Gene Expression
Nebulas
Gene Expression Nebulas概要: Our work illustrates how high-resolution molecular and spatial profiling of COVID-19 patient tissues collected during rapid autopsies can serve as a hypothesisgenerating tool to identify key mediators driving the pathophysiology of COVID-19 for diagnostic and therapeutic target testing. Here we employ bulk RNA sequencing to identify key regulators of COVID-19 and list specific mediators for further study as potential diagnostic and therapeutic targets. We use single-nuclei RNA sequencing to highlight the diversity and heterogeneity of coronavirus receptors within the brain, suggesting that it will be critical to expand the focus from ACE2 to include other receptors, such as BSG and ANPEP, and we perform digital spatial profiling of lung and lymph node tissue to compare two patients with different clinical courses and symptomatology.
项目整体设计: Three technical replicates for olfactory bulb and prefontal cortex tissues from Patient 1.
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| 生长方案: | - |
| 处理方案: | - |
| 提取方案: | Nuclei were isolated from fresh frozen autopsy tissue following the 10x Genomics (Pleasanton, CA) recommended protocol using 0.1% Nonident NP40 lysis buffer. Suspensions were filtered through a 40 um mesh to remove debris and concentrated to a density of 1x10^6 nuclei/mL in Dulbecco's PBS + 0.04% BSA (Sigma Aldrich). Nuclei were processed according to Chromium 3’ Gene Expression V3 Kit (10X Genomics, Pleasanton, CA) using manufacturer’s guidelines. An estimated 15,000 nuclei were loaded onto each channel with a targeted cell recovery of 10,000 nuclei/sample. This was followed by sequencing on a S4 NovaSeq chip (Illumina Inc., San Diego, CA). Qubit 3 (Fisher Scientific) and 2100 Bioanalyzer (Agilent Technologies, Santa Clara, CA) were used for quality check of cDNA. The output BAM file, a binary text file containing the sequence alignment data from sequencing, was processed through 10X Genomics Cell Ranger software v3.1.0. Sequencing generated scRNA-seq data with ~41,000 2x100bp reads per nucleus and 63,653 total cells sequenced |
| 建库方案: | - |
| 分子类型: | polyA(+) 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: | - |
| 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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