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Transcriptome profiling of HEK 293T cells depleted of endogenous miRNAs

ABSTRACT: To assess the impact of AdV-VP55 mediated degredation of host miRNAs on the cellular transcriptome.

ORGANISM(S): Homo sapiens

PROVIDER: GSE73718 | GEO | 2016/01/30

SECONDARY ACCESSION(S): PRJNA297763

REPOSITORIES: GEO

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Small RNA deep sequencing of HEK 293T cells treated with an Adeno vector encoding the Vaccinia virus VP55 protein

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Project description:This SuperSeries is composed of the SubSeries listed below.

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Transcriptome profiling of HEK 293T cells and BJ foreskin fibroblasts depleted of endogenous miRNAs

Project description:Transcriptome profiling of HEK 293T cells and BJ foreskin fibroblasts depleted of endogenous miRNAs

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Tumorigenic effects of TLX overexpression in HEK 293T cells.

Project description:BackgroundThe human orphan receptor TLX (NR2E1) is a key regulator of neurogenesis, adult stem cell maintenance, and tumorigenesis. However, little is known about the genetic and transcriptomic events that occur following TLX overexpression in human cell lines.AimsHere, we used cytogenetics and RNA sequencing to investigate the effect of TLX overexpression with an inducible vector system in the HEK 293T cell line.Methods and resultsConventional spectral karyotyping was used to identify chromosomal abnormalities, followed by fluorescence in situ hybridization (FISH) analysis on chromosome spreads to assess TLX DNA copy number. Illumina paired-end whole transcriptome sequencing was then performed to characterize recurrent genetic variants (single nucleotide polymorphisms (SNPs) and indels), expressed gene fusions, and gene expression profiles. Lastly, flow cytometry was used to analyze cell cycle distribution. Intriguingly, we show that upon transfection with a vector containing the human TLX gene (eGFP-hTLX), an isochromosome forms on the long arm of chromosome 6, thereby resulting in DNA gain of the TLX locus (6q21) and upregulation of TLX. Induction of the eGFP-hTLX vector further increased TLX expression levels, leading to G0-G1 cell cycle arrest, genetic aberrations, modulation of gene expression patterns, and crosstalk with other nuclear receptors (AR, ESR1, ESR2, NR1H4, and NR3C2). We identified a 49-gene signature associated with central nervous system (CNS) development and carcinogenesis, in addition to potentially cancer-driving gene fusions (LARP1-CNOT8 and NSL1-ZDBF2) and deleterious genetic variants (frameshift insertions in the CTSH, DBF4, POSTN, and WDR78 genes).ConclusionTaken together, these findings illustrate that TLX may play a pivotal role in tumorigenesis via genomic instability and perturbation of cancer-related processes.

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small RNA-seq in HEK-293t cells

Project description:The effect of NF90 on the abundance of miRNAs was measured using small RNA-seq.

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Core clock regulators in dexamethasone-treated HEK 293T cells at 4 h intervals.

Project description:ObjectiveThe study of the circadian clock and its mechanisms is easily facilitated through clock resetting in cell culture. Among the various established synchronizers of the circadian clock in cell culture (temperature, serum shock, glucocorticoids), the artificial glucocorticoid Dexamethasone (DEX) is the most widely used. DEX treatment as a protocol to reset the circadian clock in culture gives simple readout with minimal laboratory requirements. Even though there are many studies regarding clock resetting in culture using DEX, reference points or expression patterns of core clock genes and their protein products are scarce and sometimes contradict other works with similar methodology. We synchronise a cell line of human origin with DEX to be used for studies on circadian rhythms.ResultsWe treat HEK 293T cells with DEX and describe the patterns of mRNA and proteins of core clock regulators, while making a clear point on how CLOCK is less than an ideal molecule to help monitor rhythms in this cell line.

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