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Update Table S1 legend and mention in methods #115

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merged 4 commits into from
Apr 4, 2024
Merged

Update Table S1 legend and mention in methods #115

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35509af
update legend to mention 10X kits
allyhawkins Apr 3, 2024
f57a517
mention Table S1 in data generation section
allyhawkins Apr 3, 2024
91cf459
add kit
allyhawkins Apr 4, 2024
1787a72
Merge branch 'main' into allyhawkins/include-kits-table
allyhawkins Apr 4, 2024
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3 changes: 2 additions & 1 deletion content/04.methods.md
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Expand Up @@ -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

Expand Down Expand Up @@ -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
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2 changes: 1 addition & 1 deletion content/100.figure-table-legends.md
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Expand Up @@ -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.
<br><br>

<!-- Table S2 -->
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