Genomic Expression Archive
Single-cell submission guide
How to submit single-cell data
For single-cell gene expression data, submit raw data to DRA and processed data to GEA. Submit de-multiplexed (divided) sample and data files in the case of dozens cells (samples). In the case of more number of cells and de-multiplexed data affect reproducibility, submit multiplexed (mixed) sample and data files.
Regarding the 10x Genomics data files, please refer to What format of 10x Genomics data should I submit to NCBI GEO/SRA?.
Library information
In both de-multiplexed and multiplexed submissions, describe methods, name and version of kit (e.g., Smart-seq2, 10x, Drop-seq) used for single-cell library construction in Library Construction Protocol of the DRA Experiment. For 10x technology, describe version of 10x chemistry (e.g., v1, v2).
Data file formats
Submit raw data in fastq or bam to DRA. Include barcode sequences.
For 10x bam files without barcode sequences, submit fastq instead. Please see Generating FASTQs with cellranger mkfastq
GEA Experiment Type
Select ‘RNA-seq of coding RNA from single cells’ or ‘RNA-seq of non coding RNA from single cells’. GEA Experiment Type
De-multiplexed submission
BioSample
Create a sample for each cell in BioSample and describe cell-specific information in sample attributes.
| *sample_name | … | single_cell_identifier | inferred_cell_type | single_cell_well_quality |
|---|---|---|---|---|
| sample 1 | … | cell 1 | cell type A | OK |
| sample 2 | … | cell 2 | cell type B | OK |
| sample 3 | … | cell 3 | not applicable | 2 cells |
DRA
Submit fastq or bam de-multiplexed for each cell (sample).
GEA
Submit processed data files de-multiplexed for each cell (sample).
Loupe Browser files for data visualization and analysis (cloupe.cloupe) may be included (Understanding Outputs).
Multiplexed submission
BioSample
Create a sample for each library (usually contains hundreds to thousands of cells) in BioSample.
| *sample_name | … | tissue |
|---|---|---|
| library 1 | … | liver |
| library 2 | … | heart |
| library 3 | … | brain |
DRA
Submit fastq or bam including barcode sequences. For 10x bam files without barcode sequences, submit fastq (Generating FASTQs with cellranger mkfastq).
GEA
Since there is no information about the individual cells at the sample
annotation or file level, include the analysis results, cell-specific
attributes, read count matrix and barcode sequences in processed data
files.
Loupe Browser files for data visualization and analysis (cloupe.cloupe) may be included (Understanding Outputs).