CITE-Seq of COVID-19 Human Lungs

Gail H. Deutsch1, Ravi Misra2, Thomas J. Mariani2, Gloria Pryhuber2
1University of Washington, 2University of Rochester Medical Center, *Corresponding author
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Description Single-cell CITE-Seq of human COVID-19 infected and control lungs, spanning lifespan, using an optimized protocol for 10X Genomics Single Cell 3' (v3.1) CITE-Seq analysis. This protocol describes the steps necessary for preparing generating sequencing data following staining single cells with ADT-tagged antibodies (including library preparation, sequencing steps, and mapping steps).
Dataset ID LMEX0000004406
Assay Type Single-cell RNA-seq
Organism Human
Stages Child | Adolescent | Adult | 65+ years
Cell Count 302922
Technology 10x Genomics Chromium Single Cell Gene Expression
FileDescriptionSize
COVID_ADT.h5adTotalVI denoised surface-protein object, HDF5 AnnData, gzip compressed. 261,101 cells x 56 antibody-derived tags over the authors' 54 cell states and 50 libraries. X holds log2 of one plus the denoised value and layers['denoised_linear'] the linear values; no counts-per-ten-thousand step is applied, because rescaling a 56-plex panel by its own total would destroy the absolute abundance TotalVI recovers. The cells are the intersection of the ADT matrix, the gene-expression object and the author annotations.124.6 MB
COVID_RNA.h5adGene-expression object over the SAME 261,101 cells as the ADT object, HDF5 AnnData, gzip compressed. 261,101 cells x 35,545 genes, the authors' 54 cell states, 50 libraries. X holds log2 counts per ten thousand and layers['counts'] the raw integer counts it was rebuilt from; obsm carries the UMAP.5145.6 MB
COVID_library_metadata.tsvLibrary metadata for the 50 libraries, one row each, with the donor, COVID history, sex, reported race, lung lobe, age and death type. The rows account for all 261,101 cells in both objects.5.7 KB
LungMAP IDAlt IDSpeciesSexRaceAgeAge GroupHealth Status
LMSPCOVID0000001D105_CBL_MIX_2Homo sapiensFemaleWhite0.5 years31 days-1 yearNo COVID history
LMSPCOVID0000002D116_RML_MIX_02Homo sapiensFemaleBlack/AA40 years18+ yearsNo COVID history
LMSPCOVID0000003D122_RML_MIX_2Homo sapiensMaleHispanic31 years18+ yearsNo COVID history
LMSPCOVID0000004D239_CBL_MIX_3Homo sapiensMaleBlack/AA37 years18+ yearsNo COVID history
LMSPCOVID0000005D271_RML_MIX_02Homo sapiensMaleWhite53 years18+ yearsNo COVID history
LMSPCOVID0000006D274_RUL_MIX_2Homo sapiensMaleAsian70.2 years65+ yearsEarly Pneumonia
LMSPCOVID0000007D283_RML_MIX_2Homo sapiensMaleWhite69 years65+ yearsNo COVID history
LMSPCOVID0000008D291_RUL_MIX_3Homo sapiensMaleWhite24.6 years18+ yearsNo COVID history
LMSPCOVID0000009D292_RUL_MIX_3Homo sapiensFemaleWhite25 years18+ yearsNo COVID history
LMSPCOVID0000010D298_RUL_MIX_2Homo sapiensMaleWhite53.4 years18+ yearsLate Pneumonia
LMSPCOVID0000011D300_CBL_MIX_2Homo sapiensFemaleHispanic9.3 years1-11 yearsNon-COVID Death, Past Hx
LMSPCOVID0000012D303_RML_MIX_2Homo sapiensMaleWhite50.5 years18+ yearsEarly Pneumonia
LMSPCOVID0000013D305_RUL_MIX_2Homo sapiensFemaleWhite67 years65+ yearsNo COVID history
LMSPCOVID0000014D307_CBL_MIX_2Homo sapiensMaleBlack/AA15 years11-18 yearsNo COVID history
LMSPCOVID0000015D312_RUL_MIX_3Homo sapiensMaleWhite53.6 years18+ yearsNo COVID history
LMSPCOVID0000016D314_LUL_MIX_2Homo sapiensFemaleHispanic24.6 years18+ yearsNon-COVID Death, Past Hx
LMSPCOVID0000017D316_RUL_MIX_02Homo sapiensFemaleWhite51.5 years18+ yearsLate Pneumonia
LMSPCOVID0000018D318_RML_MIX_3Homo sapiensFemaleBlack/AA65 years65+ yearsEarly Pneumonia
LMSPCOVID0000019D326_CBL_MIX_2Homo sapiensMaleWhite0.3 years31 days-1 yearNo COVID history
LMSPCOVID0000020D329_RUL_MIX_2Homo sapiensMaleWhite Hispanic58 years18+ yearsLate Pneumonia
LMSPCOVID0000021D331_RUL_MIX_2Homo sapiensMaleWhite53.5 years18+ yearsNon-COVID Death, Recent Hx
LMSPCOVID0000022D334_CBL_MIX_2Homo sapiensMaleHispanic14.4 years11-18 yearsNon-COVID Death, Recent Hx
LMSPCOVID0000023D335_CBL_MIX_04Homo sapiensFemaleAsian41 years18+ yearsNon-COVID Death, Past Hx
LMSPCOVID0000024D337_CBL_MIX_2Homo sapiensFemaleWhite0.6 years31 days-1 yearNo COVID history
LMSPCOVID0000025D341_RUL_MIX_2Homo sapiensFemaleHispanic56.8 years18+ yearsNo COVID history
LMSPCOVID0000026D342_RUL_MIX_3Homo sapiensMaleBlack/AA58.8 years18+ yearsNon-COVID Death, Past Hx
LMSPCOVID0000027D346_RUL_MIX_2Homo sapiensMaleWhite59 years18+ yearsNo COVID history
LMSPCOVID0000028D353_CBL_MIX_2Homo sapiensMaleAsian52.9 years18+ yearsLate Pneumonia
LMSPCOVID0000029D356_RUL_MIX_3Homo sapiensMaleWhite65.8 years65+ yearsNo COVID history
LMSPCOVID0000030D357_RUL_MIX_02Homo sapiensFemaleHispanic53 years18+ yearsNon-COVID Death, Recent Hx
LMSPCOVID0000031D359_CBL_MIX_2Homo sapiensMaleWhite1.1 years1-11 yearsNo COVID history
LMSPCOVID0000032D360_RML_MIX_2Homo sapiensFemaleBlack/AA67.8 years65+ yearsEarly Pneumonia
LMSPCOVID0000033D366_RUL_MIX_02Homo sapiensFemaleWhite39.3 years18+ yearsNon-COVID Death, Past Hx
LMSPCOVID0000034D369_RUL_MIX_2Homo sapiensFemaleWhite37 years18+ yearsLate Pneumonia
LMSPCOVID0000035D370_RUL_MIX_2Homo sapiensFemaleHispanic13 years11-18 yearsNon-COVID Death, Recent Hx
LMSPCOVID0000036D373_RUL_MIX_2Homo sapiensMaleWhite66.1 years65+ yearsNo COVID history
LMSPCOVID0000037D375_RUL_MIX_2Homo sapiensMaleHispanic64.4 years18+ yearsNon-COVID Death, Past Hx
LMSPCOVID0000038D376_RUL_MIX_04Homo sapiensFemaleAsian25 years18+ yearsNo COVID history
LMSPCOVID0000039D381_RUL_MIX_2Homo sapiensFemaleWhite62.1 years18+ yearsNon-COVID Death, Past Hx
LMSPCOVID0000040D383_RUL_MIX_2Homo sapiensMaleWhite43 years18+ yearsNon-COVID Death, Past Hx
LMSPCOVID0000041D386_RUL_MIX_2Homo sapiensMaleWhite44.5 years18+ yearsLate Pneumonia
LMSPCOVID0000042D387_CBL_MIX_2Homo sapiensMaleWhite10.5 years1-11 yearsNo COVID history
LMSPCOVID0000043D388_RUL_MIX_01Homo sapiensMaleWhite24.9 years18+ yearsLate Pneumonia
LMSPCOVID0000044D389_RUL_MIX_2Homo sapiensMaleHispanic59 years18+ yearsLate Pneumonia
LMSPCOVID0000045D391_CBL_MIX_2Homo sapiensFemaleWhite16.9 years11-18 yearsNo COVID history
LMSPCOVID0000046D396_RUL_MIX_2Homo sapiensMaleWhite24.9 years18+ yearsNon-COVID Death, Recent Hx
LMSPCOVID0000047D398_RUL_MIX_02Homo sapiensFemaleWhite44 years18+ yearsLate Pneumonia
LMSPCOVID0000048D403_RUL_MIX_02Homo sapiensFemaleAsian49.6 years18+ yearsNo COVID history
LMSPCOVID0000049D404_CBL_MIX_2Homo sapiensFemaleMore than 1 race9.6 years1-11 yearsNo COVID history
LMSPCOVID0000050D408_CBL_MIX_2Homo sapiensMaleWhite3.1 years1-11 yearsNon-COVID Death, Recent Hx