CATlas-datasets Hub
Call for contributions to the CATlas
To expand the single cell multi-omics data-resource, we admire receive the dataset by accepting submissions from researchers with existing single-cell datasets. Submitted datasets will be made publicly available on the CATlas Portal.
We accept submissions of single-cell ATAC, single-cell hic, 10x multiome, Paired-Tag or Others across multi-sepcies datasets. Researchers are recommend process their data by
scanpy, avaliable at (https://github.com/scverse/scanpy), cicero, avaliable at (https://github.com/cole-trapnell-lab/cicero-release),
SCENIC+, avaliable at (https://github.com/aertslab/SCENICplus), SnapATAC2, avaliable at (https://github.com/kaizhang/SnapATAC2),
monocle, avaliable at (https://github.com/cole-trapnell-lab/monocle3),
and submit the output, along with cell (see Submitting Cell Metadata) metadata, expression (see Submitting expression Matrix) Matrix and bigwig(see Submitting bigwig).
Submitters must take the following steps:
1. Complete an intake form to determine dataset eligibility: . We will contact you within several working days of your submission to notify you of your eligibility and provide additional information required for submission.
2. Process the dataset you will submit following the corrsponding file format
3. Transfer the single cell metadata, expression matrix and other necessary datasets to the CATlas.
| Metadata Field | Description |
|---|---|
Cell ID |
Unique ID for each cell, eg.MM_566.GCGGTGTATGCCGGATCAAGTT |
Cell Type |
The cell type or label assigned to the cell |
Cell Type Name |
The detail name of cell types |
Cell Cluster |
(Optional) |
UMAP_1 |
Replaceable: tsne_1 or pca_1. Coords for each cell |
UMAP_2 |
Replaceable: tsne_2 or pca_2. Coords for each cell |
Example Cell_matrix.tsv file
| Cell ID | Cell Type | Cell Type Name | Cell Cluster | UMAP_1 | UMAP_2 |
|---|---|---|---|---|---|
| Cell1 | A1 | B1 | C1 | ... | ... |
| Cell2 | A2 | B2 | C2 | ... | ... |
| Cell3 | A3 | B3 | C3 | ... | ... |
| ... | ... | ... | ... | ... | ... |
| Field | Description |
|---|---|
File format |
A matrix in a tab-separated format (often denoted by '\t' or a tab character). |
NxM matrix |
Describes the dimensions of the matrix where N is the number of genes and M is the number of cells. |
N: gene |
Gene name or gene id for the first value in each row. |
M: cell id |
Expression value for genes across all cells. |
Example expressionMatrix.tsv file
| Cell1 | Cell2 | Cell3 | Cell4 | ... |
|---|---|---|---|---|
| gene1 | A1 | B1 | C1 | ... |
| gene2 | A2 | B2 | C2 | ... |
| gene3 | A3 | B3 | C3 | ... |
| ... | ... | ... | ... | ... |
| Field | Description |
|---|---|
bigwig |
Each bigwig file named by celltypes. |
Example files
Celltype1.bw
Celltype2.bw
Celltype3.bw