Schema for Blood PBMC Donor - Blood PBMCs binned by blood donor from Hao et al 2020
  Database: hg38    Primary Table: bloodHaoDonor Data last updated: 2022-05-12
Big Bed File: /gbdb/hg38/bbi/bloodHao/donor.bb
Item Count: 22,710
Format description: BED6+5 with additional fields for category count and median values, and sample matrix fields
fieldexampledescription
chromchr1Reference sequence chromosome or scaffold
chromStart166070019Start position in chromosome
chromEnd166166969End position in chromosome
nameFAM78BName or ID of item
score0Score from 0-1000, typically derived from total of median value from all categories
strand-+ or - for strand. Use . if not applicable
name2ENSG00000188859.6Alternative name for item
expCount8Number of categories
expScores0.00110842,0.00016115,0,0.000162235,0,0,0.000133962,0Comma separated list of category values

Sample Rows
 
chromchromStartchromEndnamescorestrandname2expCountexpScores
chr1166070019166166969FAM78B0-ENSG00000188859.680.00110842,0.00016115,0,0.000162235,0,0,0.000133962,0
chr1166475771166490039LINC016750-ENSG00000234142.180.00049688,0.000909892,0.000756504,0.000527262,0.000654184,0.00110846,0.00119454,0.000712951
chr1166840088166854473POGK0+ENSG00000143157.1180.0934585,0.0872169,0.0922903,0.0978523,0.153801,0.147062,0.145592,0.12874
chr1166856509166876327TADA10-ENSG00000152382.580.0203317,0.0179052,0.0186414,0.0196618,0.0347114,0.0298306,0.0290699,0.0282232
chr1166908190166975324ILDR20-ENSG00000143195.1280,0,0.000236408,0,0.000551055,0.000904841,0.00091348,0.000316867
chr1166989108167022214MAEL0+ENSG00000143194.1280,0,0,0,0,0.000453976,0.000341734,0.000321354
chr1167052835167090631GPA330-ENSG00000143167.1180.0120218,0.0125743,0.00918513,0.00987337,0.00977859,0.0114774,0.0105143,0.0145889
chr1167219830167220512AL451050.20-ENSG00000272205.180.0021404,0.00153777,0.00222223,0.00234246,0.00259815,0.002384,0.00222832,0.00205964
chr1167220828167427345POU2F10+ENSG00000143190.2280.0717299,0.0711976,0.0845629,0.0717745,0.131605,0.12688,0.114135,0.117656
chr1167430639167518538CD2470-ENSG00000198821.1080.444919,0.412275,0.516573,0.278435,0.559925,0.50032,0.38146,0.666244

Blood PBMC Donor (bloodHaoDonor) Track Description
 

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