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