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

PRJNA623281: Identification of Candidate COVID-19 Therapeutics using hPSC-derived Lung Organoids

来源: NCBI / GSE148113
提交时间: Apr 06 2020
释放时间: Aug 11 2020
最后更新时间: Dec 11 2020

概要: The SARS-CoV-2 virus has caused already over 3.5 million COVID-19 cases and 250,000 deaths globally. There is an urgent need to create novel models to study SARS-CoV-2 using human disease-relevant cells to understand key features of virus biology and facilitate drug screening. As primary SARS-CoV-2 infection is respiratory-based, we developed a lung organoid model using human pluripotent stem cells (hPSCs) that could be adapted for drug screens.

项目整体设计: We performed a high throughput screen using hPSC-derived lung organoids and identified FDA-approved drug candidates, including imatinib and mycophenolic acid, as inhibitors of SARS-CoV-2 entry.

GEN 数据集:
GEND000478
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方案
生长方案: hESC cultures were maintained in an undifferentiated state at 37 in a 5% CO2/air environment until stem cells reached about 90% confluence.
处理方案: hPSC differentiation into endoderm was performed in serum-free differentiation (SFD) medium of DMEM/F12 (3:1) (Life Technologies) supplemented with 1N2 (Life Technologies), 1B27 (Life Technologies), 50 g/ml ascorbic acid, 2 mM Glutamax (Gibco), 0.4 monothioglycerol, 0.05% BSA at 37 in a 5% CO2/5% O2/95% N2 environment. hPSCs were treated with Accutase and plated onto low attachment 6-well plates (Corning), re-suspended in endoderm induction medium containing 10 Y-27632, 0.5 ng/ml human BMP4 (R&D Systems), 2.5 ng/ml human bFGF, 100 ng/ml human Activin A (R&D Systems), for 72-76 hours dependent on the formation rates of endoderm cells. On day 3 or 3.5, the endoderm bodies were dissociated into single cells using 0.05% Trypsin/0.02% EDTA and plated onto fibronectin-coated, 24-well tissue culture plates (~100,00050,000 cells/well). For induction of anterior foregut endoderm, the endoderm cells were cultured in SFD medium supplemented with 1.5 dorsomorphin dihydrochloride (R&D Systems) and 10 SB431542 (R&D Systems) for 36 hours, and then switched to 36 hours of 10 SB431542 and 1 IWP2 (R&D Systems) treatment. For induction of early stage lung progenitor cells (day 65), the resulting anterior foregut endoderm was treated with 3 CHIR99021 (CHIR, Stem-RD), 10 ng/ml human FGF10, 10 ng/ml human KGF, 10 ng/ml human BMP4 and 50-60 nM all-trans retinoic acid (ATRA), in SFD medium for day 80. The day 105 culture was maintained in a 5% CO2/air environment. On days 15 and 16, the lung field progenitor cells were replated after one minute trypsinization onto fibronectin-coated plates, in the presence of SFD containing 3 CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human FGF7, 10 ng/ml human BMP4, and 50 nM ATRA. Day 165 cultures of late stage lung progenitor cells were maintained in SFD media containing 3 CHIR99021, 10 ng/ml human FGF10, 10 ng/ml human KGF, in a 5% CO2/air environment. For differentiation of mature lung cells (day 25 to 55) in 3D culture, cultures were re-plated and embedded in 90% Matrigel after brief trypsinization in SFD media containing maturation components containing 3 CHIR99021, 10 ng/ml human FGF10; 10 ng/ml human KGF, 50 nM Dexamethasone, 0.1 mM 8-bromo-cAMP (Sigma Aldrich) and 0.1 mM IBMX (3,7-dihydro-1-methyl-3-(2-methylpropyl)-1H-purine-2,6-dione, Sigma Aldrich).
提取方案: -
建库方案: Library was constructed according to the user manual of Chromium Single Cell 3Library & Gel Bead Kit v2
测序信息
分子类型: Poly(A)+ 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
基本信息:
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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
文章
Identification of SARS-CoV-2 inhibitors using lung and colonic organoids.
Nature . 2020-10-28 [PMID: 33116299]