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Integrative multi-omics landscape of fluoxetine action across 27 brain regions [bulk RNA-seq]

ABSTRACT: Integrative multi-omics landscape of fluoxetine action across 27 brain regions [bulk RNA-seq]

PROVIDER: PRJNA800072 | ENA |

REPOSITORIES: ENA

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Integrative multi-omics landscape of fluoxetine action across 27 brain regions

Project description:We constructed a comprehensive multi-omics map of the molecular effects of fluoxetine (an SSRI antidepressant), in 27 rat brain regions. We profiled gene expression (bulk RNA-seq, 210 datasets) and chromatin state (bulk chromatin immunoprecipitation sequencing (ChIP-seq) for the histone marker H3K27ac, 100 datasets) in a broad, unbiased panel of 27 brain regions across the entire rodent brain, in naive and fluoxetine-treated animals. We complemented this approach with single-cell RNA-seq (scRNA-seq) analysis of two brain regions. Using diverse integrative data analysis techniques we characterized the complex and multifaceted effects of fluoxetine on region-specific and cell-type-specific gene regulatory networks and pathways. Remarkably, we observed profound molecular changes across the brain (>4,000 differentially expressed genes and differentially acetylated ChIP-seq peaks each) that were highly region-dependent. We leveraged this atlas to identify fluoxetine-moduated genes and gene-regulatory loci, predict enriched motifs that suggest potential upstream regulators, and validate global mechanisms of fluoxetine action.

2022-09-04 | GSE193040 | GEO

Integrative multi-omics landscape of fluoxetine action across 27 brain regions [bulk RNA-seq]

2022-09-04 | GSE194289 | GEO

Integrative multi-omics landscape of fluoxetine action across 27 brain regions (single cell profiling for 2 regions)

Project description:We constructed a comprehensive multi-omics map of the molecular effects of fluoxetine (an SSRI antidepressant) in 27 rat brain regions. We profiled gene expression (bulk RNA-seq, 210 datasets) and chromatin state (bulk chromatin immunoprecipitation sequencing (ChIP-seq) for the histone marker H3K27ac, 100 datasets) in a broad, unbiased panel of 27 brain regions across the entire rodent brain, in naive and fluoxetine-treated animals. We complemented this approach with single-cell RNA-seq (scRNA-seq) analysis of two brain regions (20 datasets). Remarkably, in the single-cell RNA-seq profiling we observed profound changes in the transcripts of hippocampal dorDG and venDG (~500 DEGs in specific cell types). Using diverse integrative data analysis techniques we characterized the complex and multifaceted effects of fluoxetine on region-specific and cell-type-specific gene regulatory networks and pathways. We leveraged this atlas to identify fluoxetine-modulated genes and gene-regulatory loci, predict enriched motifs that suggest potential upstream regulators, and validate global mechanisms of fluoxetine action.

2022-09-04 | GSE197622 | GEO

Integrative multi-omics landscape of fluoxetine action across 27 brain regions

Project description:Integrative multi-omics landscape of fluoxetine action across 27 brain regions

| PRJNA794169 | ENA

Integrative multi-omics landscape of fluoxetine action across 27 brain regions (single cell profiling for 2 regions)

Project description:Integrative multi-omics landscape of fluoxetine action across 27 brain regions (single cell profiling for 2 regions)

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Integrative Omics Analysis for Colorectal Cancer and Metastasis

Project description:The pathogenesis of Colorectal cancer (CRC) metastasis remains unclear.We collect clinical data from our center and use Integrative omics to analyze and predict candidate biomarkers of colorectal cancer and distant metastasis.

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RNA-sequencing Analysis of GBM Neurosphere Cells with Fluoxetine or DMSO treatment

Project description:To determine fluoxetine-induced transcriptional signatures in GBM cancer cells, we performed RNA-sequencing analysis of three GBM patient-derived neurosphere cancer cell lines after fluoxetine or DMSO treatment. Genes with differential expression and associated transcriptional signatures were analyzed and identified in three cancer cell lines.

2021-10-24 | GSE158674 | GEO

Fluoxetine dosed macaque proteomics

Project description:We have established proteome and phosphoproteome landscapes of two brain sections of juvenile rhesus monkeys in response to long-term fluoxetine treatment following discontinuation of drug dosing.

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Asymmetry of STAT action in driving IL-27 and IL-6 transcriptional outputs and cytokine specificity

Project description:IL-6 and IL-27 have antagonistic and overlapping functions, signal through a shared receptor subunit and employ the same downstream STAT proteins. To evaluate the degree of specificity and redundancy for these cytokines, we quantified global transcriptomic changes induced by the two cytokines and determined the relative contributions of STAT1 and STAT3 using genetic models and ChIP-seq. We found a high degree of overlap of the transcriptomes induced by IL-6 and IL-27 and extremely few examples in which the cytokines acted in opposition. Using STAT deficient cells and T cells from patients with gain-of-function STAT1 mutations, we show that STAT3 was responsible for the overall transcriptional output driven by both cytokines, whereas STAT1 was the driver of cytokine specificity. STAT1 did not compensate for the lack STAT3; on the contrary, much of STAT1 binding to chromatin was STAT3 dependent. Thus, STAT1 shapes the specific cytokine signature superimposed upon STAT3’s action. Integrated analysis of transcriptome and transcription factor binding data from cytokine treated CD4+T cells

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Juvenile fluoxetine evoked gene expression changes in the rat medial prefrontal cortex

Project description:To understand the consequences of chronic exposure to fluoxetine during juvenile life on global transcriptional changes withing the rat medial prefrontal cortex in adulthood. To understand the consequences of chronic exposure to fluoxetine during juvenile life on global transcriptional changes withing the rat medial prefrontal cortex in adulthood.

2024-06-30 | GSE270731 | GEO

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