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Submission Help

Stereo-seq Spatiotemporal Omics Data Archiving Operation

1. Database Address

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

2. Operation Steps

1. Log in

BGI employees can log in using the BGI channel.

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 datasubs@cngb.org to delete the process and resubmit.
  • To modify the Submitter, Compliance Information (application), please contact datasubs@cngb.org 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 datasubs@cngb.org 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.

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'.
      • In the template file for analyzing data, all the data files listed must be uploaded and an MD5 list file must be prepared. The MD5 list file is uniformly named with the online submission process number, for example, "sts0000110.md5.list".
    • Other data:
      • Fill in the template of other (auxiliary data), provide the file name, file type, 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 datasubs@cngb.org to delete it and submit again.
  2. After submission, the Submitter and the Compliance Information (application), project information (Study) can be modified by contacting datasubs@cngb.org 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 datasubs@cngb.org 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 datasubs@cngb.org to explain the specific situation.

IV. About Data Citation

The assigned project number (STTxxxxxxx) can be used for citation in the article and can be referenced as follows:

The data that support the findings of this study have been deposited into STOmis DB[1] of China National GeneBank DataBase (CNGBdb) [2] with accession number STTxxxxxxx.

[1] Xu, Z., Wang, W., Yang, T., Li, L., Ma, [2] Chen FZ, You LJ, Yang F, et al. CNGBdb: China National GeneBank DataBase. Hereditas. 2020;42(08):799-809. doi:10.16288/j.yczz.20-080.

V. Dataset

In addition to providing archiving services for spatiotemporal analysis data, it also supports the creation and visualization of spatiotemporal datasets. For more information, please refer to the following examples:

  • High-quality datasets: STDS0000235
  • Standard Data Set: STDS0000247 (archived item STT0000039)

VI. 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.

Analysis Information Filling Requirements

Analysis Template 4:

  1. The files in the template information cannot contain duplicates.
  2. 'Tissue section alias', 'expression type' and 'filtered feature-spot matrix (bin size=1)' are required.
  3. 'Microscope slide image' and 'registered image' file information of a single slice must exist or not exist at the same time.
  4. An expression matrix containing at least one of 'SquareBin' and 'CellBin'.
  5. 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'.
  6. When filling in the CellBin matrix information, 'filtered feature-spot matrix: cell bin' and 'cell annotation: cell bin' all fields are required.

MD5 List File:

  1. The archived project only needs one MD5 list file, and the file naming rule is sts0000xxx.md5.list; if the archive number is sts0000123, the file name is sts0000123.md5.list.
  2. 'MD5.list' field of Template 4. The MD5 list file needs to be uploaded to the upload directory. Note that the file is in text format and does not contain additional suffixes.
  3. The MD5 list file content needs to contain each file in the Analysis template information. The content of each line is: file name + md5 value, which can be separated by spaces or tabs.