diff --git a/content/04.methods.md b/content/04.methods.md index 4e2b359..4b4032e 100644 --- a/content/04.methods.md +++ b/content/04.methods.md @@ -7,6 +7,7 @@ Single-cell or single-nuclei libraries were generated using one of the commercia For bulk RNA-seq, RNA was collected and sequenced using either paired-end or single-end sequencing. For spatial transcriptomics, cDNA libraries were generated using the Visium kit from 10x Genomics. All libraries were processed using our open-source pipeline, `scpca-nf`, to produce summarized gene expression data. +A detailed summary with the total number of samples and libraries collected for each sequencing method broken down by project is available in Table S1. ### Metadata @@ -86,7 +87,7 @@ The normalized ADT data are available in the `altExp` of the processed object. ### Processing HTO data from multiplexed libraries To identify which cells come from which samples in a multiplexed library, we applied three different demultiplexing methods: genetic demultiplexing, HTO demultiplexing using `DropletUtils::hashedDrops()`, and HTO demultiplexing using `Seurat::HTODemux()`. -We do not provide separate `SingleCellExperiment` objects for each sample in a library. +We do not provide separate `SingleCellExperiment` objects for each sample in a library. Each multiplexed library object contains the counts data from all samples and the results from all three demultiplexing methods to allow users to select which method(s) to use. #### Genetic demultiplexing diff --git a/content/100.figure-table-legends.md b/content/100.figure-table-legends.md index 3d75225..4913ca0 100644 --- a/content/100.figure-table-legends.md +++ b/content/100.figure-table-legends.md @@ -101,7 +101,7 @@ This table provides descriptions and sample and library counts for each project `Total number of samples (S)`: Number of samples associated with the project. `Total number of libraries (L)`: Number of libraries associated with the project. Due to additional sequencing modalities and/or multiplexing, projects may have more libraries than samples. -All remaining columns give the number of libraries (as designated with `(L)`) with the given suspension type or additional modality. +All remaining columns give the number of libraries (as designated with `(L)`) with the given suspension type, 10x kit version, or additional modality.