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

PRJNA377736: Tracing the temporal-spatial transcriptomic landscapes of the human fetal digestive tract by single cell RNA-seq analysis [fetal tissues]

来源: NCBI / GSE95630
提交时间: Mar 02 2017
释放时间: Apr 05 2018
最后更新时间: May 15 2019

概要: The development of digestion tract is critical for proper digestion of food and absorbance of nutrient for an individual. It includes the spatial segregation into esophagus, stomach, small and large intestine. The temporal-spatial gene expression profiles of human digestion tract in vivo have never been analyzed at single-cell resolution.Here we analyzed esophagus, stomach, small intestine (SI) and large intestine (LI) from multiple human embryos between 6 and 25 weeks of gestation by single cell RNA-seq analyses.We firstly identified 51 clusters of different types of cells using t- Distributed Stochastic Neighbor Embedding (t-SNE) analysis.Moreover,cell type of each organ were identified according to the known marker genes and new cell types were further analyzed.The dynamic change of each cell type were tracked during the human embryonic digestive tract development.We found HOX family geens paly different roles in the regulation of digestion tract developemnt. In addition, Hedgehog,TGF尾 and BMP signaling pathway are essential for SI and LI development in human fetal. The function of nutrient digestion and absorption was increased as the SI development in human fetal.Finally, we demonstrated that the immune system was established at late stage of human fetal and verified the immune-like cells,such as T cell, B cells and macrophage. In summary, by using single cell RNA seq technique, we identified the waves of signaling pathways and critical cell types for the human digestion tract development.

项目整体设计: Single cell transcriptome profiles of four main human organs (esophagus, stomach, small and large intestine) from 6 week to 25 week gestation of digestion system were generated by next generation sequencing using Illumina HiSeq X Ten

GEN 数据集:
GEND000213
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方案
生长方案: For every embryo, the main organs of digest system, including esophagus, stomach, small intestine (SI), large intestine (LI), were dissected. For 11W to 25W small intestine, the villi and crypt were separated by shaving off the villi carefully with a surgical blade. The mesenterium of small intestine and large intestine were torn off carefully under a microscope. The middle section of dissected esophagus, SI and LI was used to collect single cells. And the corpus of stomach was used to collect single cells. The selected tissue pieces were washed by PBS for several times considering there many microorganisms and mucus in digest system even in the early development stage. Then the selected tissue pieces were minced to small pieces by surgical scissors, after which the minced tissues were digested to single cells by using 2mg/mL Collagenase/Dispase for 30-40 min at 37. When digest intestine crypt, 2mM EDTA was firstly used to insure the release of the cells from intestine crypt. 40m strainer was used to filter large tissue debris. Then the cell suspension in the solution of Collagenase/Dispase was centrifuged at 800g for 5min at 4 and the cell pellet was re-suspended in 1% HSA.
处理方案: -
提取方案: After pick single cells using mouth pipette, they were transferred to cold scRNA-seq lysis buffer immediately. Subsequently, the lysis buffer were shocked for 3min at 72 to make sure the release of RNA.
建库方案: -
测序信息
分子类型: poly(A)+ RNA
库的片段类型: SINGLE
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
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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
Tracing the temporal-spatial transcriptome landscapes of the human fetal digestive tract using single-cell RNA-sequencing.
Nature cell biology . 2018-05-25 [PMID: 29802404]