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README.md

README.md

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

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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