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RNA-seq of OVCAR3 and CCL218 cancer cells with evolved hydroxychloroquine resistance

ABSTRACT: OVCAR3 and CCL218 cells were passaged in the presence or absence of hydroxychloroquine. Drug pulse chases were used, with 48h of drug exposure followed by replacement of fresh media. Cells were allowed to grow to near confluence and then another drug pulse-chase was performed. After 15 hydroxychloroquine pulse-chases, cells were allowed to proliferate for 7 days in drug-free media so that transient drug effects were no longer present. Cells were then pelleted and cell pellets were processed for concomitant bulk RNA-seq, whole-exome-sequencing, and single-cell RNA-seq. This project represents the bulk transcriptomic sequencing and analysis.

ORGANISM(S): Homo sapiens

PROVIDER: GSE245133 | GEO | 2024/03/18

REPOSITORIES: GEO

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single-cell RNA-seq of OVCAR3 and CCL218 cancer cells with evolved hydroxychloroquine resistance

Project description:OVCAR3 and CCL218 cells were passaged in the presence or absence of hydroxychloroquine. Drug pulse chases were used, with 48h of drug exposure followed by replacement of fresh media. Cells were allowed to grow to near confluence and then another drug pulse-chase was performed. After 15 hydroxychloroquine pulse-chases, cells were allowed to proliferate for 7 days in drug-free media so that transient drug effects were no longer present.

2024-03-18 | GSE245329 | GEO

Genome-scale CRISPR-Cas9 screen of OVCAR3 and CCL218 cancer cells with or without hydroxychloroquine

Project description:A Brunello CRISPR-Cas9 library screen was performed with OVCAR3 and CCL218 cells in the presence or absence of hydroxychloroquine. Drug pulse chases were used, with 48h of drug exposure followed by replacement of fresh media. Cells were allowed to grow to near confluence and then another drug pulse-chase was performed. After each pulse-chase, a pool of cells were collected for sgRNA quantitation. Three pulse chases were performed. Cell pellets were processed for genomic DNA and sgRNA sequences amplified by PCR for NGS-based quantitation. Once quantified by NGS analysis, MAGeCK MLE analysis was performed to determine which sgRNAs were most associated with resistance or sensitization to hydroxychloroquine.

2024-03-18 | GSE245215 | GEO

Thiouracil Pulse-chase, Tachyzoites and Bradyzoites mRNA stability data

Project description:Pulse chase measurements using thiouracil (DTU) labeling via UPRT and chasing with uracil Data from tachyzoites is labeled "DTU Pulse Chase". Two independent pulse chase experiments were performed in tachyzoites, pulse chase 1 and 2. Duplicate arrays at each timepoint were performed for pulse chase 2 (2 a and b). Data from bradyzoites are labeled "DTU Bradyzoite Pulse Chase". Two independent pulse chase experiments were performed in bradyzoites and a single set of arrays were performed for each experiment. Just one chase timepoint was used in the bradyzoite experiments, the 2 hour chase. An RNA stablity experiment design type examines stability and/or decay of RNA transcripts. Keywords: RNA_stability_design

2005-07-16 | GSE2947 | GEO

Transcription profiling of Toxoplasma gondii thiouracil pulse-chase, tachyzoites and bradyzoites mRNA stability data

2005-07-07 | E-SMDB-2949 | biostudies-arrayexpress

EC_tagging pulse-chase to measure mRNA decay in Drosophila larval neuroblasts and neurons

Project description:Nascent RNA was tagged with EU, via EC feeding, in targeted cells (neuroblasts or neurons) then purified after the initial pulse labeling or after a chase using media containing excess unmodified uridine

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Thiouracil Pulse-chase, Tachyzoites and Bradyzoites mRNA stability data

2005-07-16 | E-GEOD-2947 | biostudies-arrayexpress

Hydroxychloroquine inhibits trained immunity

Project description:Hydroxychloroquine inhibits trained immunity

| PRJNA670179 | ENA

Hydroxychloroquine inhibits trained immunity

Project description:We demonstrate that hydroxychloroquine inhibits trained immunity at the functional and epigenetic level and is accompanied by reduced expression of interferon-stimulated genes. Trained immunity comprises a functional adaptation induced by epigenetic reprogramming which facilitates the anti-viral innate immune response.

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Hydroxychloroquine inhibits responses to group A streptococcus in peripheral blood mononuclear cells

Project description:Immune responses to group A streptococcus in humans can lead to the development of acute rheumatic fever and rheumatic heart disease. Immune pathways that are activated by group A streptococcus are potential targets for inhibiting autoimmune responses to group A streptococcus. This experiment tests the impact of the drug hydroxychloroquine on immune responses to group A streptococcus in peripheral blood mononuclear cells

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RNASET2-silenced and control OVCAR3 cell clones injected into nude mice.

Project description:To investigate the molecular pathways underlying RNASET2-mediated tumor suppression in vivo, we investigated the gene expression profile of tumor samples obtained from control and RNASET2-silenced OVCAR3 xenografts, respectively. In order to evaluate the contribution of human cancer cells and the murine host stroma to RNASET2-mediated tumorigenesis responses, total RNA extracted from tumor xenografts derived from six independent OVCAR3 cell clones (three parental and three RNASET2-silenced clones) was fluorescently labeled and hybridized to human Agilent whole-genome microarrays. Control and RNASET2-silenced OVCAR3 were injected subcutaneously into nude mice. After 39 days mice were sacrified, tumors were extracted and total RNA purified.

2013-05-01 | E-GEOD-43029 | biostudies-arrayexpress

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