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Submission Help

Stereo-seq Spatiotemporal Omics Data Archiving Operation

Ⅰ. Database Address

  1. Spatiotemporal Database STOmics DB: https://db.cngb.org/stomics
  2. Spatiotemporal Archive System: https://db.cngb.org/stomics/submission/data_archive

Ⅱ. Operation Steps

1. Log in

Users can log in using multiple login methods

2. Create a Process

Click [New submission], create a submission process. Please note that the process will not be created in the following cases: 1. The process has been created but not completed, that is, there is a process with the "Unfinished" status in the submission record. 2. The submitter modification permission has been enabled, but the submission of the modified information has not yet been completed. 3. The submitter information has not been reviewed.

3. Submitter, Project and Other Related Information Online

Follow the instructions and submit the Submitter, Submission Type, and Submission Form step by step. Fill in compliance information (Submission Application), project information (Study), according to the actual situation, and in the last step (Overview) click Submit to complete the filling of the above information.

Please note when filling in:

  • Submitter, Submission Type, compliance information (Submission Application) once you fill out the application, you cannot go back and modify it.
  • To modify the submission type, you can only contact P_STOmicsDB@genomics.cn to delete the process and resubmit.
  • To modify the Submitter, Compliance Information (application), please contact P_STOmicsDB@genomics.cn to obtain modification permissions.

4. Fill Out the Offline Template and Send the Email

  1. Template download: https://ftp.cngb.org/pub/stomics/template/
  2. Download templates for samples, sections, experiments & sequencing (optional, not required), analysis (select by technology type), and other (auxiliary data). Two templates are provided for sections, and the "withSampleName" template is generally used. If you have submitted samples to OSTomitics DB, you can also use the "withSampleAccession" template.
  3. Reference example: https://ftp.cngb.org/pub/stomics/example/
  4. The completed template file must be sent to P_STOmicsDB@genomics.cn . for timely review and feedback. At the same time, the data file upload method must be informed so that the data can be checked.
  5. If the template file exceeds 10M, it needs to be split into two batches for submission. If you encounter such a situation, you will need to cooperate with the new process.
  6. Analysis Information Filling Requirements
    sheet: 4.STOmicsAnalysisStereo-seq.V2.0.xlsx:
  • The files in the template information cannot contain duplicates.
  • 'Tissue section alias', 'expression type' and 'filtered feature-spot matrix (bin size=1)' are required.
  • 'Microscope slide image' and 'registered image' file information of a single slice must exist or not exist at the same time.
  • An expression matrix containing at least one of 'SquareBin' and 'CellBin'.
  • When filling in the SquareBin matrix information, 'filtered feature-spot matrix' and 'bin size (matrix)' are required; 'bin size (matrix)' and 'bin size (annotation)' numbers must be the same; If no annotation file is included, both 'cell annotation' and 'bin size (annotation)' are filled in with 'not applicable'.
  • When filling in the CellBin matrix information, 'filtered feature-spot matrix: cell bin' and 'cell annotation: cell bin' all fields are required.

5. Data File Upload

  1. Go to https://db.cngb.org/mycngbdb/services to query the data upload method.

Remark:
If you upload data through the cluster, you can use a cluster account that is not your own, that is, there is a cluster account upload directory under /zfssz6/BIGDATA_WAREHOUSE/bigdata_ods/for_cngb/cnsa/upload, and you need to entrust a colleague of this account to transfer the data files.

  1. Data type and format requirements:

    • Experimental sequencing data:

      • Sequencing data: fastq format is required, and the file name suffixes include '.fastq.gz', '.fastq.bz2', '.fq.gz', '.fq.bz2'.
      • When submitting sequencing data, you are required to provide a corresponding mask file, which supports file name suffixes '.h5' and '.bin'.
      • Supports bam archives and file name suffix '.bam'.
      • The reference sequence required for alignment supports reference genome and reference annotation files. There are two archiving methods: one is the data number of the public database, and the other is a custom sequence file (need to be uploaded).

    • Spatiotemporal downstream analysis data:

      • The matrices include chip matrix (raw feature-spot matrix), original matrix without non-tissue regions (filtered feature-spot matrix (bin size=1)), and downstream analysis matrix. Supported file name suffixes are '.gem', '.gef', '.gem.gz'.
      • The annotation file must correspond to the downstream analysis matrix. The format requirements are as follows, and the file name suffixes supported are '.csv', '.tsv', '.csv.gz', '.tsv.gz'.
      • The downstream analysis matrix and its corresponding annotation file support two different methods (Square Bin and Cell Bin), one of which must be selected.
      • Images support microscope images and registered images, and file name suffixes include '.jpg', '.jpeg', '.png', '.tiff', '.tif', '.tiff.gz', '.tif.gz', '.czi', '.czi.gz'.

    • Other data:

      • Fill in the template of other (auxiliary data), provide the file name, file type, Corresponding slice (separate them with semicolons ';' to correspond to multiple slices), MD5 value and related description information to archive.

III. About Modification or Update

  1. Technical Type (Submission type) once selected, it cannot be modified and you can only contact P_STOmicsDB@genomics.cn to delete it and submit again.
  2. After submission, the Submitter and the Compliance Information (application), project information (Study) can be modified by contacting P_STOmicsDB@genomics.cn to obtain modification permissions and make changes online.
  3. If you need to modify the template files and data files submitted offline, you can email the modified form files to P_STOmicsDB@genomics.cn and the data files will be updated through the original upload method.
    • When modifying offline template files, please note that sample name and tissue section alias are used as unique identifiers of samples and slices and cannot be modified.
    • If a sample or slice number has already been assigned, modifying the number is not supported.
    • Offline template files do not support additions or deletions. If you need to add data, please create a new process and link it to an existing project; if you need to delete information, please contact P_STOmicsDB@genomics.cn to explain the specific situation

IV. Frequently Asked Questions

  1. Sample determination duplication: remove sample information in the name, sample title, and description fields if repeated. You need to distinguish them by modifying the required fields or adding optional fields.
  2. The reviewer link is a temporary link that becomes invalid upon expiration and cannot be cited in the article.

Contact

For assistance, contact P_STOmicsDB@genomics.cn.
We provide detailed guidance and support to ensure a smooth process for data submission and visualization creation.

Support Hours: Monday to Friday, 9:00 AM - 6:00 PM (GMT+8).