PanglaoDB
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oscar-franzen
oscar-franzen
metadata and data from the database
PanglaoDB
This repo contains data and metadata from the database https://PanglaoDB.se
data directory
Files contain comma-delimited tables without headers.
sample_clusters directory
Contains cell clustering results.
cell_type_abbrev.txt
Maps cell types to abbreviations.
| Column | Description |
|---|---|
| 1 | Cell type |
| 2 | Abbreviation |
cell_type_annotations.txt
Mapping cell clusters to cell types.
| Column | Description |
|---|---|
| 1 | SRA accession |
| 2 | SRS accession |
| 3 | Cluster index |
| 4 | Cell type annotation |
| 5 | P-value from Hypergeometric test |
| 6 | Adjusted p-value (BH) |
| 7 | Cell type Activity Score |
cell_type_annotations_markers.txt
Markers that were used to determine the cell type.
| Column | Description |
|---|---|
| 1 | SRA accession |
| 2 | SRS accession |
| 3 | Cluster index |
| 4 | Gene symbol |
cell_type_desc.txt
Cell types and their descriptions.
| Column | Description |
|---|---|
| 1 | Cell type |
| 2 | Biological description of this cell type |
| 3 | Possible synonyms |
clusters_to_number_of_cells.txt
Clusters to number of cells
| Column | Description |
|---|---|
| 1 | SRA accession |
| 2 | SRS accession |
| 3 | Cluster index |
| 4 | Number of cells |
cyclone.txt
Results from cell cycle analysis based on cyclone.
| Column | Description |
|---|---|
| 1 | SRA accession |
| 2 | SRS accession |
| 3 | Cluster index |
| 4 | % cells in G1 |
| 5 | % cells in G2M |
| 6 | % cells in S |
expressed_tx_list.txt
Expressed transcription factors.
| Column | Description |
|---|---|
| 1 | SRA accession |
| 2 | SRS accession |
| 3 | Cluster index |
| 4 | Gene encoding the transcription factor |
genes.txt
Gene symbols used.
| Column | Description |
|---|---|
| 1 | Ensembl gene ID |
| 2 | Gene symbol |
germ_layers.txt
Cell types to organs and germ layers.
| Columns | Description |
|---|---|
| 1 | Cell type |
| 2 | Germ layer |
| 3 | Organ |
metadata.txt
Sample metadata.
| Columns | Description |
|---|---|
| 1 | SRA accession |
| 2 | SRS accession |
| 3 | Tissue origin of the sample |
| 4 | scRNA-seq protocol |
| 5 | Species |
| 6 | Sequencing instrument |
| 7 | Number of expressed genes |
| 8 | Median number of expressed genes per cell |
| 9 | Number of cell clusters in this sample |
| 10 | Is the sample from a tumor? (1 true otherwise false) |
| 11 | Is the sample from primary adult tissue? |
| 12 | Is the sample from a cell line? |
mito.txt
Mitochondrial expression.
| Columns | Description |
|---|---|
| 1 | SRA accession |
| 2 | SRS accession |
| 3 | Cluster index |
| 4 | z-score |
| 5 | P-value |
| 6 | Adjusted p-value |
| 7 | Mean perc mito reads |
regulons.txt
| Columns | Description |
|---|---|
| 1 | SRA accession |
| 2 | SRS accession |
| 3 | Cluster index |
| 4 | Transcription factor gene |
| 5 | TF binding site motif |
| 6 | Confidence (AUC) |
| 7 | Genes controlled by this TF |
Contact
- Oscar Franzén [email protected]
Reference
- Franzén,O., Gan,L.-M. and Björkegren,J.L.M. PanglaoDB: a web server for exploration of mouse and human single-cell RNA sequencing data. Database (2019) Vol. 2019: doi:10.1093/database/baz046
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