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

PRJNA684327: Single-cell RNA sequencing of Tocilizumab-treated peripheral blood mononuclear cells as an in vitro model of inflammation

来源: NCBI / GSE163014
提交时间: Dec 10 2020
释放时间: Dec 11 2020
最后更新时间: Jan 27 2021

概要: COVID-19 has posed a significant threat to global health. Early data has revealed that IL-6, a key regulatory cytokine, plays an important role in the cytokine storm of COVID-19. Multiple trials are therefore looking at the effects of Tocilizumab, an IL-6 receptor antibody that inhibits IL-6 activity, on treatment of COVID-19, with promising findings. As part of a clinical trial looking at the effects of Tocilizumab treatment on kidney transplant recipients with subclinical rejection, we performed single-cell RNA sequencing of comparing stimulated PBMCs before and after Tocilizumab treatment. We leveraged this data to create an in vitro cytokine storm model, to better understand the effects of Tocilizumab in the presence of inflammation. Tocilizumab-treated cells had reduced expression of inflammatory-mediated genes and biologic pathways, particularly amongst monocytes. These results support the hypothesis that Tocilizumab may hinder the cytokine storm of COVID-19, through a demonstration of biologic impact at the single-cell level

项目整体设计: Examination of peripheral blood mononuclear cells (PBMCs) from 15 human kidney transplant recipients, diagnosed with subclinical rejection on their 6-month post-transplant protocol biopsy and randomized to either continue standard of care (Tacrolimus, mycophenolate, and steroid) immunosuppression (control arm, 8 patients) or standard of care plus Tocilizumab (Tocilizumab treatment arm, 7 patients)

GEN 数据集:
GEND000423
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生长方案: PBMCs were isolated from blood samples by Ficoll-PaqueTM PLUS density gradient centrifugation and frozen in fetal bovine serum containing 10% (vol/vol) dimethyl sulfoxide. Cells were frozen and not thawed until the day of the experiment when they were used directly for in vitro stimulation.
处理方案: Cells were stimulated with soluble anti-CD3 and anti-CD28 antibodies at 37 Celsius, 5% CO2 for 24 hours. Unstimulated PBMCs were incubated under identical conditions to reduce any confounding from incubation conditions other than stimulation.
提取方案: Cells were multiplexed into pools of cells from different patients with the intent of using in silico genetic demultiplexing tools to recover more single cells and reduce batch effect. No samples from the same person were multiplexed into the same pool. Pools were loaded onto the 10x Genomics controller using several lanes per pool, and processed using standard protocols, including cell lysis, reverse transcription, amplification and library generation.
建库方案: Libraries were constructed using standard protocols from 10x Genomics.
测序信息
分子类型: Poly(A)+ 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: -
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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
Single-Cell RNA Sequencing of Tocilizumab-Treated Peripheral Blood Mononuclear Cells as an in vitro Model of Inflammation.
Frontiers in genetics . 2020-01-01 [PMID: 33469465]