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Analysis of polysomal enrichment and depletion of mRNA in untreated and TGF-beta treated MCF-10A and MCF7 cells

ABSTRACT: We have performed sucrose-gradient-based isolation of polysomal fractions from untreated and TGF-beta treated MCF-10A and MCF7 cells, subjected these fractions to RNA-seq, and also sequenced total mRNA from each cell line in the treated and untreated condition

ORGANISM(S): Homo sapiens

PROVIDER: GSE81955 | GEO | 2016/09/24

SECONDARY ACCESSION(S): PRJNA323495

REPOSITORIES: GEO

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Gene expression from total and polysomal RNA fractions after ATO treatment in LN229 cells.

Project description:Arsenic trioxide (ATO) treatment leads to activation of mRNA translation through the MAPK-interacting kinase (MNK) signaling pathway. Polysomal fractionation and microarray analysis allows for identification of transcripts undergoing active translation. We identified the genes differentially enriched in untreated and ATO treated fractions. In this dataset, we include expression data in untreated and ATO treated LN229 cells using either the total or polysomal RNA.

2018-01-01 | GSE100523 | GEO

Colon cancer progression-polysomal difference

Project description:Two colon cancer cell lines are under study. SW480 and SW620. The first one is derived from primary cancer, SW620 are from lymphnode metastatic sites. they both comes from the sampe patient. Polisomal RNA fractions from the two isogenic colon cancer cells lines was purified by sucrose gradient and hybridized on affymetrix hgu133a chips. this study is complementary to the series GSE1323 were total RNA was used instead. Comparison between the polysomal fraction chips and the total RNA chips is performed and the analysis proposed in a paper from the authors (at the moment in preparation). Keywords: other

2005-11-08 | GSE2509 | GEO

Transcriptome wide analysis of translation efficiency in MCF7 cells using polysome profiling with and without eIF4A inhibition by hippuristanol treatment

Project description:To identify mRNAs that are most translationally repressed following eIF4A inhibition and those that are relatively insensitive, polysome profiling was carried with and without eIF4A inhibition by hippuristanol treatment. Polysomal, sub-polysomal and total RNA was sequenced and we used a Bayesian model to identify mRNAs that with greatest confidence had shifted from the polysomal into the sub-polysomal fractions, from the sub-polysomal into the polysomal fractionsand those mRNAs that did not change in their polysomal to sub-polysomal ratio, following hipp treatment, which were termed eIF4A-dependent, eIF4A-antidependent and eIF4A-independent mRNAs respectively

2019-11-21 | GSE134888 | GEO

Translatome of aged mouse NEBD – stage oocytes determined using a new polysomal profiling method

Project description:We provide complete translatome of mouse oocytes from aged females after the breakdown of nuclear envelope (NEBD). RNAseq of polysomal and non-polysomal RNA was determined by using a novel approach combining polysomal fractionation of 200 NEBD-staged oocytes in small SW55Ti centrifugation tubes in the absence of any external spike and qRT-PCR analysis of ribosomal RNA in collected fractions. We compared these data to the translatome of same stage oocytes from young females (GSE121358). We report that genome-wide translatome profiling reveals considerable numbers of transcripts that are differentially translated in oocytes obtained from aged compared to young females. Additionally, we show the majority of aberrantly translated mRNAs in older oocytes have roles associated with cell cycle regulation. Indeed, we demonstrate the differential translation rates of four specific maternal age related transcripts (Sgk1, Castor1, Aire and Eg5) are associated with distinct localization patterns around the newly forming meiotic spindle.

2021-01-01 | GSE151836 | GEO

Transcriptome and translatome profiling of MCF7 vector cells after p53 activation

Project description:Several genome-wide transcriptome analyses that focused on p53-induced cellular responses in many cellular contexts have continued to expand the already vast p53-regulated transcriptional networks. To investigate post-transcriptional controls as an additional dimension of p53-directed gene expression responses we performed translatome analysis by polysomal profiling on MCF7 cells treated with Doxorubicin and Nutlin-3a. A comparison between the transcriptome and the translatome revealed a large number of uncoupled genes, whose transcription changes did not correlate with translation changes. Overall, we establish p53 as a master regulator of translational control and identify many p53 target genes affecting translation that can contribute to p53-dependent cellular responses. Keywords: p53, transcriptome, translatome, polysomal RNA, subpolysomal RNA, uncoupling, Doxorubicin, Nutlin-3a Total RNA (tot) was extracted from MCF7 vector cells after 16h of treatment with Doxorubicin (1.5uM) and Nutlin-3a (10uM) or DMSO (solvent, as control treatment). Polysomal profiling was performed after the same conditions. We collected all subpolysomal mRNA fractions (sub) and the polysomal ones (pol) after sucrose gradient fractionation of cytoplasmic lysates to analyze separately mRNAs that are not actively translated from those that are considered in active translation, respectively. Experiments were performed in three biological replicates.

2014-04-17 | E-GEOD-50650 | biostudies-arrayexpress

5 cell lines - Deep proteome analysis of 5 cell lines (WI38, Hep2G, MCF-10A, MDA-MB-231, MCF7), using peptide isolectic focusing fractionation.

Project description:Deep proteome analysis of 5 cell lines (WI38, Hep2G, MCF-10A, MDA-MB-231, MCF7), using peptide isolectic focusing fractionation.

2015-07-20 | PXD002400 | Pride

Temporally-regulated tRNA-derived small RNAs are associated primarily with non-polysomal fractions in Drosophila

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2018-02-12 | GSE35443 | GEO

RNA-seq analysis of MCF-10A human mammary epithelial cells following MYC activation

Project description:We profiled gene expression and splicing changes in MCF-10A human mammary epithelial cells expressing MYC fused to a portion of estrogen receptor (MYC-ER) (Eilers et al., 1989; Littlewood et al., 1995). We performed RNA-seq, in triplicate, on 3D-grown MCF-10A MYC-ER cells at 0, 8, and 24 hours (h) after 4-OHT-induced MYC activation. As a control for 4-OHT-induced effects, 3D-grown parental MCF-10A cells lacking the MYC-ER fusion protein were treated with 4-OHT at the same timepoints.

2022-07-11 | GSE181968 | GEO

Transcriptional and translational status of genes responding to drought stress

Project description:Transcriptional and translational status of genes responding to drought stress - Drought-stressed plants were compared to non-stressed plants, using total, polysomal or non-polysomal RNAs. Keywords: treated vs untreated comparison

2008-10-29 | GSE13366 | GEO

Transcription profiling of human colorectal adenocarcinoma samples transfected with a miR-10a repressor to identify candidate target genes of miR-10a

Project description:MiR-10a inhibits colon cancer invasion and metastasis. To search the candidate target genes of miR-10a, SW480 cells were transfected with miR-10a blockage to suppress miR-10a activity and the differentially expressed genes were detected by cDNA microarray analysis. Some of the up-regulated genes may be candidate target genes of miR-10a.

2009-02-20 | E-MEXP-2061 | biostudies-arrayexpress

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