Overview

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Basic processing of the raw data were performed by the University of Illinois at Chicago Research Informatics Core (UICRIC).

We adhere to a general policy for acknowledgements and authorship as established by the Association for Biomolecular Resource Facilities (ABRF) , and we support the following statement from the ABRF.

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File Description Type
Visium_HD_3prime_Mouse_Kidney.zip SpaceRanger output for Visium_HD_3prime_Mouse_Kidney result

Sample list
Sample OriginalID
Visium_HD_3prime_Mouse_Kidney Visium_HD_3prime_Mouse_Kidney

Method: Processing of 10X Genomics Visium data with SpaceRangerhttps://www.10xgenomics.com/support/software/space-ranger/latest

Whole transcriptome is mapped to tissue on a microscope image.

Reference sequence database : mm10

CellRanger reference genome for mouse mm10, November 19, 2020.

Figure 1 . Gene expression (GEX) sample summary

Table 1 . Data processing summary statistics of gene expression samples

Table 1 . Data processing summary statistics of gene expression samples
Sample Reads Mapped Confidently to Genome Reads Mapped Confidently to Transcriptome Total Genes Detected Valid Barcodes Valid UMI Sequences Number of Reads Number of Squares Under Tissue 2 µm Number of Bins Under Tissue 8 µm Number of Bins Under Tissue 16 µm Number of Cells Median Genes per Cell Median UMIs per Cell Median Cell Area (μm²) Median Nucleus Area (μm²) Mean UMIs Under Tissue per Square 2 µm Mean UMIs Under Tissue per Bin 8 µm Mean UMIs Under Tissue per Bin 16 µm Mean Genes Under Tissue per Square 2 µm Mean Genes Under Tissue per Bin 8 µm Mean Genes Under Tissue per Bin 16 µm
Visium_HD_3prime_Mouse_Kidney 0.8216008740353596 0.7399878736144156 20957 0.8791618810312359 0.9947524507028236 520565667 6753403 423482 106302 277215 238 310 84 24 20.749393602011363 331.06829570088036 1319.5468570676042 18.52003678737899 236.8115575160226 759.6465635641824

Citations