Good morning, Bioconductor team:

I am using the pbmc_10x dataset from the SingleCellMultiModal package found in the following link

https://bioconductor.org/packages/release/data/experiment/vignettes/SingleCellMultiModal/inst/doc/scMultiome.html

Within the website it is mentioned that the cell types were produced by 10X. I have two questions:

1) Could you please provide the exact link to the 10X dataset from which this dataset was sourced?

2) Could you please provide a reference to a publication or other document that confirms who and how the labels were obtained?

Thank you for your time,

Javier

If you check the underlying code a bit you find that there is a file with data sources:

modes_file <- system.file("extdata", "metadata.csv", package = "SingleCellMultiModal", mustWork = TRUE)

# Read it and scan for multiome
available <- read.csv(modes_file)
available[grep("Multiome", available$DataProvider),]
#>    DataType     ResourceName
#> 68 pbmc_10x pbmc_rna_tenx.h5
#>                                                RDataPath DispatchClass
#> 68 SingleCellMultiModal/pbmc_10x/v1.0.1/pbmc_rna_tenx.h5        H5File
#>    RDataClass                                  Maintainer
#> 68 TENxMatrix Marcel Ramos <marcel.ramos@roswellpark.org>
#>                                                                              DataProvider
#> 68 10X Genomics, Single Cell Multiome ATAC + Gene Expression Dataset by Cell Ranger 1.0.0
#>    Coordinate_1_based TaxonomyId      Species SourceVersion
#> 68                 NA       9606 Homo sapiens         1.0.1
#>                                                                                                                                  SourceUrl
#> 68 https://cf.10xgenomics.com/samples/cell-arc/1.0.0/pbmc_granulocyte_sorted_10k/pbmc_granulocyte_sorted_10k_filtered_feature_bc_matrix.h5
#>    SourceType Genome BiocVersion
#> 68       HDF5     NA        3.14
#>                                            Description         Title
#> 68 pbmc_rna_tenx data specific to the PBMC_10X project pbmc_rna_tenx
Created on 2025-04-08 with reprex v2.1.1