Description

This track displays data from Single-cell reconstruction of the early maternal-fetal interface in humans. Using droplet-based 10x and plate-based Smart-seq2 single cell RNA-sequencing (scRNA-seq) ~70,000 cells were profiled from first-trimester placentas with matched decidual cells and maternal peripheral blood mononuclear cells (PBMC).

This track collection contains nine bar chart tracks of RNA expression in the human placenta, decidua, and maternal PBMCs where cells are grouped by cell type (Placenta Cells, Placenta Cells Ss2), detailed cell type (Placenta Detail, Placenta Detail Ss2), cell location (Placenta Loc, Placenta Loc Ss2), stage (Placenta Stage), and placenta and decidua cells (Placenta Mat/Fet, Placenta Mat/Fet Ss2). The default tracks displayed are Placenta Cells, Placenta Loc, Placenta Loc Ss2, and Placenta Mat/Fet Ss2.

Display Conventions

The cell types are colored by which class they belong to according to the following table.

Cells that fall into multiple classes will be colored by blending the colors associated with those classes. The colors will be purest in the Placenta Cells and Placenta Cells Ss2 subtracks, where the bars represent relatively pure cell types. They can give an overview of the cell composition within other categories in other subtracks as well.

Method

Tissue was collected from 5 placentas (6-14 gestational weeks) and 11 deciduas. Additionally, blood was drawn from 6 of the donors (D4-D9) and enriched for PBMCs using a Ficoll-Paque gradient. Decidual and placental tissue were both first macroscopically separated. Decidual tissue was then chopped before enzymatic dissociation. Placental villi was scraped from the chorionic membrane before enzymatic dissociation. Decidual and blood cells were enriched for certain populations using an antibody panel prior to Smart-seq2 library preparation. Cells from blood decidua and placenta were enriched using FACS prior to 10x Genomics v2 library preparation. Smart-seq2 libraries were sequenced on an Illumina HiSeq2000. 10x libraries were sequenced on an Illumina HiSeq4000.

The cell/gene matrix and cell-level metadata was downloaded from the UCSC Cell Browser. The UCSC command line utility matrixClusterColumns, matrixToBarChart, and bedToBigBed were used to transform these into a bar chart format bigBed file that can be visualized. The coloring was done by defining colors for the broad level cell classes and then using another UCSC utility, hcaColorCells, to interpolate the colors across all cell types. The UCSC utilities can be found on our download server.

Data Access

The raw bar chart data can be explored interactively with the Table Browser or the Data Integrator. For automated analysis, the data may be queried from our REST API. Please refer to our mailing list archives for questions, or our Data Access FAQ for more information.

Credit

Thanks to Roser Vento-Tormo, Mirjana Efremova, and to the many authors who worked on producing and publishing this data set. The data were integrated into the UCSC Genome Browser by Jim Kent and Brittney Wick then reviewed by Jairo Navarro. The UCSC work was paid for by the Chan Zuckerberg Initiative.

References

Vento-Tormo R, Efremova M, Botting RA, Turco MY, Vento-Tormo M, Meyer KB, Park JE, Stephenson E, Polański K, Goncalves A et al. Single-cell reconstruction of the early maternal-fetal interface in humans. Nature. 2018 Nov;563(7731):347-353. PMID: 30429548