Human Intestine Cancer (FPPE)

5 µm section from Human Intestinal Cancer. FFPE tissue purchased from BioIVT Asterand Human Tissue Specimens.

Libraries were prepared following the Visium Spatial Gene Expression Reagent Kits for FFPE User Guide (CG000407 Rev A).

Sequencing instrument: Illumina NovaSeq 6000, flow cell HCCVHDSX2 (lanes 1-2)
Sequencing depth: 77,288 reads per spot
Sequencing configuration: 28 bp read 1 (16 bp Visium spatial barcode, 12 bp UMI), 50 bp read 2 (transcript), 10 bp i7 sample barcode and 10 bp i5 sample barcode
Dual-Index set: SI-TS-B1
Slide: V10L13-021
Area: B1

Key metrics were:

View summary metrics about the sequencing quality and detected cells

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Output Files Format details	Size	md5sum
Genome-aligned BAM	10.8 GB	9e903eaab48e99feac83eca8a531de9a
Genome-aligned BAM index	8.44 MB	d3f86e57425dd2a78806077f3187be6c
Per-molecule read information	337 MB	6f812229b058151a6cb1b656a41e800f
Feature / barcode matrix HDF5 (filtered)	20 MB	3d3cb57045aecab3911cf3aeb51b0cb4
Feature / barcode matrix (filtered)	62.3 MB	7de1e434881f206a0fc432c251c70a0d
Feature / barcode matrix HDF5 (raw)	33.8 MB	9980c8c51ae3e7cb3783825e89dd10e5
Feature / barcode matrix (raw)	90.8 MB	94dc0bd61b12b22bd43c63175e21aee3
Clustering analysis	25 MB	d692a1b1f1917cf55dfc199c0797b956
Spatial imaging data	11.5 MB	e2d3ec0283143125223a23371bc36db2
Spatial Enrichment (Moran's I)	1.79 MB	7a41c767ee37cfc8d9b6126809b59f09
Summary CSV	925 B	05b0cdfab69e27cc2756f510a7cc0dbf
Summary HTML	8.24 MB	4564e0c1b6008092b39d9e9b585391e7
Loupe Browser file	435 MB	ae730b2c05ba29264fd2a7e56f96601d

Spatial Gene Expression Dataset by Space Ranger 1.3.0