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Obtain and add files to the project

The project includes Human Breast Cancer (Block A Section In Situ Replicate 1) and Human Breast Cancer (Block A Section In Situ Replicate 2) output files  files in one project. 

• Obtain the filtered Count matrix files (h5 or HDF5) files and Spatial outputs Xenium Output Bundles (Figure 1) for each sample. 

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• Navigate the options to select 10x Genomics Visium Space Ranger output Xenium Output Bundle as the file format for input. 

Choose to import 10x Genomics Visium Space Ranger output Xenium for your project (Figure 2).

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• Click Transfer files on the homepage, under settings, or during import (Figure 3). 

Proceed to transfer files as shown below using the 10x Genomics Visium Space Ranger outputs importer Xenium importer (Figure 3).

• Navigate to the appropriate files for each sample (Figure 4). Please note that the 10x Genomics Space Ranger output can be count matrix data as 1 filtered .h5 file per sample or sparse matrix files for each sample as 3 files (two .csv with one .mtx or two .tsv with one .mtx for each sample). The spatial output files should be in compressed format (.zip). The high resolution image can be uploaded and is optional. 

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The Xenium output bundle should be included for each sample using Browse (Figure 4). The whole folder can be used, or a folder containing 5 files (cell_feature_matrix.h5, cells.csv.gz, cell_boundaries.csv.gz, transcripts.csv.gz, morphology.ome.tif) can be added per sample. Once added, the Cells and Features values will update. 

Once the download completes, the sample table will appear in the Metadata tab, with one row per sample (Figure 5).

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