How to access the cell type annotation

[onebeingmay]

Dear Tabula team, I downloaded the processed data from https://figshare.com/projects/Tabula_Muris_Senis/64982 and loaded the data into R using Seurat's ReadH5AD function. When I checked the meta.data I cannot find the cell type annotation? For example, https://github.com/czbiohub/tabula-muris/blob/master/22_markers/droplet_Lung_cell_ontology_class_classes.csv listed the cell type annotation, but I don't know which column it corresponds to in the meta.data? Here is an example of the meta.data of the lung droplet data set:

age cell cell.ontology.class cell.ontology.id free.annotation method mouse.id nFeatures_RNA sex subtissue tissue tissue.free.annotation nCount_RNA louvain cluster.names leiden AAACCTGAGCGTAATA-1-11-0-0 2 MACA_18m_F_LUNG_50_AAACCTGAGCGTAATA 0 4 0 0 6 2470 0 2 0 0 6594.1533203125 33 35 35 AAACGGGTCGCCCTTA-1-11-0-0 2 MACA_18m_F_LUNG_50_AAACGGGTCGCCCTTA 0 4 0 0 6 1821 0 2 0 0 5138.74755859375 8 8 8 AAAGATGAGCAGACTG-1-11-0-0 2 MACA_18m_F_LUNG_50_AAAGATGAGCAGACTG 6 7 6 0 6 1333 0 2 0 0 4399.15380859375 5 2 2 AAAGATGAGCCGTCGT-1-11-0-0 2 MACA_18m_F_LUNG_50_AAAGATGAGCCGTCGT 8 8 8 0 6 1455 0 2 0 0 4933.3740234375 4 1 1 AAAGCAACATGGTAGG-1-11-0-0 2 MACA_18m_F_LUNG_50_AAAGCAACATGGTAGG 5 3 5 0 6 3322 0 2 0 0 7091.1279296875 6 3 3 AAATGCCAGGAGTTGC-1-11-0-0 2 MACA_18m_F_LUNG_50_AAATGCCAGGAGTTGC 6 7 6 0 6 1300 0 2 0 0 4612.63916015625 5 2 2

Thank!

[aopisco]

@onebeingmay we don't recommend using ReadH5AD as other members in the community run into similar issues. I'd suggest for you to first convert the file to loom and then use sceasy:

sceasy:::convertFormat('filename.loom', from="loom", to="anndata",
                       outFile='filename.h5ad')

if you would like help creating the loom files please let me know

[onebeingmay]

@aopisco Thank you for your quick response! Did you mean if I first convert the downloaded h5ad objects to loom then back to h5ad using

sceasy:::convertFormat('filename.loom', from="loom", to="anndata",
                       outFile='filename.h5ad')

to load the cell type annotation information correctly? May I know which column of the meta.data is the cell type annotation (listed in https://github.com/czbiohub/tabula-muris/blob/master/22_markers/droplet_Lung_cell_ontology_class_classes.csv)? The column names I found include: [1] "age" "cell" "cell.ontology.class" "cell.ontology.id" "cellid"
[6] "free.annotation" "method" "mouse.id" "plate" "sex"
[11] "subtissue" "tissue" "well" "nFeatures_RNA" "nCount_RNA"
[16] "louvain" "cluster.names" "leiden" "cluster.number" Thanks!

[aopisco]

@onebeingmay my mistake, I meant first convert to loom then convert to single cell experiment

sceasy:::convertFormat('filename.loom', from="loom", to="sce",
                       outFile='filename.rds')

the file you are pointing to is from Tabula Muris and not Tabula Muris Senis. For that file -- which will not match Tabula Muris Senis -- the cell type annotations are in cell.ontology.class

[onebeingmay]

@aopisco My mistake. So does Tabula Muris Senis provide cell type information? Does the hdad files from https://figshare.com/projects/Tabula_Muris_Senis/64982 contain cell type annotation information? Thank you!

[aopisco]

yes, exactly, if you're looking for a single organ I recommend you use the ones split by tissue here

[onebeingmay]

Thanks @aopisco . I downloaded the tabula-muris-senis-facs-processed-official-annotations-Lung.h5ad from your link and the columns of the metadata include [1] "FACS.selection" "age" "cell" "cell.ontology.class" "cell.ontology.id"
[6] "free.annotation" "method" "mouse.id" "sex" "subtissue"
[11] "tissue" "nFeatures_RNA" "nCount_RNA" "louvain" "leiden"
May I know which column is the cell type annotation?

[aopisco]

cell.ontology.class

[onebeingmay]

Thanks! The cell.ontology.class contains 32 categories (number 0-31). Does Tabula Muris Senis provide a mapping from these numbers to actual cell type name (i.e. lung endothelial cell, stromal cell, T cell, B cell etc)?

[aopisco]

you are getting to this result because you are importing the file to R and that is not compatible. There are cell labels and not numbers -- that lung object match what you can search here: https://tabula-muris-senis.ds.czbiohub.org/lung/facs/

[onebeingmay]

Thank you! I load the data using scanpy and now can see the correct labels.

[aopisco]

Closing the issue for now as this sounds resolved! Feel free to re-open

[Nidane]

may i ask how would u guys suggest to convert the h5ad file into a loom file ? thanks!