Gene Expression Nebulas
基于标准化流程分析的转录图谱综合数据库

Gene Expression Nebulas

多物种转录图谱整合数据库

PRJNA669693: scRNA-seq analysis of SARS-CoV-2 infected human islets (human)

来源: NCBI / GSE159556
提交时间: Oct 19 2020
释放时间: Apr 27 2021
最后更新时间: Jul 27 2021

概要: Recent clinical data has suggestedsed a bi-directional relationship between Coronavirus disease 19 (COVID-19) and diabetes. Here, we showdemonstrateed the detection of SARS-CoV-2 in pancreatic endocrine cells in autopsy samples derived fromof COVID-19 patients. Single cell RNA-seq and immunostaining confirmed that multiple types of pancreatic islet cells can be infected byare susceptible to SARS-CoV-2, eliciting a cellular stress response and the induction of chemokines. SARS-CoV-2 infection causes the increase of chemokine response, cell stress, and interferon signal. Upon SARS-CoV-2 infection, beta cells show a the decreased expression of insulin and the increased expression of alpha and acinar cell markers, including glucagon and , and acinar cell markers, including PRSS1/trypsin1, respectfully, suggesting which suggests that infected beta cells undergocellular dedifferentiation. This was furtherCorroboration of these findings could be further validated using theinex vivo using single cell sequencing of pancreatic tissue from autopsy of COVID-19 patients autopsies. Trajectory analysis identifiedindicated that the EIF2 pathway that changess along withmediates beta cell dedifferentiation. Furthermore, a, and a high content screen identified trans-integrated stress response inhibitor (trans-ISRIB) that as decreasinges poly-hormonal cells. Finally, trans-ISRIB treatmentwhich rescueds beta cell dedifferentiation upon SARS-CoV-2 exposure. Together, it, suggestings that SARS-CoV-2 infection causes EIF2 pathway-mediated beta cell dedifferentiation. Altogether, tThis study provides a potential mechanism of new onset diabetes in upon the development of COVID-19.

项目整体设计: Human islets were infected with SARS-CoV-2 and analyzed using scRNA-seq

GEN 数据集:
GEND000407
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方案
生长方案: The pancreatic organs were obtained from the local organ procurement organization under the United Network for Organ Sharing (UNOS). The islets were isolated in the Human Islet Core at University of Pennsylvania following the guidelines of Clinical Islet Transplantation consortium protocol (Ricordi et al., 2016). Briefly, the pancreas was digested following intraductal injection of Collagenase & Neutral Protease in Hanks’ balanced salt solution. Liberated islets were then purified on continuous density gradients (Cellgro/Mediatech) using the COBE 2991 centrifuge and cultured in CIT culture media and kept in a humidified 5% CO2 incubator.
处理方案: Approximately 1 × 10^6 untreated, control or integrated stress response inhibitor treated (ISRIB) treated, and Sal003 treated primary human pancreatic islet cells were infected with passage-3 SARS-CoV-2 at an MOI of 1 for 24 h in CIT culture media. After 24 hours, infected and mock infected pancreatic islets were dissociated into a single cell suspension using Accutase cell detachment solution (Innovative Cell Technologies) and incubation at 37C for ~20 minutes followed by gentle pipetting to break apart groups of cells.
提取方案: Target cell inputs of 10,000 cells for each condition were then loaded into a Chromium Controller using Chromium Next GEM (Gel Bead-In Emulsion) single Cell 5’ Library & Gel Bead Kit v1.1 (10x Genomics) according to manufacturer’s instructions. After generation of GEMs, cDNA synthesis and subsequent library preparation of all samples was completed using the Chromium Single Cell 5’ Library Kit v1.1 (10x Genomics) according to manufacturer’s instructions.
建库方案: The 10X Libraries (Single Cell 5’ R2-only library) were sequenced on the Illumina NovaSeq6000 sequencer with pair-end reads (28 bp for read 1 and 91 bp for read 2).
测序信息
分子类型: polyA(+) RNA
库的片段类型: PAIRED
库的链类型: -
测序平台: ILLUMINA
测序仪型号: Illumina NovaSeq 6000
链特异性: -
样本
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数据来源 GEN样本编号 GEN数据集编号 系列编号 项目编号 样本编号 样本名称 生物样本编号 样本访问号 实验访问号 释放时间 提交时间 最后更新时间 物种 种族 族裔 年龄 年龄单位 性别 来源名称 组织 细胞类型 细胞亚型 细胞系 疾病 疾病状态 发育阶段 突变/变异 表型 Condition Detail 生长方案 处理方案 提取方案 建库方案 分子类型 库的片段类型 链特异性 库的链类型 加标(Spike-In) 测序方法 测序平台 测序仪型号 细胞数 测序片段数 碱基数 平均测序片段长度_1 平均测序片段长度_2 唯一比对率 多重比对率 覆盖度
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