Submitting Single-cell Data

Prerequisites

Note

Accessing the Single-cell Page

Create a profile [1] following the steps in Biodata profile creation. Then, access the Single-cell [2] page via any of the following methods:

Using the Components Button

Click the single-cell-component-button component button in the Components [3] column as shown below:

Single-cell profile component button

Button to access the Single-cell page (highlighted)


Using the Components Icon Navigation Pane

The component icon navigation pane provides a quick access to other components associated with the same profile. It appears on the inner right pane of the screen when you are viewing a component’s page. The icons displayed in the navigation pane correspond to the components associated with the profile.

If you are unsure what each icon represents, you can perform any of the following:

  • Hover over the icon in the component icon navigation pane to see a tooltip with the component’s name

  • Refer to the component button image above

  • Refer to the What are profile components? FAQ

Note

  • The navigation pane will not display the icon associated with the page that is currently being viewed.

  • If a component has subcomponents, a dropdown menu is shown when at least two items are available. However, if you are viewing a subcomponent’s page and only one item remains, that item is displayed directly in the navigation pane.

../../_images/single-cell-icon-pointer.png

Navigation pane showing the Single-cell component icon

Upload Data

  1. Click the dropdown menu to choose a checklist [4]. Hover over each option to view its description.

    Supported Single-cell checklists include the following. Click below collapsible-item-arrow to view all types.

    View all types of Single-cell submissions
    Types of Single-cell submissions

    Type

    Abbreviation

    COPO Identifier

    Single-cell Ribonucleic Acid Sequencing Darwin Core

    scRNA-Seq DwC

    version_dwc_sc_rnaseq

    Single-cell Ribonucleic Acid Sequencing Functional Annotation of Animal Genomes

    scRNA-Seq FAANG

    version_faang_sc_rnaseq

    Single-cell Ribonucleic Acid Sequencing Minimum Information about any (x) Sequence

    scRNA-Seq MIxS

    version_mixs_sc_rnaseq

    Single-cell Ribonucleic Acid Sequencing Tree of Life

    scRNA-Seq ToL

    version_tol_sc_rnaseq
    Available sample checklist options within a Biodata profile

    Checklist options for Single-cell submissions


  2. Click the single-cell-blank-manifest-download-button button to download a blank manifest [5].

    A manifest is a spreadsheet file used to record metadata for submission.

  3. Fill in the downloaded manifest then, click add-single-cell-manifest-button button to upload a completed Single-cell manifest from your local (computer) system.

    Note

    Please ensure that the manifest that you are uploading matches the checklist type selected in step 1. You will encounter errors if the uploaded manifest does not correspond with the selected dropdown menu checklist option.

    Pointer to 'Add Study from Spreadsheet' button

    Click “Add study from spreadsheet” button to open an upload dialogue


  4. A dialogue is displayed. Click the upload-single-cell-manifest-button button in the dialogue to choose a spreadsheet file from your local system.

    Upload Single-cell Spreadsheet dialogue

    Click ‘Upload manifest’ button


  5. The uploaded data is shown in a preview before final submission. Click the finish-button button to finalise the upload.

    Dialogue with uploaded Single-cell data

    Single-cell upload preview


  6. The new single-cell data will be displayed on the Single-cell page after a successful validation.

    Note

    • The first record in the STUDY tab is selected by default.

    • Each tab represents a worksheet in the manifest. Only worksheets with data appear as tabs.

    Single-cell data uploaded

    Single-cell page showing the uploaded data


Submit Data

Note

  • Follow the steps in Upload Data to upload data before proceeding with the submission.

  • The following repositories are supported for Single-cell submissions:

    • European Nucleotide Archive (ENA) via submit-record-button-ena button

    • Zenodo via submit-record-button-zenodo button

  1. After uploading data, select a row in the data table under the STUDY tab.

    Then, click the submit-record-button-ena button to submit the selected record to ENA or submit-record-button-zenodo button to submit to Zenodo.

    Hint

    The first row of the data table under the STUDY tab is selected by default. Selected rows are indicated by a blue background colour.

    Note

    Please ensure that the selected record is under the desired checklist option. If not, choose another option from the dropdown menu, then select a row in the data table.


  2. Wait for the submission process to be completed. The submitted record’s status and accessions can be viewed in the data table’s respective columns. See the sections below for details.


Make Data Public

  1. Submissions are private by default. You can make the data publicly accessible by referring to the steps in the Publishing Data at Data Level section.

View Submission Status

Hint

The Data status & progress legend, located on the right side of the data table, shows the different stages of submission processing. Hover over the info-icon to see description for each status.

For more details, see the How can I check the status of my data submissions? FAQ section.

The submission will be scheduled for processing after the submit-record-button-ena or submit-record-button-zenodo button is clicked. The row of the submitted record will be highlighted in green indicating that the submission has been successful.

If the submission was unsuccessful or has not been assigned any accessions, the table row will be highlighted in red. Its status is indicated in the following columns:

  • Status for Ena - Displays the ENA status assigned to the project

  • Status for Zenodo: Displays the Zenodo status assigned to the project

View Accessions

Accessions are unique identifiers assigned to submissions after they have been successfully submitted to public repositories.

The accession columns are:

  • Accession for Ena - Displays the ENA accession assigned to the project

  • Accession for Zenodo: Displays the Zenodo accession assigned to the project

Clicking any accession in the data table will open the corresponding record in the associated repository. You can also find the same record by searching for the accession directly in the repository.

Tip

Alternatively, click the accessions-component-icon icon located in the top-right corner of the data table to navigate to the Accessions page that displays accessions for all submissions.