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This table has entries for any uploads you have in progress. Click to resume or see more details about the status.
| Share ID | Status | Dataset type | Title | Actions |
|---|
Enter metadata
Use the form or provided template to enter metadata for your dataset.
Upload dataset
Choose your dataset format and upload directly or provide a supported URL (soon).
Build track hub
Setup basic track configuration for Gosling.
Dataset processing
Your dataset is processed and checked on the server.
Finalize submission
Your dataset gets fully integrated into the system here.
Curate dataset
Get the most out of your dataset by doing curation steps here.
The 'metadata' is the data describing your dataset, including things like title, authorship, sequencing protocols used, etc. This is the first step in uploading a dataset to the portal. All data uploaded are initially private to only your account (you can change this later in the Dataset Explorer)
Enter the metadata manually below OR fill out and upload from a spreadsheet template.
If a GEO ID is available, enter it here and the rest can be autofilled.
Please check the form above and correct these issues.
Choose the format of your dataset and upload it here. You can also provide a URL to a supported dataset (soon).
These are simple, plain-text files in a bundle, usually compressed with tar/gzip or zip.
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Similar in format to 3-tab but rather than individual files each is a different tab in an Excel spreadsheet. Mostly for bulk RNA-seq data as it doesn't initial-scale very well for even medium-sized datasets.
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This is a binary format used by the Seurat package in R. If you've already been working with your dataset in R, including clustering and other analyses, this is the format to choose.
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Usually created by the Scanpy package in Python, this is a binary format that is very efficient for large datasets. If you've been working with your dataset in Python, this is the format to choose.
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Special considerations are needed for spatial datasets, as each platform has a different file requirement. Select a platform below to see specific instructions.
You can also upload in one of the other formats but will not be able to take advantage of special features. This is also an option for spatial data from a platform we currently do not support.
If a UCSC track hub 'hub.txt' file is linked, it and its associated metadata and track files will be cloned to the server. Currently, only BigBed and BigWig files are supported.
Track hub information is converted into a spec that can be read in by the Gosling epigenome viewer.
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Required if providing a track hub URL
Hub file contains relative file references
Your hub.txt file contains relative or local file paths that will not be automatically prepopulated.
You will need to upload or link these files manually in the track configuration step after clicking "Configure Trackhub".
Before proceeding, you may want to consider updating your hub.txt file to use "one file" mode so that the track information can be populated if you plan to upload track files.
Please double-check that the hub and track information is correct before proceeding. Contents will be copied over to the server.
Your dataset is being processed on the server. This may take a few minutes, depending on the size of the dataset. You can close your browser at any time and return to the uploader to check on the progress.
Your dataset has been processed and is ready to be submitted.
Please use the Feedback link on the left and provide this error message:
Your dataset has been submitted and is now available in the Dataset Explorer.
Right now your dataset is stored in the system but there are no visualizations created so users can explore it. Curation is the process of creating these visualizations, which can include things like bar charts, UMAPs, heatmaps, etc.
Click the button to redirect to the gene expression page, where you can view a display after searching a gene.
tar cvf spatialdata.tar spatialdata_filtered_feature_bc_matrix.h5 clusters.csv spatial
tar cvf spatialdata.tar binned_outputs/feature_slice.h5 clusters.csv binned_outputs/square_008um