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Transcription profiling of membrane-bound and cytosolic polysomes isolated from human MCF-7 cells

ABSTRACT: RNA from MCF-7 cells was fractionated by sucrose density gradient centrifugation to separate RNA associated with membrane-bound polysomes from RNA associated with free polysomes. These two populations were hybridized in triplicate to U133A microarrays.

ORGANISM(S): Homo sapiens

SUBMITTER: Carol Westbrook

PROVIDER: E-GEOD-1400 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Publications

Membrane-associated and secreted genes in breast cancer.

Stitziel Nathan O NO Mar Brenton G BG Liang Jie J Westbrook Carol A CA

Cancer research 20041201 23

The identification of membrane-associated and secreted genes that are differentially expressed is a useful step in defining new targets for the diagnosis and treatment of cancer. Extracting information on the subcellular localization of genes represented on DNA microarrays is difficult and is limited by the incomplete sequence and annotation that is available in existing databases. Here we combine a biochemical and bioinformatic approach to identify membrane-associated and secreted genes express ...[more]

PMID: 15574777

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MCF-7 Fractionated RNA

Project description:RNA from MCF-7 cells was fractionated by sucrose density gradient centrifugation to separate RNA associated with membrane-bound polysomes from RNA associated with free polysomes. These two populations were hybridized in triplicate to U133A microarrays. Keywords: repeat sample

2004-12-01 | GSE1400 | GEO

Translatome analysis of TRM6/61 overexpressing C6 rat cells.

Project description:Lysates from control or Trm6/61 overexpressing cells were fractionated on sucrose gradient to isolate polysomes. RNA extracted from heavy polysomal fractions was analyzed by microarray versus total RNA

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Project description:H1s are induced to differentiate into the trophoblast (TE) lineage, and polysome analysis performed at 0hr (Undifferentiated), 12hr TE and 24hr TE. The whole cell extract (WCE) is a cytoplasmic lysate of the cell . G1-G4 represent RNAs that were found in different fractions of a sucrose gradient, which represents monosomes, polysomes, etc. Thus the WCE is used as the denominator so that for a particular transcript, we can express G1, for example, as a fraction of the total RNA.

2014-07-21 | E-MTAB-1653 | biostudies-arrayexpress

Comparative analysis of mRNA distribution in heavy and light polysomes in wild type and Dicer1 knockout cells

Project description:To gain a global view of translational inhibition by microRNA (miRNA), we isolated polysomes from wild type and Dicer1 knockout HCT116 human cells using sucrose gradient fractionation technique. The polysome fraction was separated into light (9mer or less) and heavy (10mer or more) subfractions. RNA samples were extracted from both subfractions and subjected to RNA-seq analysis. A general shift from light to heavy subfractions was detected for miRNA targted mRNAs.

2020-05-21 | GSE134818 | GEO

Transcription profiling by array of membrane-bound and cytosolic polysomes from Homo sapiens MCF-7 cells

| S-ECPF-GEOD-1400 | biostudies-other

Polysomes

2013-04-05 | E-GEOD-45797 | biostudies-arrayexpress

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

Project description: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

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Translatome and transcriptome profiling of FK866 response in Jurkat cells

Project description:We treated Jurkat cells for 48 hr with a sublethal dose of FK866 (5 nM) and DMSO (Mock, control treatment). RNA samples for microarrays derived from fractionated samples by sucrose gradient (sub-polysomes, polysomes), giving us the chance to perform an analysis among polysomal/subpolysomal distribution in treated or untreated cells and the possibility to identify the multi-level gene expression regulation effects of FK866. We are interested to find differentially expressed genes, in the early phase of cell response to FK866, and genes that account for a specific post-transcriptional regulation exerted by the cell in response to the drug. Keywords: polysomal profiling, translatome profiling, polysomal RNA, subpolysomal RNA, translational profiling, polysome profiling, post-transcriptional regulation, FK866, translational efficiency.

2015-04-01 | GSE53772 | GEO

Ribosome profiling on polysomes extracted via sucrose gradient and IP

Project description:Technical feasibility study to determine data quality and reproducibilty. Ribosome profiling was performed by either sucrose gradient (SG) or immunoprecipitation (IP).

2016-02-17 | GSE74511 | GEO

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