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

PRJNA352390: Single-cell RNA-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta

来源: NCBI / GSE89497
提交时间: Nov 03 2016
释放时间: Jul 24 2018
最后更新时间: May 15 2019

概要: In this study, we isolated human villous stromal cells (STRs), CTBs, the STB, and EVTs at the first and second trimester of pregnancy and monitored the transcriptome dynamics of 1567 cells at single-cell resolution. We identified 14 subtypes of placental cells and characterized their functions, especially the unexpected secretion of 102 polypeptide hormone using bioinformatics analyses and immnunostaining verifications. Our study builds a strong foundation for understanding how the human placenta develops and functions to maintain a healthy pregnancy.

项目整体设计: single cell transcriptome profiles of stomal cells and trophoblast cells from 8 week and 24 week gestation of placenta were generated by next generation sequencing using Illumina Hiseq4000.

GEN 数据集:
GEND000058
测序方法:
物种:
组织:
健康状况:
细胞类型:
发育阶段:
方案
生长方案: -
处理方案: Extravillous trophoblast of weeks 24 of human placenta tissues were harvested from the hospital put into DMEM supplemented with 5% FBS. the tissue was transferred to the lab on ice within 1 h; Cytotrophoblast of weeks 8 of human placenta tissues were harvested from the hospital put into DMEM supplemented with 5% FBS. the tissue was transferred to the lab on ice within 1 h; TMR-positive CD8+ sorted T-cells of human placenta tissues were harvested from the hospital put into DMEM supplemented with 5% FBS. the tissue was transferred to the lab on ice within 1 h; Extravillous trophoblast of weeks 8 of human placenta tissues were harvested from the hospital put into DMEM supplemented with 5% FBS. the tissue was transferred to the lab on ice within 1 h; Stromal cell of weeks 8 of human placenta tissues were harvested from the hospital put into DMEM supplemented with 5% FBS. the tissue was transferred to the lab on ice within 1 h
提取方案: Chrion were scraped from human placenta and the remaining villi were collected and minced into small pieces. The tissue were digested with an enzyme cocktail (0.125% trypsin 0.04% Dnase and 0.05% type Ⅳ collagenase) for 8 min twice at 37℃ Cell suspension were collected by filtering the ezyme mixture with 70 μm cell strainer and the enzyme reaction were stopped by addition of 5% DMEM. cells were centrifuged at 1200 g at 4 ℃ on a percoll gradient (7 layers: 10%, 20%, 30%, 40%, 50%, 60% and 70%) and cells from 30% - 50% percoll gradient were collected and washed with DMEM. EVT and CTB were sorted with MACS with PE-conjucted HLA-G and CDH1 antibody combined with anti-PE beads,STB were purified with mouth pipette based on their big size from the cell population and the remaning HLA-G and CDH1 double negative cells were stromal cells. For isolation of EVT from the basal plate of the 24 w placenta, basal plate were scaped from the placenta, minced and digested with the method as described above,finally 24 w EVT were purified by MACs with HLA-G antibody.
建库方案: the single cells were picked into 2ul cell lysis buffer using mouse pipet, then the transcriptome was amplified by modified smart-seq2 protocol which added in barcode for each cell. the amplified cDNAs were sheared into 300bp fragments, the 3' end of the cDNAs were enriched to build library with KAPA Hyper Prep Kits for Illumina
测序信息
分子类型: rRNA- RNA
库的片段类型: paired
库的链类型: Reverse; -
测序平台: Illumina
测序仪型号: Illumina HiSeq 4000
链特异性: Specific; Unspecific
样本
基本信息:
样本描述:
生物条件:
实验变量:
方案:
测序信息:
质量评估:
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-seq reveals the diversity of trophoblast subtypes and patterns of differentiation in the human placenta.
Cell research . 2018-07-24 [PMID: 30042384]