PRJNA345620: Term placenta single cell transcriptome
概要: We provide single cell transcriptomes from the placental-uterine interface. Tissue was collected at term C-section (no labor) from two healthy pregnancies, from villous part of the placenta. Cells were disassociated and processed using Fluidigm technology. RNA-seq was performed on RNA from 33+54 single cells, at approx. 3.5 mio paired reads per cell. Clustering resulted in 4 trophoblast and a single immune cell clusters. As the placenta is an epitome of cell signaling, we combined the present cell-level transcriptomes with uterine cell transcriptomes to study the potential inter-cell communication. To this end, we inferred the cell-cell-interactome by assessing the gene expression of receptor-ligand pairs across cell types. We find among the signals transmitted a predominance of growth and immune signals, and suggest a delicate balance of enhancing and suppressive signals. Finally, this study provides a rich resource of gene expression profiles of term intravillous and extravillous trophoblasts.
项目整体设计: Single cell mRNA-seq of placenta from two term healthy pregnancies.
| 生长方案: |
- |
| 处理方案: |
Tissue underwent serial trypsin and collagenase digests and the resulting cell suspension was layered on a continuous Percoll gradient. Cells were collected from the 20-60% fractions. Collected cells were filtered through a 40um cell filter and underwent Trypan blue exclusion to assess viability. Cell suspension at 3x10^5 cell/ml was submitted to Cincinnati Children's gene expression core for single cell capture using Fluidigm integrated fluidic circuit. |
| 提取方案: |
C1 Single-Cell Auto Prep Integrated Fluidic Chip for mRNA-seq (17-25 micron cell size selection). |
| 建库方案: |
Nextera XT DNA Library Preparation Kit - manufacturer's recommendation. |
| 分子类型: |
poly(A)+ RNA |
| 库的片段类型: |
paired |
| 库的链类型: |
- |
| 测序平台: |
Illumina |
| 测序仪型号: |
Illumina HiSeq 2500 |
| 链特异性: |
Unspecific |
| 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 |
Single-cell transcriptomics of the human placenta: inferring the cell communication network of the maternal-fetal interface.
Genome research . 2017-02-07 [PMID:
28174237]
