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Comparative gene expression profiling analysis of RNA-seq data for mCherryHigh and DTC populations compared to mCherryLow metastatic populations [mCherry Pops and DTCs]

ABSTRACT: To investigate characteristics of the Gstt1high metastatic subppulation in pancreatic cancer, lung metastatic cell line was generated to express mCherry from the Gstt1 endogenous promoter. Mice were injected via tail vein with mixed populations until evidence of metastatic disease, or 5 days after injection for DTC sorting. Upon evidence of metastatic disease, mice were euthanized and lung tissues were digested followed by sorting of mCherry tumor cell populations (top 15-20%) gated on GFP. DTCs were collected 5 days after injection by gating and sorting on GFP. We then performed gene expression profiling analysis using data obtained from RNA-seq comparing mCherryHigh and low populations.

ORGANISM(S): Mus musculus

PROVIDER: GSE232197 | GEO | 2024/04/01

REPOSITORIES: GEO

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Project description:Hearing loss is most commonly caused by the destruction of mechanosensory hair cells in the ear. This condition is usually permanent: Despite the presence of putative hair-cell progenitors in the cochlea, hair cells are not naturally replenished in adult mammals. Unlike those of the mammalian ear, the progenitor cells of nonmammalian vertebrates can regenerate hair cells through- out life. The basis of this difference remains largely unexplored but may lie in molecular dissimilarities that affect how progenitors respond to hair-cell death. We analyzed gene expression in hair-cell progenitors of the lateral-line system. We developed a transgenic line of zebrafish called alpl:mCherry that expresses a red fluorescent protein in the presumptive hair-cell progenitors known as mantle cells. Fluorescence-activated cell sorting from the skins of transgenic larvae, followed by microarray-based expression analysis, revealed a constellation of transcripts that are specifically enriched in these cells versus hair cells and non-fluorescent skin cells. Gene expression analysis after hair-cell ablation uncovered a cohort of genes that are differentially regulated early in regeneration, suggesting possible roles in the response of progen- itors to hair-cell death. These results provide a resource for studying hair-cell regeneration and the biology of sensory progenitor cells. Two sets of analyses were performed. The first compared baseline expression levels in four sorted cell types from two different transgenic lines of zebrafish, alpl:mCherry;pou4f3:GFP and alpl:mCherry:ET20. alpl:mCherry;pou4f3:GFP larvae express GFP in hair cells and mCherry in mantle cells. alpl:mCherry:ET20 larvae express GFP in most mantle cells and mChery in all mantle cells. The four cell types compared were GFP+ hair cells, mCherry+ mantle cells, mCherry+/GFP+ mantle cells from alpl:mCherry:ET20 larvae, and non-fluorescent (NF) cells. Two hair-cell, five mCherry+ mantle cell, four mCherry+/GFP+ mantle cell, and six NF cell samples were analyzed. This excludes a few samples that were discardced based on failure to cluster by principal component analysis. A second analysis, separately imported, compared gene expression in mCherry+ mantle cells and NF cells at four time points following chemical ablation of hair cells with copper sulfate. These were one, three, five, and eleven hours after treatment (hpCu). Untreated samples served as controls. For mCherry+ cells, five untreated and four each of 1 hpCu, 3 hpCu, 5 hpCu and 11 hpCu were analyzed. For NF cells, six untreated, seven 1 hpCu, and four each of 3 hpCu, 5 hpCu and 11 hpCu samples were analyzed. Untreated mCherry+ and NF cells were shared between both analyses.

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Comparative gene expression profiling analysis of RNA-seq data for mCherryHigh and DTC populations compared to mCherryLow metastatic populations [mCherry Pops and DTCs]

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