
What the sources say
- Not checked — no full text of the sourcecites [3] source
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
- The authors state this as an assumption: The transcription and translation rates a and b have static or slowly varying heterogeneous distributions f(a) and g(b) across cells.
A conclusion the paper draws from its own results — it cites no other source for it, so there is none to check. The quote shows it is in the paper.
In the paper
“Given that some proteins and most mRNAs of functional genes are present at low copy numbers in a bacterial cell, the single molecule sensitivity afforded by our measurements is necessary for the understanding of stochastic gene expression and regulation.”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Conclusion
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
None of the sources cited for this claim have been checked yet.
In the paper
“In E. coli, mRNA is typically degraded within minutes (Table S6) (18), whereas most proteins, including fluorescent proteins, have a lifetime longer than the cell cycle (34).”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Simultaneous RNA and protein measurements in single cells
What the sources say
- Not checked — no full text of the sourcecites [18] source
- Not matchedcites [34]
Couldn’t be matched to a paper in Crossref, so it can’t be checked.
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
What the paper did — it cites no source for this, so there is none to check. The quote shows it is in the paper.
In the paper
“Out of the 1,400 strains attempted, 1,018 strains were confirmed by sequencing and showed no significant growth defects.”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Single-molecule imaging of a YFP reporter library
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: unclear — It is unclear whether the paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
In the paper
“Because the same probe is used for all strains, the optimized hybridization efficiency is unbiased for every measured gene (18).”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Single-molecule RNA counting
What the sources say
- Not checked — no full text of the sourcecites [18] source
plain- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
A claim is checked only against the cited paper’s full text, never its abstract, and none is available for its sources.
In the paper
“While single cell mRNA profiling has been carried out with cDNA microarray (6) and mRNA-seq (7), these studies did not have single molecule sensitivity and are not suitable for bacteria, which express mRNA at low copy numbers (8).”
§ Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells** > Abstract
What the sources say
plaindirect- Asserted: passes — The authors put it forward as true.
- Checkable: passes — It can be checked against evidence.
- Load-bearing: passes — The paper’s conclusions depend on it.
- Based: passes — The paper gives a reason why it holds.
It may state two separate claims as one.
The authors state this as an assumption.
Gene expression dynamics follow a kinetic scheme with transcription, translation, mRNA degradation, and protein degradation rates.
“We consider the kinetic scheme”
The authors state this as an assumption.
The transcription and translation rates a and b have static or slowly varying heterogeneous distributions f(a) and g(b) across cells.
“Assuming that there exist static or slowly varying heterogeneities of a and b, with distributions f (a) and g(b), respectively, the protein distribution is”
Claims other papers make about this one
Each is checked against this paper’s own text: does it say what the citing paper says it does?
The source backs part of the claim, not all of it — or backs it for a different population, condition or comparison.
In the citing paper
“Stochastic simulations are necessary when reactions involving few particles such as those in genetic information processing and the charging of the tRNAs can lead to large variations in the state of the cell (Taniguchi et al., 2010).”
From Fundamental behaviors emerge from simulations of a living minimal cell (2022) · cites this paper as Taniguchi et al., 2010
Experimental — accuracy not yet measuredThe cited source says what the claim attributes to it.
In the citing paper
“Although transcriptomic profiling has provided insights into Tex cell biology, mRNA abundance is not always a faithful proxy of protein expression across various organisms18–22.”
From Proteotoxic stress response drives T cell exhaustion and immune evasion (2025) · cites this paper as [22]
In the citing paper
“This finding contrasts with data from bacteria where productive protein expression is achieved with such low mRNA concentrations (Taniguchi et al., 2010).”
From Quantitative Analysis of Fission Yeast Transcriptomes and Proteomes in Proliferating and Quiescent Cells (2012) · cites this paper as Taniguchi et al., 2010
In the citing paper
“These methods hold promise for elucidating the epigenetic controls of cellular identity186,187.”
From Revealing the vectors of cellular identity with single-cell genomics (2016) · cites this paper as [187]
Citations
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Analytical Techniques for Single-Cell Studies in Microbiology
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Gene-Drug Interactions and the Evolution of Antibiotic Resistance
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Sparse learning of Markovian population models in random environmentsPreprint
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“[2014]) and furthermore, appears plausible in the context of gene expression Taniguchi et al. [2010]. Throughout the remaining paper we assume”
BackgroundCYANIDIALES ECOLOGY: BIODIVERSITY AND TRANSCRIPTOMICS IN YELLOWSTONE NATIONAL PARK
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Empirical noise-mean fitness landscapes and the evolution of gene expressionPreprint
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“Unfortunately, transcription and translation do not always correlate [51] or are at least time-delayed [52] and conclusions can be challenging.”
BackgroundMathematical Models of Gene ExpressionPreprint
Robert, P. (2019) · arXiv (Cornell University) · doi:10.48550/arxiv.1905.02578 · Cited by 1
“See Taniguchi [37].”
Adiabatic reduction of a model of stochastic gene expression with jump Markov processPreprint
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Elf, J., & Barkefors, I. (2018) · arXiv (Cornell University) · doi:10.48550/arxiv.1809.03265 · Cited by 1
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“and fluorescence microscopy, one usually obtains data of protein concentrations, instead of protein copy numbers [11]. Let V >0 be a scaling parameter which usually denotes the average cell volume [30] or maximal protein copy number [31, 32], and let X V(t) = N(t)=V denote the concentration of the protein at time t…”
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Metadata
- Authors
- Taniguchi, Y., Choi, P. J., Li, G.-W., Chen, H., Babu, M., Hearn, J., Emili, A., & Xie, X. S.
- Affiliations
- Harvard University (US)
- University of Toronto (CA)
- Corresponding author
- Taniguchi, Yuichi
- Choi, Paul J.
- Li, Gene-Wei
- Chen, Huiyi
- Xie, X. Sunney
- Venue
- Science
- Published
- 2010-07-30
- Volume
- 329
- Issue
- 5991
- Pages
- 533-538
- ISSN
- 0036-8075 (ISSN-L)
- 1095-9203
- PMC
- PMC2922915
- OpenAlex
- W2053460598
- Cited by
- 1,982
- References
- 33
- Citations by year
- 2026: 60 · 2025: 77 · 2024: 85 · 2023: 91 · 2022: 102 · 2021: 110 · 2020: 122 · 2019: 127 · 2018: 153 · 2017: 117 · 2016: 158 · 2015: 157 · 2014: 156 · 2013: 171 · 2012: 161
- FWCI
- 60.66
- Type
- journal article
- Language
- en
- Open access
- green
- www.ncbi.nlm.nih.gov
- Locations
- Science (publishedVersion)
- PubMed (publishedVersion)
- PubMed Central (acceptedVersion)
- Funders
- National Institutes of Health (DP1OD000277)
- Canadian Institutes of Health Research (77639_1)
- Topics
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Gene Regulatory Network Analysis
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Biophysics › Advanced Fluorescence Microscopy Techniques
- Life Sciences › Biochemistry, Genetics and Molecular Biology › Genetics › Bacterial Genetics and Biotechnology
- Keywords
- Escherichia coli, single-cell proteomics, single-cell transcriptomics, gamma distribution, transcription rate, extrinsic noise, intrinsic noise, mRNA-protein correlation, gene expression variation
- MeSH terms
- Escherichia coli, Luminescent Proteins, Microscopy, Fluorescence, RNA, Bacterial, RNA, Messenger, Saccharomyces cerevisiae, Transcription, Genetic, Protein Biosynthesis, Gene Library, Gene Expression, In Situ Hybridization, Fluorescence, Proteome, Gene Expression Profiling, RNA Stability, Escherichia coli Proteins, Microfluidic Analytical Techniques
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