Uploading data in classic mode during study creation

How to upload data during study creation

The following guide assumes you have chosen the classic upload experience.

Step 1. Upload the raw count expression matrix

1. Choose either dense or sparse for the type of matrix you are uploading.
2. Select the species for the file being uploaded.
3. Select the unit for the file being uploaded.
4. Experimental input type of the biosample. Choose from "Whole-cell", "Single Nuclei" or "Bulk".
5. Choose the library preparation protocol used for the uploaded matrix file. If the library preparation protocol you need is not available, contact us.
6. Choose the modality of the expression data. If the modality you need is not available, contact us.
7. Optionally enter a description of the file.

If you upload a sparse matrix, you will also need to upload a 10x features file and a 10x barcodes file.

Click "Choose file" to select your file, then "Save" to begin the upload of the file. This is a two-step process,
(1) the file is uploaded using the browser
(2) the file is checked and loaded into the portal.

Uploading a file can take a little time depending on the size of the file and your connection speed. During this step please do not navigate away from the page as it will cancel your upload. You are welcome to use your browser in other tabs or other windows of the browser. Once the file has successfully loaded into the portal, it is then moved to the Terra workspace associated with your study.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal.

Note: Your study will not have visualizations generated until this file is uploaded.

Step 2. Upload the processed expression files

In order to upload a processed expression file, an upload of a raw count expression matrix is required. If you want to upload a processed file and haven’t yet uploaded a raw count file you will have the option to:

1. Return to the step to upload a raw count matrix
2. Request an exemption which will require filling out a form to ask to be exempt from needing to upload a raw count matrix.

Otherwise follow the same steps as in the raw count file upload step for your process expression file upload. Note: processed expression files are necessary for gene expression visualization.

Step 3. Upload the study metadata file

1. Choose a metadata file to upload
2. SCP requires the use of SCP conventional names in metadata files. (The Yes option is selected by default). For more information about conventional names. 
3. Add a description (optional)

Click "Save & Upload" to begin the process of uploading the file. The process for uploading and parsing files is the same as expression matrices. As before, please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal.

Note: Your study will not have visualizations generated until this file is uploaded.

Step 4. Upload cluster file

1. Choose a cluster file to upload
2. Enter a name (optional). The name will be used to refer to the plot in the portal.
3. Enter a description of the ordination (optional). The description should comment on the biology being displayed and the method of generating the plot. 
4. Enter axes for the plot:
   • The Z-axis is optional and only used for 3D plots. 
   • You can also optionally provide the domain of each axis if you would like your plots to render a certain way. If not, the portal will size each plot automatically based on the input data provided.

You can load as many cluster files as you would like.

Click "Save & Upload" to begin the process of uploading the file. The process for uploading and parsing files is the same as previous files. As before, please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal.

Note: Your study will not have visualizations generated until this file is uploaded.

The following file types under the section "Other files" are all optional. To jump past these descriptions click here.

Spatial transcriptomics

1. Choose a spatial file to upload

From the "Corresponding clusters" dropdown, indicate the cluster file (if any) that should be displayed side-by-side with your spatial file.

     2. Optionally add a name, description, and axis labels.

 

Click "Save & Upload" to begin the process of uploading the file. The process for uploading and parsing files is the same as previous files. As before, please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal.

Coordinate labels

1. Choose a coordinate label file to upload. This is not a cluster file but an annotation for overlaying on top of a scatter plot.
2. Select the corresponding cluster/spatial data. The coordinates of the label must be in the same range as the corresponding data for them to show.
3. Optionally add a description (which will appear below the image)

Click "Save & Upload" to begin the process of uploading the file. The process for uploading and parsing files is the same as previous files. As before, please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal.

Reference images

1. Choose an image file to upload. These will appear alongside the visualizations of a study.
2. Optionally add a name, the corresponding data, and a description.

Click "Save & Upload" to begin the process of uploading the file. The process for uploading and parsing files is the same as previous files. As before, please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal.

Sequence files

For Non-Human Data

1. Make sure "Primary Human Data" is set to "No"
2. Upload a couple, small files. If you are loading large or many files, there are better ways to upload to the portal (more here). Please compress (gzip) your files before loading. This is important to allow more efficient upload and download of data for portal users.
3. Choose file type (i.e. fastq) and species
4. Optionally add a description.

Click "Save & Upload" to begin the process of uploading the file. The process for uploading and parsing files is the same as previous files. As before, please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal.

For Human Data

The portal should not store human sequence data, this should be stored in an external biological sequence archive of your choice and then linked to your portal study. After securely storing the data in an external repository, you may link that repository here.

1. To store a link, select "Yes" for "Primary Human Data?". 
2. Add the link (URL) to the file or study,
3. Add a name for the linked resource
4. Optionally add a description of the sequenced sample(s)

Click "Save & Upload" to begin the process of uploading the file. The process for uploading and parsing files is the same as previous files. As before, please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal.

Precomputed expression stats

1. Choose a precomputed expression file to upload. 
2. Optionally add a name and a description for the file.

You can load as many precomputed expression files as you would like. Panels of genes are often important results in analysis. These gene lists can be derived by many methods (eg. differential expression, enrichment analysis, and expert knowledge). Multiple lists of precomputed expression stats can be uploaded which will allow others to explore the genes in the list

Click "Save & Upload" to begin the process of uploading the file. The process for uploading and parsing files is the same as previous files. As before, please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal.

Documentation & other files

If you would like to share a file we have not mentioned so far, please share it here. 

1. Upload a file
2. Choose the file type, such as "Documentation", if the file type you would like to add is not listed please contact us.
3. Optionally add a description of the file

Click "Save & Upload" to begin the process of uploading the file. The process for uploading and parsing files is the same as previous files. As before, please do not navigate away from the page during the upload.

After completing the upload a notification will be shown on your screen. An email will follow once your file is checked and loaded into the portal.

Finished!

Once you are satisfied with your uploaded files you can click “View study” to view your study summary page.

If you loaded the required visualization files you may click on "Explore" and explore your data online!

If you want to come back to your study to add, update, or remove files you can do so from the “Settings” tab and clicking the “Upload/Edit data” button. The settings tab will also show a summary of your study, including uploaded files, some information in your files like clusters, and study permissions, as well as links to your study in the portal and in Terra.