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

PRJNA745903: SARS-CoV-2 infects the brain vasculature in COVID-19 patients and a hiPSC-derived model of the blood-brain barrier

来源: NCBI / GSE179923
提交时间: Jul 12 2021
释放时间: Jul 14 2021
最后更新时间: Jan 24 2022

概要: We report the transcriptional changes of an hipsc-derived model of the blood-brain barrier to infection with SARS-CoV-2. Furthermore, the neurovascular niche was isolated from human brain biopsies to compare the transcriptional signatures of hipsc-derived endothelial cells and human neurovascular niche.

项目整体设计: hipsc-derived endothelial cells were either mock infected of exposed to SARS-CoV-2.

GEN 数据集:
GEND000473
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方案
生长方案: The hiPSC line WISCi004-B/IMR90-4 was used to differentiate BCECs. a single cell suspension of hiPSCs was prepared with Accutase. The cell suspension was centrifuged at 300 x g for 5 min and cells were seeded in mTeSRTM1 supplemented with 10 µM Y-27632 onto Matrigel-coated 6-well plates. The seeding density was optimized for each hiPSC line. For the differentiation of hiPSCs to BCECs, the neurodevelopmental process in vivo has to be recapitulated in vitro. For brain-capillary endothelial-like cells, a co-differentiation of neural and endothelial cells was initiated by treatment with so-called unconditioned medium. After 2-3 days when optimal cell densities of 2-4x104 cells/cm2 were reached, medium was switched to unconditioned medium in order to initiate co-differentiation of BCECs and neuronal cells (referred to as day 0 of differentiation throughout the manuscript). Unconditioned medium was composed of 78.5% DMEM/F12 , 20% KnockOutTM serum replacement, 1% MEM NEAA, 0.5% L-glutamine, and 0.1 mM β-mercaptoethanol. A daily change of unconditioned medium for 5 days was followed by double feeding at day 6 with endothelial cell (EC) medium supplemented with 20 ng/ml hbFGF and 10 µM retinoic acid to expand the BCECs. EC medium was composed of Human Endothelial-SFM and, if not stated otherwise, 0.5% B27 Supplement as described recently (Neal et al., 2019). After 48 h without medium change, cells were dissociated with Accutase for 30 min and seeded at a cell density of 1x106 cells/cm2 onto collagen IV/fibronectin-coated transwell insert in EC medium supplemented with 20 ng/mL hFGF and 10 µM RA. This seeding step at day 8 in combination with the collagen IV/fibronectin-coating allows for an efficient purification of BCECs. At day 9, hiPS-BCECs were adapted to EC medium without hFGF and RA (in transwell systems with 200 µl of medium apical and 800 µl basolateral) for 24 h. TEER measurements were performed to evaluate the integrity of the generated in vitro BBB to be used for further applications.
处理方案: At day 10 of differentiation hipsc-derived BCECs were either mock infected or exposed to SARS-CoV-2. After 24 hours cells were harvested and total RNA was extracted according to the manufacturer’s instructions using the NucleoSpin® RNA Kit (#740955.250, Macherey-Nagel). RNA concentration and quality was determined using a NanoDrop™ 1000 Spectrophotometer (ThermoFisher Scientific) and samples were stored at -80 °C until further use.
提取方案: NEBNext Ultra RNA Library Prep Kit (Illumina)
建库方案: -
测序信息
分子类型: polyA(+) RNA
库的片段类型: PAIRED
库的链类型: Forward
测序平台: ILLUMINA
测序仪型号: Illumina NovaSeq 6000
链特异性: Specific
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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