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

PRJNA625444: Identification of Lead Drug Candidates for COVID-19 based on Drug Screening Using Human Pluripotent Stem Cell-Derived Cells/Organoids

来源: NCBI / GSE148697
提交时间: Apr 15 2020
释放时间: Jan 01 2021
最后更新时间: Feb 11 2021

概要: We systematically probed which cell types are permissive to SARS-CoV-2 infection. Transcriptomic analysis following SARS-CoV-2 infection of hPSC-derived lung organoids revealed upregulation of chemokines but not type I/III interferon signaling, similar to what was seen in primary human COVID-19 pulmonary infection.

项目整体设计: Using 10x genomics to measure single-cell RNA sequence (scRNA-seq) to comprehensively characterize the lung microenvironment in 4 lung tissues from the same COVID-19 severe patient.

GEN 数据集:
GEND000428
测序方法:
物种:
组织:
健康状况:
细胞类型:
细胞系:
发育阶段:
方案
生长方案: Protocols for maintenance of hPSCs and generation of lung cells were slightly modified from previous studies (Chen et al., 2019; Huang et al., 2014). Pancreatic endocrine cell differentiation was performed using INSGFP/W MEL-1 cells. Cells were cultured on Matrigel-coated 6-well plates in StemFlex medium (Gibco Thermo Fisher).; Protocols for maintenance of hPSCs and generation of lung cells were slightly modified from previous studies (Chen et al., 2019; Huang et al., 2014). Pancreatic endocrine cell differentiation was performed using INSGFP/W MEL-1 cells. Cells were cultured on Matrigel-coated 7-well plates in StemFlex medium (Gibco Thermo Fisher).; Protocols for maintenance of hPSCs and generation of lung cells were slightly modified from previous studies (Chen et al., 2019; Huang et al., 2014). Pancreatic endocrine cell differentiation was performed using INSGFP/W MEL-1 cells. Cells were cultured on Matrigel-coated 8-well plates in StemFlex medium (Gibco Thermo Fisher).; Protocols for maintenance of hPSCs and generation of lung cells were slightly modified from previous studies (Chen et al., 2019; Huang et al., 2014). Pancreatic endocrine cell differentiation was performed using INSGFP/W MEL-1 cells. Cells were cultured on Matrigel-coated 9-well plates in StemFlex medium (Gibco Thermo Fisher).; Protocols for maintenance of hPSCs and generation of lung cells were slightly modified from previous studies (Chen et al., 2019; Huang et al., 2014). Pancreatic endocrine cell differentiation was performed using INSGFP/W MEL-1 cells. Cells were cultured on Matrigel-coated 10-well plates in StemFlex medium (Gibco Thermo Fisher).; Protocols for maintenance of hPSCs and generation of lung cells were slightly modified from previous studies (Chen et al., 2019; Huang et al., 2014). Pancreatic endocrine cell differentiation was performed using INSGFP/W MEL-1 cells. Cells were cultured on Matrigel-coated 11-well plates in StemFlex medium (Gibco Thermo Fisher).
处理方案: Mock infected versus SARS-CoV-2 infected
提取方案: Total RNA was extracted in TRIzol (Invitrogen) and DNase I treated using Directzol RNA Miniprep kit (Zymo Research) according to the manufacturer’s instructions.
建库方案: RNAseq libraries of polyadenylated RNA were prepared using the TruSeq RNA Library Prep Kit v2 (Illumina) or TruSeq Stranded mRNA Library Prep Kit (Illumina) according to the manufacturer’s instructions.
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:
样本描述:
生物条件:
实验变量:
方案:
测序信息:
质量评估:
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 Candidate COVID-19 Therapeutics using hPSC-derived Lung Organoids.
bioRxiv : the preprint server for biology . 2020-05-05 [PMID: 32511403]