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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Protrusion vs cell-body mRNA analysis by RNA-seq

ABSTRACT: We quantified the distribution of cellular mRNAs between protrusions and cell-body of MDA-MB-231 breast carcinoma cells by RNA-seq, using a filter based fractionation method. In this method, cells are seeded on top of 3micrometer transwell filters to enable protrusions to form but to prevent the cell-bodies passing through due to the small size of the pores, thus resulting in separation of protrusions and cell-bodies on opposite sides of the filter, from which RNA can be prepared separately. RNA samples for Illumina sequencing were generated in duplicates from two biological replicate experiments (two protrusions and two cell-body).

INSTRUMENT(S): Illumina HiSeq 2000

ORGANISM(S): Homo sapiens

SUBMITTER: Faraz Mardakheh

PROVIDER: E-MTAB-2546 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Combining transcriptome and proteome analysis to identify and characterize the RpoS regulon in Pseudomonas fluorescens

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2019-11-12 | PXD010845 | Pride

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Quantitative proteomics analysis of actin-rich protrusions and cell-bodies in migratory cells

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2020-10-20 | PXD021239 | Pride

QUANTSEQ 3' sequencing of protrusions and cell bodies of control (NT) or LARP6 siRNA (LARP6 KD) transfected MDA-MB231 breast cancer cells

Project description:To assess how LARP6 affects mRNA localisation to cell-protrusions, we transfected MDA-MB231 cells with either non-targeting control siRNA or LARP6 siRNA for 72 hrs, before fractionating the cells into protrusion and cell-bodies, and analysed total RNA from each fraction via Lexogen QUANTSEQ FWD 3' mRNA sequencing. Protrusion induction was done for 2 hrs on 3 micron transwell filters (Corning). The experiment was performed twice using two independent batches of cells, and sequencing was carried out on an Illumina NextSeq 500 sequencer.

2020-10-30 | E-MTAB-9520 | biostudies-arrayexpress

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Protrusion vs Cell-body pulsed-SILAC proteomics

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2015-10-09 | PXD002649 | Pride

Random-primed mRNA-sequencing transcriptomic dataset for 70 primary human cardiomyocyte cell samples

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