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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genome-wide measurement of mRNA lifetime in Escherichia coli

ABSTRACT: We measured the mRNA abundance in E.coli using RNAseq to calculate mRNA lifetimes. The data is used in support of a larger paper on the proteome and transcriptome of E.coli. Comparison of mRNA abundance over time, after the addition of transcription inhibitor, rifampicin. Center: Harvard University

ORGANISM(S): Escherichia coli

SUBMITTER: Huiyi Chen

PROVIDER: E-GEOD-21341 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Quantifying E. coli proteome and transcriptome with single-molecule sensitivity in single cells.

Taniguchi Yuichi Y Choi Paul J PJ Li Gene-Wei GW Chen Huiyi H Babu Mohan M Hearn Jeremy J Emili Andrew A Xie X Sunney XS

Science (New York, N.Y.) 20100701 5991

Protein and messenger RNA (mRNA) copy numbers vary from cell to cell in isogenic bacterial populations. However, these molecules often exist in low copy numbers and are difficult to detect in single cells. We carried out quantitative system-wide analyses of protein and mRNA expression in individual cells with single-molecule sensitivity using a newly constructed yellow fluorescent protein fusion library for Escherichia coli. We found that almost all protein number distributions can be described ...[more]

PMID: 20671182

Similar Datasets

genome-wide measurement of mRNA lifetime in Escherichia coli

Project description:We measured the mRNA abundance in E.coli using RNAseq to calculate mRNA lifetimes. The data is used in support of a larger paper on the proteome and transcriptome of E.coli.

2010-07-30 | GSE21341 | GEO

Real-time quantitative PCR analysis of gene expression in the cerebellum of MeCP2 A140V mutant mice

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-02-01 | E-GEOD-35694 | biostudies-arrayexpress

Reference Design time-course

Project description:E.coli K-12 W3110 was grown in LB medium and harvested at each time point. And time series microarray experiments were performed based on reference desgin. In reference design, the control sample is collected at one representative time point. Combining with data from sequential design, more acculate and reliable expression series could be collected. Keywords: Reference design The control sample is collected at one representative time point.

2011-03-31 | E-GEOD-6033 | biostudies-arrayexpress

Real-time quantitative PCR analysis of the expression of chromatin modification enzyme genes in 4 week-old male MeCP2 A140V mutant mouse cerebellum

Project description:The goal of this study was to identify cerebellar gene expression differences between mutant MeCP2 A140V mice and their wild type littermates.The PCR array used for these experiments was the Mouse Epigenetic Chromatin Modification Enzymes Array (Catalog# PAMM-085A) from SABiosciences. Mice used in this study were 4 week old males. Total RNA was extracted from whole cerebella of 4 week old male MeCP2 A140V hemizygous mutant mice and their wild type littermates. For this study, cerebella from 3 mice of each genotype were used and RNA from the cerebellum of each mouse was analyzed separately (ie., triplicate biological replicates). The RNA was purified to remove genomic DNA and was then reverse transcribed for use in quantitative RT-PCR analysis of gene expression using the SABiosciences RT2 profiler PCR array system. The PCR array used for these experiments was the Mouse Epigenetic Chromatin Modification Enzymes Array (Catalog# PAMM-085A).

2015-02-01 | E-GEOD-35689 | biostudies-arrayexpress

Real-time quantitative PCR analysis of the expression of chromatin modification enzyme genes in 2 week-old male MeCP2 A140V mutant mouse cerebellum

Project description:The goal of this study was to identify cerebellar gene expression differences between mutant MeCP2 A140V mice and their wild type littermates. The PCR array used for these experiments was the Mouse Epigenetic Chromatin Modification Enzymes Array (Catalog# PAMM-085A) from SABiosciences. Mice used in this study were 2 week old males. Total RNA was extracted from whole cerebella of 2 week old male MeCP2 A140V hemizygous mutant mice and their wild type littermates. For this study, cerebella from 3 mice of each genotype were used and RNA from the cerebellum of each mouse was analyzed separately (ie., triplicate biological replicates). The RNA was purified to remove genomic DNA and was then reverse transcribed for use in quantitative RT-PCR analysis of gene expression using the SABiosciences RT2 profiler PCR array system. The PCR array used for these experiments was the Mouse Epigenetic Chromatin Modification Enzymes Array (Catalog# PAMM-085A).

2015-02-01 | E-GEOD-35688 | biostudies-arrayexpress

Real-time quantitative PCR analysis of the expression of chromatin modification enzyme genes in 2 week old male MeCP2 A140V mutant mouse brain cortex

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2015-02-01 | E-GEOD-35767 | biostudies-arrayexpress

Real-time quantitative PCR analysis of the expression of chromatin modification enzyme genes in 4 week old male MeCP2 A140V mutant mouse brain cortex

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2015-02-01 | E-GEOD-35768 | biostudies-arrayexpress

Real-time quantitative PCR analysis of gene expression in the cortex of MeCP2 A140V mutant mice

Project description:This SuperSeries is composed of the SubSeries listed below. Refer to individual Series

2015-02-01 | E-GEOD-35773 | biostudies-arrayexpress

High-throughput Solexa sequencing of total RNA from Escherichia coli wild type and M-bM-^HM-^Ffnr strain (PK4854)

Project description:Investigation of whole genome gene expression level changes in a Escherichia coli MG1655 K-12 M-bM-^HM-^Ffnr mutant, compared to the wild-type strain. The mutations engineered into this strain produce a strain lacking the FNR protein. A RNA-seq study using total RNA recovered from two separate cultures of Escherichia coli MG1655 K-12 WT and two separate cultures of the M-bM-^HM-^Ffnr mutant strain.The results are further described in the article "Genome-scale Analysis of E.coli FNR Revealse the Complexity of Bacterial Regulon Structure".

2013-06-20 | E-GEOD-41190 | biostudies-arrayexpress

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Project description:This study explores the effects of prolonged stationary phase, on whole genome expression of Escherichia coli. In summary these results imply that prolonged stationary phase cells have shown less growth rate compared to fresh cells due to the low abundance of transcripts for translation initiation factor infC, and for all the seven rrn operons of 5S, 16S, 23S ribosomal RNA which further delayed in protein synthesis leading to low biomass in prolonged stationary phase cells. 28 days old E.coli cells were grown in the presence of LB broth and LB broth supplemented with 10% v/v glycerol. RNA was extracted from these samples, cDNA was prepared, fragmented cDNA was labled with labeling reagent and hybridized with Affymetrix E.coli2.0 genome array chips.Data was analysed to get the effect of glycerol on E.coli gene expression

2013-09-12 | E-GEOD-50828 | biostudies-arrayexpress

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