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Ribosome profiling on SUM159PT cells grown in vitro or in vivo

ABSTRACT: SUM159PT cells were grown either in vitro (in culture) or in vivo (mouse), after which RPL10a tagged with GFP was used to perform extraction by immoprecipitation and subsequent ribosome profiling

ORGANISM(S): Homo sapiens

PROVIDER: GSE74512 | GEO | 2016/02/17

SECONDARY ACCESSION(S): PRJNA300625

REPOSITORIES: GEO

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Ribosome profiling on SUM159PT cells grown in vitro or in vivo

Project description:SUM159PT cells were grown either in vitro (in culture) or in vivo (mouse), after which RPL10a tagged with GFP was used to perform extraction by immoprecipitation and subsequent ribosome profiling Two batches of in vitro grown cells, each having 2 replicates. Two batches of in vivo grown cells from tumors grown in two individual mice, each having tumors on left (first batch) and right side (second batch). Extraction and ribosome profiling was done independently for the two batches of samples.

2016-02-17 | E-GEOD-74512 | biostudies-arrayexpress

Profiling the endothelial translatome in vivo using ‘AngioTag’ zebrafish

Project description:We profiled the gene expression patterns of undisturbed endothelial cells in living animals using a novel ‘AngioTag’ zebrafish transgenic line that permits isolation of actively translating mRNAs from endothelial cells in their native environment. This transgenic line uses the endothelial cell-specific kdrl promoter to drive expression of an epitope tagged Rpl10a 60S ribosomal subunit protein, allowing for Translating Ribosome Affinity Purification (TRAP) of actively translating endothelial cell mRNAs. We also collected the whole embryo translatome using the TRAP protocol and a ubiquitously expressed tagged Rpl10a, and the endothelial transcritome by collecting the GFP+ endothelial cells that had the kdrl promoter driving GFP.

2019-03-29 | GSE121973 | GEO

Homo sapiens strain:SUM159PT

Project description:SUM159PT cell line transcriptome

| PRJNA224979 | ENA

The translatome of adult cortical axons is regulated by learning in vivo

Project description:Local protein synthesis has not been believed to occur in adult forebrain axons. We have used translating ribosome affinity purification (TRAP) to capture mRNA from the distal amygdaloid projections of auditory cortical axons. An eYFP-tagged ribosomal protein (rpL10a) was expressed in the adult rat auditory cortex via a lentiviral vector, and rats were given Pavlovian fear conditioning or control training two hours before collection of auditory cortex and amygdala. The eYFP tag alone was used as an IP control. Polysome extraction and eYFP immunoprecipitation were performed according to published protocols (Heiman et al., 2008 Cell 135:78; Kratz et al. 2014 Genome Res. 24:1396).

2019-12-19 | GSE124592 | GEO

A stem cell roadmap of ribosome heterogeneity reveals a function for RPL10A in mesoderm production

Project description:Recent findings suggest that the ribosome itself modulates gene expression. However, whether ribosomes change composition across cell types or control cell fate remains unknown. Here, employing quantitative mass spectrometry during human embryonic stem cell differentiation, we identify dozens of ribosome composition changes underlying cell fate specification. We observe upregulation of RPL10A/uL1-containing ribosomes in the primitive streak followed by progressive decreases during mesoderm differentiation. An Rpl10a loss-of-function allele in mice causes striking early mesodermal phenotypes, including posterior trunk truncations, and inhibits paraxial mesoderm production in culture. Ribosome profiling in Rpl10a loss-of-function mice reveals decreased translation of mesoderm regulators, including Wnt pathway mRNAs, which are also enriched on RPL10A/uL1-containing ribosomes. We further show that RPL10A/uL1 regulates canonical and non-canonical Wnt signaling during stem cell differentiation and in the developing embryo. These findings reveal unexpected ribosome composition modularity that controls differentiation and development through the specialized translation of key signaling networks.

2022-08-31 | GSE177520 | GEO

Methods comparison for ribosome profiling

Project description:Assessment of the effecacy of direction extraction of ribosome-protected mRNA fragments for ribosome profiling

2015-07-01 | GSE68008 | GEO

Gene expression profile at single cell level of SUM149PT, SUM185PE, SUM229PE, SUM159PT and SUM1315MO2 cell lines

Project description:SUM149PT, SUM185PE, SUM229PE, SUM159PT and SUM1315MO2 are triple negative breast cancer cell lines. They were sequenced to test the contrastive learning-based algorithm we developed to predict Afatinib sensitivity in TNBC.

2024-03-25 | GSE228275 | GEO

Methods comparison for ribosome profiling

Project description:Assessment of the effecacy of direction extraction of ribosome-protected mRNA fragments for ribosome profiling Immortalized human lymphocytes were analyzed by ribosome profiling protocols with or without ribosome purification

2015-07-01 | E-GEOD-68008 | biostudies-arrayexpress

Gene expression profiling of MDA231, BT549, and SUM159PT cells after selumetinib treatment or DUSP4 siRNA knockdown

Project description:MDA231, BT549, and SUM159PT basal-like breast cancer cell lines were transfected with non-targeting siRNA (siCONTROL), siRNA targeting DUSP4 (siDUSP4), or siCONTROL + 4 or 24 hr of 1uM selumetinib. Cells were harvested at 96 hr post-siRNA transfection. Data were Log2 RMA normalized.

2013-09-03 | GSE41816 | GEO

RNA-seq profiling of the Tg(myo6b:GFP-2A-rpl10a-3xHA) zebrafish hair cell IP vs. whole fish IN

Project description:We have developed and tested the efficiency of the Tg(myo6b:GFP-2A-rpl10a-3xHA) zebrafish to specifically enrich for and evaluate the translatome of inner ear and lateral line sensory hair cells (IP) compared to the whole fish transcriptome (IN). We show through RNA-seq that HA-tagged ribosome immunoprecipitation significantly enriches for RNA transcripts of known zebrafish hair cell expressed transcripts.

2018-04-24 | GSE102861 | GEO

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