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

PRJNA629482: Single cell RNA sequencing reveals fetal ovary development in Macaca fascicularis

来源: NCBI / GSE149629
提交时间: Apr 30 2020
释放时间: Jan 01 2021
最后更新时间: Jan 11 2021

概要: The germ cells are vital for reproduction and heredity. However, the mechanisms for female germ cell development in primates, especially in late embryonic stage, has remained elusive. Here, we performed single-cell RNA sequencing of 12471 cells from fetal ovaries. We identified five cell types (germ cell, granulosa cell, theca cell, endothelial cell, macrophage cell), and explored the interactions between germ cells and niche cells. Interestingly, we demonstrated that two waves of oogenesis occur during fetal ovary development and ZGLP1 could activate oogenic program and is essential for meiosis initiation. Furthermore, late formed double strand breaks (DSBs) mediated by PRDM9 may lead to the apoptosis of germ cells during cyst breakdown process. Moreover, our study identified the origin of theca cells that may derive from Leydig cell like cells in fetal ovaries. Overall, our work provides new insights into the molecular and cellular basis of fetal ovary development at single-cell resolution.

项目整体设计: Single cell RNA sequencing on fetal ovary cells was performed from Macaca fascicularis.

GEN 数据集:
GEND000004 GEND000602
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方案
生长方案: -
处理方案: -; The ovaries samples for scRNA-seq were from two fetal female Macaca fascicularis (embryonic day 84 and 116). For each single cell sequencing experiment, two ovaries were washed twice in 1× PBS, and subjected to a standard digestion procedure through Tumor Dissociation Kit, human (Miltenyi Biotec # 130-095-929). First, the ovaries were cut into small pieces of 2–4 mm, and transferred into the gentleMACS C Tube containing the enzyme mix (4.7 mL DMEM, 200 µL Enzyme H, 100 µL Enzyme R, and 25 µL Enzyme A). Then, the C Tube was attached onto the sleeve of the gentleMACS dissociator. After termination of the program, C Tube was detached from the gentleMACS Dissociator. The sample was incubated for 30 minutes at 37 °C under continuous rotation using the MACSmix Tube Rotator. Next, C Tube was attached onto the sleeve of the gentleMACS dissociator and then perform a short centrifugation step to collect the sample material at the bottom of the tube. Resuspend sample and apply the cell suspension to a MACS SmartStrainer (70 µm) placed on a 50 mL tube and wash cell MACS SmartStrainer (70 µm) with 20 mL DMEM. Finally, centrifuge cell suspension at 300×g for 7 minutes, aspirate supernatant completely and resuspend cells as required for further applications.
提取方案: Cell instrument to generate a single cell Gel bead in Emulsion(GEM). Single cell RNA libraries were prepared for sequencing according to standard Illumina protocols accompanying the Single Cell 3’ Reagent Kits v3 (10X Genomics)","Cell instrument to generate a single cell Gel bead in Emulsion(GEM). Single cell RNA libraries were prepared for sequencing according to standard Illumina protocols accompanying the Single Cell 3’ Reagent Kits v3 (10X Genomics); RNAs were prepared for sequencing
建库方案: Then, count matrix was imported into the R package Seurat and quality control was performed to remove outlier cells and genes. Cells with 200-3000 detected genes were retained. Genes were retained in the data if they were expressed in ≥ 3 cells. After applying these quality control criteria, 11742 cells and 19204 genes remained for downstream analyses. Additional normalization was performed in Seurat on the filtered matrix to obtain the normalized count. Highly variable genes across single cells were identified and principal component analysis (PCA) was performed to reduce the dimensionality on the top 18 principal components. Then, cells were clustered at a resolution of 0.6 and visualized in 2-dimension using Uniform Manifold Approximation and Projection (UMAP)." "Then, count matrix was imported into the R package Seurat and quality control was performed to remove outlier cells and genes. Cells with 200-3000 detected genes were retained. Genes were retained in the data if they were expressed in ≥ 3 cells. After applying these quality control criteria, 11742 cells and 19204 genes remained for downstream analyses. Additional normalization was performed in Seurat on the filtered matrix to obtain the normalized count. Highly variable genes across single cells were identified and principal component analysis (PCA) was performed to reduce the dimensionality on the top 18 principal components. Then, cells were clustered at a resolution of 0.6 and visualized in 2-dimension using Uniform Manifold Approximation and Projection (UMAP).; Cell instrument to generate a single cell Gel bead in Emulsion(GEM). Single cell RNA libraries were prepared for sequencing according to standard Illumina protocols accompanying the Single Cell 3’ Reagent Kits v3 (10X Genomics)
测序信息
分子类型: Poly(A)+ RNA; polyA(+) 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:
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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 reveals regulation of fetal ovary development in the monkey (Macaca fascicularis).
Cell discovery . 2020-12-29 [PMID: 33372178]