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Half-life determination for human B-cells (BL41)

ABSTRACT: RNA was labeled in BL41 cells by culturing cells for 60 min in media containing 100µM 4sU. Tc-RNA was separated into nt- and p-RNA. All three RNA subsets were subjected to microarray analysis. Only probe sets providing present calls in all RNA samples/subsets were included into the analysis We used microarrays to determine half-lives of mRNAs expressed in BL41 cells Keywords: Determination of mRNA half-life in human B-cells

ORGANISM(S): Homo sapiens

PROVIDER: GSE9973 | GEO | 2009/09/30

SECONDARY ACCESSION(S): PRJNA109051

REPOSITORIES: GEO

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Transcription profiling of human B-cells (BL41) for tc-, nt- and p-RNA half-life determination

Project description:RNA was labeled in BL41 cells by culturing cells for 60 min in media containing 100ÂµM 4sU. Tc-RNA was separated into nt- and p-RNA. All three RNA subsets were subjected to microarray analysis. Only probe sets providing present calls in all RNA samples/subsets were included into the analysis; We used microarrays to determine half-lives of mRNAs expressed in BL41 cells Experiment Overall Design: RNA was labeled in BL41 cells by culturing cells for 60 min in media containing 100ÂµM 4sU. Tc-RNA was separated into nt- and p-RNA. All three RNA subsets were subjected to microarray analysis.

2009-10-20 | E-GEOD-9973 | biostudies-arrayexpress

Transcription profiling of mouse NIH-3T3 cells for tc-, nt- and p-RNA half-life determination

Project description:Data from tc-, nt- and p-RNA as well as 1 and 2h of actinomycin-D treatment (5Âµg/ml) of NIH-3T3 cells used to determine half-lives. RNA was labeled for 15, 30 or 60 minutes with 4-thiouridine. After preparation of tc-RNA, thiol-labeled RNA was biotinylated using biot-HPDP and subsequently tc-RNA was separated into nt- and p-RNA using streptavidin coated magnetic beads. All three fractions were used for microarray analysis. For actinomycin-D experiments only tc-RNA was used prepared from cell before and 1 an 2h after addition of act-D. We used microarrays to analyze the effects of 1 and 3h of IFNalpha and gamma treatment in total cellular RNA Experiment Overall Design: NIH-3T3 cells ( 5th to 15th passage after thawing) were split from confluent plates 24h before start of the experiment. At the begin of the experiment about 80% confluency was reached. The experiment was started by applying fresh, prewarmed, CO2-equilibrated medium containing either 200ÂµM 4sU (for 1h labeling), 500ÂµM 4sU (for <=30min labeling) or 5Âµg/ml actinomycin-D.

2009-10-20 | E-GEOD-10011 | biostudies-arrayexpress

Expression data from NIH-3T3 cells used for half-life determination

Project description:Data from tc-, nt- and p-RNA as well as 1 and 2h of actinomycin-D treatment (5µg/ml) of NIH-3T3 cells used to determine half-lives. RNA was labeled for 15, 30 or 60 minutes with 4-thiouridine. After preparation of tc-RNA, thiol-labeled RNA was biotinylated using biot-HPDP and subsequently tc-RNA was separated into nt- and p-RNA using streptavidin coated magnetic beads. All three fractions were used for microarray analysis. For actinomycin-D experiments only tc-RNA was used prepared from cell before and 1 an 2h after addition of act-D. We used microarrays to analyze the effects of 1 and 3h of IFNalpha and gamma treatment in total cellular RNA Keywords: determination of RNA half-lives in NIH-3T3

2009-09-30 | GSE10011 | GEO

Global RNA half lives in cyanobacteria

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2019-01-01 | GSE109174 | GEO

Global analysis of mRNA isoform half-lives: identification of stabilizing and destabilizing elements in yeast

Project description:We measured half-lives of 21,248 mRNA 3’ isoforms in yeast by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process. Interestingly, the half-lives of mRNA isoforms from the same gene, including nearly identical isoforms, often vary widely. Based on clusters of isoforms with different half-lives, we identify hundreds of sequences conferring stabilization or destabilization upon mRNAs terminating downstream. One class of stabilizing element is a polyU sequence that can interact with poly(A) tails, inhibit the association of poly(A) binding protein, and confer increased stability upon introduction into ectopic transcripts. More generally, destabilization and stabilization elements are linked to the degree to which the poly(A) tail can engage in double-stranded structures. Isoforms engineered to fold into 3’ stem-loop structures not involving the poly(A) tail exhibit even longer half-lives. We suggest that double-stranded structures at the 3’ ends are a major determinant of mRNA stability. Half-lives of 21,248 mRNA 3’ isoforms in yeast were measured by rapidly depleting RNA polymerase II from the nucleus and performing direct RNA sequencing throughout the decay process.

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2014-04-02 | GSE52286 | GEO

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2023-04-03 | GSE228592 | GEO

Half-lives mRNA analysis of Stenotrophomonas maltophilia D457 and rng-deficient mutant

Project description:We calculated half-life values of mRNAs quantified by RNA-Seq by a suitable method of normalization. We determined the half-lives of more than 2200 mRNAs in the Stenotrophomonas maltophilia D457 wild-type strain and in an isogenic RNase G deficient mutant. Median half-lives were 2,74 and 3 min in the wild-type and the rng-deficient mutant respectively. We found an overall enhancement of half-life times of mRNAs when the gene encoding RNase G is lacking, showing that many RNAs are targets of RNase G in S. maltophilia. For achieving such goal, we propose a method for the normalization of RNA-Seq based studies on global bacterial mRNA decay.

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Cell cycle mRNA half-life profiling.

Project description:mRNA half-life profiling in the bacterium Caulobacter crescentus was performed in synchronized cells collected from different stages of the cell cycle including swarmer cells, stalk cells (45 min post synchrony), and predivisional cells (90 min post synchrony). For each cell population, transcription was disrupted by the antibiotic rifampicin, and RNA samples were collected at different time points to measure the mRNA half-lives.

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