Schema for Placenta Cells - Placenta and decidua cells binned by cell type 10x from Vento-Tormo et al 2018
Database: hg38 Primary Table: placentaVentoTormoCellType10x Data last updated: 2022-05-12|
Big Bed File: /gbdb/hg38/bbi/placentaVentoTormo/10x/cell_type.bb
Item Count: 28,793
Format description: BED6+5 with additional fields for category count and median values, and sample matrix fields
|chrom||chr1||Reference sequence chromosome or scaffold|
|chromStart||166069298||Start position in chromosome|
|chromEnd||166167001||End position in chromosome|
|name||FAM78B||Name or ID of item|
|score||0||Score from 0-1000, typically derived from total of median value from all categories|
|strand||-||+ or - for strand. Use . if not applicable|
|name2||NM_001017961||Alternative name for item|
|expCount||13||Number of categories|
|expScores||0.000696718,0.000568242,0,0.0137063,0,0,0.000646704,0.000824847,0,5.50314e-05,0.00790748,0.0129514,0.000148967||Comma separated list of category values|
Placenta Cells (placentaVentoTormoCellType10x) Track 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 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 Ss2, and
Placenta Mat/Fet Ss2.
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.
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
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.
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
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.
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.