牡蛎血液单细胞测序

从牡蛎的血细胞中收集了四组单细胞RNA测序数据，使用了10× Genomics单细胞捕获系统。使用Cell Ranger的STAR软件包对数据进行了对齐，以与C. hongkongensis基因组匹配。如果读数被认为是唯一映射到转录组的，那么它将用于UMI计数。所有UMI计数总和超过m/10的条形码被称为细胞。原始数据已提交至PRJNA751934和PRJNA747628。使用Seurat3.0进一步分析了单细胞RNA测序结果，以识别细胞簇和差异表达基因（DEGs）。使用Monocle（版本2.6.4）和CellphoneDB进行了细胞轨迹和通讯分析。

Four single-cell RNA sequencing (scRNA-seq) datasets were collected from the hemocytes of oysters using the 10× Genomics single-cell capture system. The data were aligned to the genome of Crassostrea hongkongensis (C. hongkongensis) using the STAR software package within Cell Ranger. Only reads uniquely mapped to the transcriptome were retained for UMI counting. Barcodes with a total UMI count exceeding m/10 were defined as cells. Raw sequencing data have been deposited under the accession numbers PRJNA751934 and PRJNA747628. Further scRNA-seq data analysis was performed using Seurat 3.0 to identify cell clusters and differentially expressed genes (DEGs). Cell trajectory analysis and cell-cell communication analysis were conducted using Monocle (version 2.6.4) and CellphoneDB, respectively.

搜集汇总

背景与挑战

背景概述

该数据集为牡蛎血细胞的单细胞RNA测序数据，使用10× Genomics系统捕获并进行了细胞聚类和差异表达分析，旨在研究血细胞对环境因素（如铜暴露）的响应。数据来源于南海珠江口，时间范围为2023年12月，已完全共享并关联一篇2022年的学术论文。