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Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Gene expression in cells expressing doxycycline-induced thymidylate synthase transgene

ABSTRACT: Gene expression was compared between a Tet-OFF transfomant expressing thymidylate synthase trasgene and its parental human colorectal cancer cell line, DLD-1, or the transformant exposed to doxycycline.

ORGANISM(S): Homo sapiens

SUBMITTER: Shinya Oda

PROVIDER: E-MTAB-3414 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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MCF7 tet-off cells treated or not with 80 ng/ml doxycycline for 12d

Project description:Tet-on and tet-off systems are among the most popular vector systems for inducible transgene expression in mammalian cells. In tet-regulated systems the expression of the transgene depends on the presence or absence of the antibiotic tetracycline or its derivative doxycycline, which are added to the cell culture medium in concentrations considered to be far below cytotoxic levels. Therefore, potential effects on the treated cells, which are exerted by the antibiotic itself and unrelated to transgene expression, are often ignored. We examined the influence of low dose doxycycline on the transcriptional profile of two independent clones of MCF7 human breast carcinoma cells, transfected with tet-off regulator and response plasmids but not harboring any transgene. Treatment with 80 ng/ml doxycycline for 12 days markedly altered gene expression in these cells. Many genes associated with interferon-signaling were up-regulated while cell cycle-associated genes were down-regulated, which was also accompanied by a reduction of cell growth. These results highlight the importance of appropriate controls when working with tet-regulated gene expression systems, to allow distinction between the effects of transgene expression and potential “side effects” of the antibiotic used for its regulation.

2011-05-20 | GSE13926 | GEO

Expression data from Î²-globin let7 HeLa tet off cells treated with doxycycline

Project description:We used microarray to determine the genes whose expression was changed at six hours after doxycycline treatment Cells were transfected with Î²-globin let7 wt constructs. Two-condition experiment; HeLa tet off cells overexpressed control vs HeLa tet off cells treated with doxycycline for six hours

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Yeast glutamine tRNA synthetase doxycycline shut-off

Project description:During protein synthesis, charged tRNAs deliver amino acids to translating ribosomes, and are then re-charged by tRNA synthetases (aaRS). In humans, mutant aaRS cause a diversity of neurological disorders, but their molecular aetiologies are incompletely characterised. To understand system responses to aaRS depletion, the yeast glutamine aaRS gene (GLN4) was transcriptionally regulated using doxycycline by tet-off control. Depletion of Gln4p inhibited growth, and induced a transcriptional GCN4 amino acid starvation response, indicative of uncharged tRNA accumulation and Gcn2 kinase activation. The GCN4 response was confirmed using SILAC proteomics, using heavy isotope labelling to identify changes in protein expression during glutamine tRNA synthetase depletion.

2020-02-12 | PXD017140 | Pride

Thymidylate synthase maintains the de-differentiated state of triple negative breast cancers

Project description:Thymidylate synthase maintains the de-differentiated state of triple negative breast cancers

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RNA-seq profiling of murine Tet-off MLL-AF9; NRAS acute myeloid leukemia at different timepoints upon doxycycline-induced MLL-AF9 down-regulation.

Project description:Using an acute myeloid leukemia (AML) mouse model driven by tet-regulated MLL-AF9 (fusion between the gene MLL1 (KMT2A/MLL) and MLLT3 (AF9)) co-expressed with oncogenic NRASG12D (Tet-off MLL-AF9), we investigated the effect of modulating the expression of the MLL-AF9 fusion oncogene on the transcriptome and proteome of established murine AML. Treatment in vitro or in vivo of these Tet-off MLL-AF9 AMLs with doxycycline (DOX) results in the efficient down-regulation of the expression of the driver oncogene MLL-AF9. RNA sequencing analysis was performed on primary Tet-Off MLL-AF9 AML cells obtained from the spleen of leukemic animals and cultured in vitro for either 2 or 4 days in the presence of doxycycline (1μg/ml) (DOX= down-regulation of MLL-AF9) or left untreated (UT).

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Transcription profiling of transgenic seeds of Medicago truncatula after introduction of mannan synthase transgene from guar

Project description:Gene expression profiling of transgenic seeds of Medicago truncatula after introduction of mannan synthase transgene from guar.

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Transcription profiling of mouse embryonic stem cells induced to express the HOXB1 transcription factor under doxycycline tet-on control

Project description:Undifferentiated mouse embryonic stem cells stably expressing the HOXB1 transcription factor under doxycycline tet-on control were differentiated into embryoid bodies. Nestin+ neuroepithelial cells were selected by transfer of the embryoid bodies to ISTFn media. Expression of HOXB1 was induced by addition of doxycycline or not induced on the seventh day of selection and also for one day after trypsination and transfer to laminin/polyornithine substrate on matrigel substrate.

2008-06-30 | E-MIMR-441 | biostudies-arrayexpress

Transcription profiling of mouse embryonic stem cells with a doxycycline-inducible Xist cDNA transgene introduced into chromosome 17

Project description:A doxycycline-inducible Xist cDNA transgene was introduced into mouse chromosome 17 at approximately 71.24Mb (NCBI Build m36). Insertion of the transgene was heterozygous, so only one copy of chromosome 17 carried the transgene, and the other chromosome 17 was wild-type. Upon doxycycline induction, the transgene is expressed, producing Xist transgene RNA which localises to autosomal material in cis, leading to silencing of genes adjacent to the transgene. Due to the heterozygous nature of transgene insertion and the cis nature of silencing, for any silenced gene, the maximum possible downregulation in expression levels was 50%. To quantify the changes in the levels of gene expression in response to Xist transgene expression, total RNA was extracted from undifferentiated and differentiated ES cells treated with doxycycline. As background control, total RNA was also prepared from uninduced cells (both undifferentiated and differentiated, cultured in parallel to doxycycline-treated cells). The total RNA was then used to make labelled cRNA, which was hybridised to an Affymetrix GeneChip Mouse Genome 430 2.0 array.

2010-05-10 | E-MEXP-2087 | biostudies-arrayexpress

Transcription profiling of mouse embryonic stem cells with a doxycycline-inducible Xist cDNA transgene introduced into chromosome 3

Project description:A doxycycline-inducible Xist cDNA transgene was introduced into mouse chromosome 3 at approximately 99.79Mb (NCBI Build m36). Insertion of the transgene was homozygous, so only one copy of chromosome 3 carried the transgene, and the other chromosome 3 was wild-type. Upon doxycycline induction, the transgene is expressed, producing Xist transgene RNA which localises to autosomal material in cis, leading to silencing of genes adjacent to the transgene. Due to the homozygous nature of transgene insertion and the cis nature of silencing, for any silenced gene, the maximum possible downregulation in expression levels was 50%. To quantify the changes in the levels of gene expression in response to Xist transgene expression, total RNA was extracted from undifferentiated and differentiated ES cells treated with doxycycline for three days. As background control, total RNA was also extracted from uninduced cells (both undifferentiated and differentiated, cultured in parallel to doxycycline-treated cells). cRNA was labelled from the total RNAs, and then hybridised to Affymetrix GeneChip Mouse Genome 430 2.0 arrays.

2010-05-10 | E-MEXP-2086 | biostudies-arrayexpress

RNA-seq analysis of DLD-1 cell lines expressing cDNAs of subunits on human mei-cohesin complexes

Project description:The study involves trabscriptome analysis using RNA-seq of stable transgenic DLD-1 cancer cell line, which express Tet-inducible combinations of mei-cohesin subunits. The following combinations of mei-cohesin genes were expressed in DLD-1 : STAG3+SMC1beta, STAG3+SMC1beta+REC8, and STAG3+SMC1beta+RAD21L The goal of the study was to investigate the RNA transcriptional response to the induction of mei-cohesin subunits in somatic cells using Tet-on inducible transgenes activated by an rtTA transgene and doxyciline.

2022-09-30 | GSE142247 | GEO

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