Processed scRNA-seq data intake form

Modified on Mon, 27 May 2024 at 10:58 AM


To ensure a smooth and efficient analysis process, please follow the instructions below to prepare your processed scRNA-seq data.

1 Data preparation instructions

1.1 Merging raw count data

  • Ensure that all raw count data from your samples are merged into a single Seurat object.
  • This merged Seurat object should include all samples that you wish to analyze.

1.2 Annotating metadata

  • The metadata within the Seurat object should be thoroughly annotated.
  • Include all relevant experimental data for each sample, such as sample ID, treatment conditions, time points, batch information, etc.
  • This metadata is crucial for accurate downstream analysis and interpretation.

1.3 Including multimodal data

  • If your dataset includes multimodal data such as CITE-seq (Cellular Indexing of Transcriptomes and Epitopes by sequencing), ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing), or HTO (Hashtag Oligos):
    • Each type of data should be represented as separate assays within the Seurat object.
    • Ensure that the assays are properly named and structured for clear identification and analysis.
    • For HTO data: Please perform the demultiplexing step yourself and annotate the hashtags to identifiable sample names within the metadata of the Seurat object. Ensure that each sample is correctly labeled for accurate downstream analysis.

2 Submission details

2.1 File format

  • Submit your data as a Seurat object file (e.g., .rds or .rda format).

2.2 File naming convention

  • Use a descriptive and unique file name, including your project name and date of submission. For example: ProjectName_ScRNASeq_20240527.rds.
    • Note: This file name will be the initial dataset name in the UniApp.

2.3 Additional documentation

  • Provide a brief description of your experiment, including:
    • Objective of the study
    • Number of samples
    • Organism
    • Key experimental conditions
    • Any additional notes that might be relevant for analysis

3 Troubleshooting

If you encounter any issues or have questions regarding the data preparation or submission process, please contact our support team at

4 Conclusion

By following these guidelines, you will help us ensure that your data is processed efficiently and accurately. We look forward to assisting you with your scRNA-seq analysis.

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