Gene Expression
Nebulas
Gene Expression NebulasSummary: 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.
Overall Design: Single cell mRNA-seq of placenta from two term healthy pregnancies.
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| Growth Protocol: | - |
| Treatment Protocol: | 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. |
| Extract Protocol: | C1 Single-Cell Auto Prep Integrated Fluidic Chip for mRNA-seq (17-25 micron cell size selection). |
| Library Construction Protocol: | Nextera XT DNA Library Preparation Kit - manufacturer's recommendation. |
| Molecule Type: | poly(A)+ RNA |
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| Library Layout: | paired |
| Library Strand: | - |
| Platform: | Illumina |
| Instrument Model: | Illumina HiSeq 2500 |
| Strand-Specific: | Unspecific |
| Data Resource | GEN Sample ID | GEN Dataset ID | Project ID | BioProject ID | Sample ID | Sample Name | BioSample ID | Sample Accession | Experiment Accession | Release Date | Submission Date | Update Date | Species | Race | Ethnicity | Age | Age Unit | Gender | Source Name | Tissue | Cell Type | Cell Subtype | Cell Line | Disease | Disease State | Development Stage | Mutation | Phenotype | Case Detail | Control Detail | Growth Protocol | Treatment Protocol | Extract Protocol | Library Construction Protocol | Molecule Type | Library Layout | Strand-Specific | Library Strand | Spike-In | Strategy | Platform | Instrument Model | Cell Number | Reads Number | Gbases | AvgSpotLen1 | AvgSpotLen2 | Uniq Mapping Rate | Multiple Mapping Rate | Coverage Rate |
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