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.

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).

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.