Gene expression analysis from splenocytes treated with mPVAT-conditioned media

The overall purpose of this study was to understand the impact of a high-fat diet on the perivascular microenvironment in Dahl S rats, a spontaneously hypertensive rat strain. Specifically, the study was designed to understand whether a high-fat diet promotes inflammation in the perivascular adipose tissue microenvironment. To address this, we collected mesenteric PVAT from Dahl S rats on either a control or a high-fat diet and used the PVAT to make conditioned media. We then cultured rat splenocytes in either mPVAT-conditioned media or in standard tissue culture media and activated them with a T cell-specific activator (anti-CD3/anti-CD28). We then isolated RNA from the splenocytes which was used for gene expression analysis by RNA-sequencing., Primary splenocytes were activated with a T cell-specific activator in the presence and absence of perivascular adipose tissue (PVAT)-conditioned media. The PVAT was collected from Dahl S rats on either a control or high-fat diet for 10 weeks. RNA from the cells was extracted using the RNeasy Mini Kit (Qiagen, Germantown, MD). Transcriptome analysis of RNA sequencing (30M raw reads/sample) was performed via Illumina platforms by Novogene (Sacramento, CA). After quality control, HISAT2 was used to map the filtered sequenced reads to the reference genome. Gene expression level is estimated by the FPKM (Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced) method. The coexpression Venn diagram was used to visualize the number of genes that are uniquely expressed within each group/sample. Differentially expressed genes (DEGs) analysis of HF condition and CTL condition was performed using the DESeq2 R package. Volcano plots were used to infer the overall distributi..., , # Gene expression analysis from splenocytes treated with mPVAT-conditioned media

[https://doi.org/10.5061/dryad.v9s4mw74c](https://doi.org/10.5061/dryad.v9s4mw74c)

Overview:  The dataset includes RNA-sequencing data from splenocytes treated with perivascular adipose tissue-conditioned media. The PVAT was collected from Dahl S rats on either a control diet or a high fat diet for 10 weeks.

Study design: The study is designed to understand the effect of the perivascular adipose tissue (PVAT) on T cell function in the context of high fat diet-induced hypertension. Male Dahl S rats were put on a control diet or high fat diet for 10 weeks after which mesenteric perivascular adipose tissue (mPVAT) was collected to make conditioned media. Splenocytes were cultured in the mPVAT-conditioned media and activated with a T cell-specific activator (anti-CD3/anti-CD28). RNA was isolated from the splenocytes for bulk RNA-sequencing. The data are organized as splenocytes treated with PVAT-CM from rats...

本研究的整体目标为解析高脂饮食对自发性高血压大鼠品系Dahl S大鼠的血管周微环境的影响。具体而言，本研究旨在探明高脂饮食是否会促进血管周脂肪组织（perivascular adipose tissue, PVAT）微环境的炎症反应。
为此，我们分别从喂食对照饮食或高脂饮食的Dahl S大鼠体内采集肠系膜血管周脂肪组织（mesenteric perivascular adipose tissue, mPVAT），并利用该组织制备条件培养基。随后，我们将大鼠脾淋巴细胞分别置于mPVAT条件培养基或标准组织培养基中培养，并使用T细胞特异性激活剂（抗CD3/抗CD28）对其进行激活。之后，我们从脾淋巴细胞中提取RNA，通过RNA测序（RNA-sequencing）开展基因表达分析。
本实验设置为：在存在或不存在PVAT条件培养基的情况下，使用T细胞特异性激活剂激活原代脾淋巴细胞。PVAT采集自喂食对照饮食或高脂饮食达10周的Dahl S大鼠。
我们使用RNeasy Mini试剂盒（Qiagen，马里兰州日耳曼敦）从细胞中提取RNA。转录组测序（每个样本含30M原始读段）的转录组分析由Novogene公司（加利福尼亚州萨克拉门托）通过Illumina平台完成。质控流程完成后，使用HISAT2将过滤后的测序读段比对至参考基因组。基因表达水平通过FPKM（Fragments Per Kilobase of transcript sequence per Millions base pairs sequenced，每百万测序碱基中每千个转录本序列的片段数）方法进行估算。
我们使用共表达维恩图可视化各组/各样本中特异性表达的基因数量。使用DESeq2 R包对高脂饮食（HF）组与对照饮食（CTL）组开展差异表达基因（differentially expressed genes, DEGs）分析。通过火山图推断整体分布……
# 经mPVAT条件培养基处理的脾淋巴细胞基因表达分析
DOI: https://doi.org/10.5061/dryad.v9s4mw74c
概述：本数据集包含经PVAT条件培养基处理的脾淋巴细胞的RNA测序数据。PVAT采集自喂食对照饮食或高脂饮食达10周的Dahl S大鼠。
研究设计：本研究旨在探明高脂饮食诱导高血压的背景下，PVAT对T细胞功能的调控作用。将雄性Dahl S大鼠分别喂食对照饮食或高脂饮食10周后，采集其肠系膜血管周脂肪组织（mPVAT）以制备条件培养基。将脾淋巴细胞置于mPVAT条件培养基中培养，并使用T细胞特异性激活剂（抗CD3/抗CD28）进行激活。随后从脾淋巴细胞中提取RNA进行批量RNA测序。数据按"经大鼠PVAT条件培养基处理的脾淋巴细胞"进行组织分类……