Is your dataset not yet in sfaira?
No
Describe the data set
Fill in below:
Link to publication: https://www.nature.com/articles/s41593-021-01005-1
Title of publication: Disentangling glial diversity in peripheral nerves at single-nuclei resolution.
First author of the publication: Aldrin K. Y. Yim
DOI preprint:
DOI journal: 10.1038/s41593-021-01005-1
Download link to any data objects required:
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Describe metadata
Optionally, you can already collect metadata information here before starting to write the data loader or to help others write one.
You can extend these lists if you find more metadata that you want to record before writing a data loader.
Note that you can also directly put this information into a draft data loader and start a pull request instead of first writing an issue.
If you know this dataset well but cannot write a loader right now, this will help other people decide if they want to write a loader for this dataset and will speed up their process.
Is this primary data (not a meta-study): Yes
Is most raw gene expression matrix normalized (if yes how)?: No
Single-cell assay used: 10x
Disease(s) of sampled individuals: none
Organ(s) sampled (ideally UBERON term): 0001322 (sciatic nerve) 0001759 (vagus nerve) 0015488 (sural nerve)
Organism(s) sampled (ideally NCBItaxon term): 10090 (Mus musculus)
Any relevant cell-wise annotation fields that are column names of a table or column names in .obs of an h5ad for example:
Cell type annotation: Todo
Additional context
Add any other context of the dataset or anticipated issues with the data loader.
Single nuclei atlas of the peripheral Nerves in M. musculus.
Single nuclei obtained by ActB-Cre/MPZ-Cre x Sun1-GFP FACS
Libraries: 10X Genomics v2 (ActB)/v3 (MPZ)
Sequencing: Illumina HiSeq 2500 or NovaSeq 6000
Caveat: this is a tissue atlas constructed from several datasets, I don't know if these should be treated as individual entries or included in their joint form. Sub datasets are:
Immune cells (CD45+ FACS sorted single cells)
Schwann cell-specific (MPZ-Cre x Sun1-GFP FACS sorted single nuclei)
Sciatic nerve (ActB-Cre x Sun1-GFP FACS sorted single nuclei)
Peripheral nerve (ActB-Cre x Sun1-GFP FACS sorted single nuclei of Sciatic + Sural + Vagus nerve)
Is your dataset not yet in sfaira?
No
Describe the data set
Fill in below:
Link to publication: https://www.nature.com/articles/s41593-021-01005-1
Title of publication: Disentangling glial diversity in peripheral nerves at single-nuclei resolution.
First author of the publication: Aldrin K. Y. Yim
DOI preprint:
DOI journal: 10.1038/s41593-021-01005-1
Download link to any data objects required:
Describe metadata
Optionally, you can already collect metadata information here before starting to write the data loader or to help others write one.
You can extend these lists if you find more metadata that you want to record before writing a data loader.
Note that you can also directly put this information into a draft data loader and start a pull request instead of first writing an issue.
If you know this dataset well but cannot write a loader right now, this will help other people decide if they want to write a loader for this dataset and will speed up their process.
Is this primary data (not a meta-study): Yes
Is most raw gene expression matrix normalized (if yes how)?: No
Single-cell assay used: 10x
Disease(s) of sampled individuals: none
Organ(s) sampled (ideally UBERON term): 0001322 (sciatic nerve) 0001759 (vagus nerve) 0015488 (sural nerve)
Organism(s) sampled (ideally NCBItaxon term): 10090 (Mus musculus)
Any relevant cell-wise annotation fields that are column names of a table or column names in .obs of an h5ad for example:
Cell type annotation: Todo
Additional context
Add any other context of the dataset or anticipated issues with the data loader.
Single nuclei atlas of the peripheral Nerves in M. musculus.
Single nuclei obtained by ActB-Cre/MPZ-Cre x Sun1-GFP FACS
Libraries: 10X Genomics v2 (ActB)/v3 (MPZ)
Sequencing: Illumina HiSeq 2500 or NovaSeq 6000
Caveat: this is a tissue atlas constructed from several datasets, I don't know if these should be treated as individual entries or included in their joint form. Sub datasets are:
Immune cells (CD45+ FACS sorted single cells)
Schwann cell-specific (MPZ-Cre x Sun1-GFP FACS sorted single nuclei)
Sciatic nerve (ActB-Cre x Sun1-GFP FACS sorted single nuclei)
Peripheral nerve (ActB-Cre x Sun1-GFP FACS sorted single nuclei of Sciatic + Sural + Vagus nerve)