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Effect of cellular and viral miRNAs on target RNA half-life in three human B-cell lines

ABSTRACT: Total, nascent and unlabeled RNA were prepared following 1h of labeling with 100 µM 4-thiouridine and 3 replicates analyzed by Affymetrix Gene ST 1.0 arrays

ORGANISM(S): Homo sapiens

PROVIDER: GSE18882 | GEO | 2010/11/04

SECONDARY ACCESSION(S): PRJNA121277

REPOSITORIES: GEO

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Effect of cellular and viral miRNAs on target RNA half-life in three human B-cell lines

Project description:Total, nascent and unlabeled RNA were prepared following 1h of labeling with 100 µM 4-thiouridine and 3 replicates analyzed by Affymetrix Gene ST 1.0 arrays Transcript half-lives were determined in DG75-eGFP, DG75-10/12 and BCBL-1 based on nascent/total RNA ratios; unlabeled RNA was analyzed in addition

2010-11-04 | E-GEOD-18882 | biostudies-arrayexpress

Dissecting primary (translation independent) from secondary (translation dependent) IFN-mediated differential gene expression

2013-07-04 | GSE30457 | GEO

Explore the effect of m6A reader YTHDF1 on RNAs half-life

Project description:In order to evaluate mRNA dynamic, we performed 4SU-TT-seq to estimate RNA synthesis and degradation rates in HEK293 cell line. After 1h exposure to the nucleoside analog 4-thiouridine (4SU), 4sU is incorporated into newly transcribed RNA, and the resulting 4sU-labeled RNAs are isolated and sequenced. The sequencing results revealed that parts of mRNAs in YTHDF1 deficient cells tends to be more stable than mRNAs from wild type

2022-11-13 | GSE143994 | GEO

Dissecting primary (translation independent) from secondary (translation dependent) IFN-mediated differential gene expression

Project description:NIH-3T3 cells were pretreated for 15 min with either DMSO (mock) or cycloheximide followed by addition of either mock, 100 U/ml IFNalpha or 100 U/ml IFNgamma for 1h. During the last 30 min, 500 µM 4-thiouridine was added to cell culture medium. Total cellular RNA was isolated using Trizol reagent and nascent RNA was purified as described (Dölken et al. RNA 2008) . Three replicates of nascent RNA were analyzed by Affymetrix Mouse Gene ST 1.0 arrays Primary (translation independent) from secondary (translation dependent) IFN-mediated differential gene expression were studied in NIH-3T3 fibroblasts by studying studying differential gene expression in presence and absence of Cycloheximide (CHX). In addition, the effect of 75 min CHX during the last 30 min of treatment was studied in nascent RNA.

2013-07-04 | E-GEOD-30457 | 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

Microarray expression data from three arterial tortuosity syndrome (ATS) patients' skin fibroblasts with recessive SLC2A10 mutations

Project description:To screen for candidate genes that may contribute to the pathogenesis of ATS Transcriptome-wide expression profiling using the Affymetrix Gene 1.0 ST platform comparing the gene expression patterns of skin fibroblasts of three ATS patients with those of three healthy individuals

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MANIO: Mechanism of wild-type and mutant p53 activation and therapeutic potential in colorectal cancer

Project description:In an attempt to find new effective p53-activating agents with antitumor activity, the anti-proliferative activity of a small chemical library of 6,7-bis(hydroxymethyl)-1H,3H-pyrrolo[1,2-c]thiazoles was investigated in a panel of human cancer cells with different p53 status. The (3S)-6,7-bis(hydroxymethyl)-5-methyl-3-phenyl-1H,3H-pyrrolo[1,2-c]thiazole (MANIO) was selected due to its noticeable selectivity to cancer cells expressing p53. The IC50 values of MANIO ranged from 0.20 – 0.97 µM or 0.088 – 2.90 µM in wtp53- or mutp53-expressing cells, respectively, to 26.20 – 48.25 µM in p53-null cells.

2022-08-30 | GSE145482 | GEO

Comparisons of Affymetrix Whole-Transcript Human Gene 1.0 ST array with standard 3' expression arrays

Project description:The recently released Affymetrix Human Gene 1.0 ST array has two major differences compared with standard 3'™ based arrays: (1) it interrogates the entire mRNA transcript, and (2) it uses cDNA targets. To assess the impact of these differences on array performance, we performed series of comparative hybridizations between the Human Gene 1.0 ST and the Affymetrix HG-U133 Plus 2.0 and the Illumina HumanRef-8 BeadChip arrays. Additionally, both cRNA and cDNA targets were probed on the HG-U133 Plus 2.0 array. The results show that the overall reproducibility is best using the Gene 1.0 ST array. When looking only at the high intensity probes, the reproducibility of the Gene 1.0 ST array and the Illumina BeadChip array is equally good. Concordance of array results was assessed using different inter-platform mappings. The Gene 1.0 ST is most concordant with the HG-U133 array hybridized with cDNA targets, thus showing the impact of the target type. Agreements are better between platforms with designs which choose probes from the 3' end of the gene. Overall, the high degree of correspondence provides strong evidence for the reliability of the Gene 1.0 ST array. Keywords: Cross-platform comparison

2008-02-01 | GSE9819 | GEO

4sU-seq of HFF exposed to salt and heat stress

Project description:Primary human foreskin fibroblasts (HFF) were exposed to either salt stress (80mM KCl) or heat stress (44ºC). Newly transcribed RNA was labelled by adding 500µM 4-thiouridine (4sU) to the cell culture media for 1h. Total cellular RNA was isolated using Trizol. Newly transcribed RNA was purified following the protocol described in Raedle et al. JoVE 2013.

2018-03-08 | GSE100469 | GEO

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