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

PRJNA715767: hPSC-derived cells to model Macrophage-mediated inflammation in COVID19 Hearts 

来源: NCBI / GSE169241
提交时间: Mar 19 2021
释放时间: Apr 16 2021
最后更新时间: Apr 16 2021

概要: hPSC-derived cells to model Macrophage-mediated inflammation in COVID19 Hearts 

项目整体设计: We systematically compared autopsy samples from non-COVID-19 donors and COVID-19 patients using RNA-seq and immunohistochemistry. We observed strikingly increased expression levels of CCL2 as well as macrophage infiltration in heart tissues of COVID-19 patients. We generated an immuno-cardiac co-culture platform containing human pluripotent stem cell (hPSC)-derived cardiomyocytes (CMs) and macrophages. We found that macrophages induce increased reactive oxygen species (ROS) and apoptosis in CMs by secreting IL-6 and TNF-α after SARS-CoV-2 exposure. Using this immuno-cardiac co-culture platform, we performed a high content screen and identified ranolazine and tofacitinib as compounds that protect CMs from macrophage-induced cardiotoxicity. We established an immuno-host co-culture system to study macrophage-induced host cell damage following SARS-CoV-2 infection, and identified FDA-approved drug candidates that alleviate the macrophage-mediated hyper-inflammation and cellular injury.

GEN 数据集:
GEND000502
测序方法:
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方案
生长方案: For monolayer-based differentiation of cardiomyocytes (CMs), hPSCs were cultured between P20-P40 and seeded at a density of 3x105 cells/well of a 6-well plate and grown for 48 hr to 90% confluence in a humidified incubator with 5% CO2 at 37℃. On day 0, the medium was replaced with RPMI 1640 supplemented with B27 without insulin and 6 µM CHIR99021. On day 1, the medium was changed to RPMI 1640 supplemented with B27 without insulin for 48 hr. Day 3, medium was refreshed to RPMI 1640 supplemented with B27 without insulin and 2 µM C59 for another 48 hr. On day 5, the medium was changed back to RPMI-B27 without insulin for 48 hr, and then switched to RPMI 1640 plus normal B27 until day 12 with a medium change every 2 days. On day 12, the medium was transiently changed to RPMI 1640 without D-glucose containing ascorbic acid, human albumin and DL-Lactate for two days to allow metabolic purification of CMs. From that day on, fresh RPMI 1640-B27 was changed every two days; Macrophages were derived from hPSCs by adapting a previously reported protocol28. hPSCs were cultured between P20-P40. First, H9 or H1 cells were lifted with ReLeSR (STEMCELL Technologies) as small clusters onto Matrigel-coated 6-well plates at low density. On day 0, IF9S medium was supplemented with 50 ng/ml BMP-4, 15 ng/ml Activin A and 1.5 µm CHIR99021. On day 2, medium was refreshed with IF9S medium with 50 ng/ml VEGF, 50 ng/ml bFGF, 50 ng/ml SCF (R&D Systems) and 10 µm SB431542 (Cayman Chemical). On day 5 and da y7, medium was changed to IF9S with 50 ng/ml IL-6 (R&D Systems), 12 ng/ml IL-3 (R&D Systems), 50 ng/ml VEGF, 50 ng/ml bFGF, 50 ng/ml SCF and 50 ng/ml TPO (R&D Systems). On day 9, cells were dissociated with TrypLE (Life Technologies) and re-suspended in IF9S medium with 50 ng/ml IL-6, 12 ng/ml IL-3 and 80 ng/ml M-CSF (R&D Systems). On day 13 and day 15, medium was changed and supplemented with 50 ng/ml IL-6, 12 ng/ml IL-3 and 80 ng/ml M-CSF. All differentiation steps were cultured at 37°C, 5% CO2.
处理方案: To analyze the gene expression of CMs co-cultured with H9-derived macrophages using RNA-seq, we used trans-well plates. CMs were seeded on the lower plate of 24 well plates and macrophages were seeded onto the upper chamber. After 24 hr, drug treatments were done to CMs and macrophages in the upper chamber were infected with SARS-CoV-2 (MOI=0.1). The trans-well chamber will allow cytokines to go through but not macrophages. 24 hpi, CMs were collected to extract total RNA. For analyzing macrophages infected with virus, macrophages were seeded onto 24 well plates and infected with SARS-CoV-2 (MOI=0.1). 24 hpi, macrophages were collected for total RNA.
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: polyA(+) RNA
库的片段类型: PAIRED; SINGLE
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
文章
Longitudinal single-cell epitope and RNA-sequencing reveals the immunological impact of type 1 interferon autoantibodies in critical COVID-19.
bioRxiv : the preprint server for biology . 2021-03-10 [PMID: 33758859]
An Immuno-Cardiac Model for Macrophage-Mediated Inflammation in COVID-19 Hearts.
Circulation research . 2021-04-15 [PMID: 33853355]