Description
This track displays data from Integrated analysis of
multimodal single-cell data. Human peripheral blood mononuclear cells
(PBMCs) taken from pre-vaccinated and post-vaccinated individuals were profiled
using both CITE-seq and ECCITE-seq. A total of 57 cell type clusters were
identified and each cluster included cells from all 24 samples with rare
exceptions. This dataset contains three annotations for cell clustering: Level
1 (8 cell types), Level 2 (30 cell types), Level 3 (57 cell types).
This track collection contains six bar chart tracks of RNA expression in PBMCs
where cells are grouped by cell type level 1
(Blood PBMC Cells), cell type level 2
(Blood PBMC Cells 2),
cell type level 3 (Blood PBMC Cells 3), donor
(Blood PBMC Donor), phase of cell cycle
(Blood PBMC Phase), or time into experiment
(Blood PBMC Time). The default track displayed
is Blood PBMC Cells.
Display Conventions
The cell types are colored by which class they belong to according to the following table.
| Color |
Cell classification |
| immune |
Cells that fall into multiple classes will be colored by blending the colors associated
with those classes.
Method
PBMC samples were taken from 8 volunteers ages 20-49 enrolled in an HIV
vaccine trial (NCT01578889). A total of 24 blood samples were collected at 3
time points: day 0 (the day before), day 3, and day 7 after the administration
of a VSV-vectored HIV vaccine. Samples were collected at these different time
points to minimize batch effects. Cells were then divided into separate
aliquots for modified versions of the 3' CITE-seq and 5' ECCITE-seq staining
protocols. In the 3' CITE-seq staining protocol, the samples are simultaneously
stained with the antibody and unique hashtag. Whereas, 5' ECCITE-seq samples
are stained first with a unique hashtag. 3' libraries were loaded into 8 lanes
of a 10x Genomics Chip B using the 10x Genomics 3' v3 kit. 5' libraries
were loaded into 2 lanes of a 10x Genomics Chip A using the 10x Genomics V(D)J
kit (v1). Both 3' and 5' libraries were pooled together and sequenced on an
Illumina Novaseq S4 flowcell. In total, 210,911 cells were profiled after
quality control and doublet filtration.
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 Yuhan Hao, Stephanie Hao, 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
Hao Y, Hao S, Andersen-Nissen E, Mauck WM 3rd, Zheng S, Butler A, Lee MJ, Wilk AJ, Darby C, Zager M
et al.
Integrated analysis of multimodal single-cell data.
Cell. 2021 Jun 24;184(13):3573-3587.e29.
PMID: 34062119; PMC: PMC8238499
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US Server