|
| Status |
Public on Oct 09, 2023 |
| Title |
Breast Cancer, Xenium In Situ Spatial Gene Expression Rep 1 |
| Sample type |
RNA |
| |
|
| Source name |
5 µm section Breast Cancer
|
| Organism |
Homo sapiens |
| Characteristics |
disease state: Breast Cancer
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Two replicate 5 μm sections were taken each for Xenium. Corresponding dissociated tumor cells for Sample #1, fresh frozen (FF) in liquid nitrogen, were also sampled from the same 2.5 cm biopsy. A 5 μm section was also taken from Sample #2 for Xenium.
|
| Label |
Xenium Human Probe Set
|
| Label protocol |
Xenium Human Probe Set
|
| |
|
| Hybridization protocol |
The Xenium samples underwent 15 rounds of fluorescent probe hybridization, imaging, and probe removal. The Xenium Analyzer captured a Z-stack of images every cycle and in every channel, which needed to be processed and stitched to build a spatial map of the transcripts across the tissue section. Decoding of transcripts was performed using a Xenium codebook ? a collection of codewords that were assigned to genes in the gene panel. In order to assign mRNAs to cells, the spatial boundaries of cells were defined by nuclear expansion.
Xenium: https://www.10xgenomics.com/support/in-situ-gene-expression/documentation/steps/assay/xenium-in-situ-gene-expression-probe-hybridization-ligation-amplification. Xenium was run on a prototype instrument.
|
| Scan protocol |
Xenium In Situ Analyzer
|
| Data processing |
Data processed using Xenium Ranger software.
Supplementary_files_format_and_content: Post-Xenium_HE_Rep1.ome.tif: Post-Xenium hematoxylin and eosin stained tissue image which can be registered to Replicate #1 Xenium data.
Supplementary_files_format_and_content: Post-Xenium_IF_Rep1.ome.tif: Post-Xenium immunofluorescence tissue image which can be registered to Replicate #1 Xenium data.
Supplementary_files_format_and_content: Post-Xenium_HE_Rep1_homography.csv: Alignment file to be used in conjunction with Post-Xenium_HE_Rep1.ome.tif for H&E registration in Xenium Explorer.
Supplementary_files_format_and_content: Post-Xenium_IF_Rep1_homography.csv: Alignment file to be used in conjunction with Post-Xenium_IF_Rep1.ome.tif for IF registration in Xenium Explorer.
|
| |
|
| Submission date |
Sep 13, 2023 |
| Last update date |
Dec 01, 2023 |
| Contact name |
Stephen Richardson Williams |
| E-mail(s) |
stephen.williams@10xgenomics.com, correspondence@10xgenomics.com
|
| Organization name |
10x Genomics
|
| Department |
Computational Biology
|
| Street address |
6230 Stoneridge Mall Rd
|
| City |
Pleasanton |
| State/province |
CA |
| ZIP/Postal code |
94588 |
| Country |
USA |
| |
|
| Platform ID |
GPL33762 |
| Series (2) |
| GSE243168 |
High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis [Xenium] |
| GSE243280 |
High resolution mapping of the tumor microenvironment using integrated single-cell, spatial and in situ analysis |
|
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7780153_Post-Xenium_HE_Rep1.ome.tif.gz |
1.3 Gb |
(ftp)(http) |
TIFF |
| GSM7780153_Post-Xenium_HE_Rep1_homography.csv.gz |
133 b |
(ftp)(http) |
CSV |
| GSM7780153_Post-Xenium_IF_Rep1.ome.tif.gz |
388.7 Mb |
(ftp)(http) |
TIFF |
| GSM7780153_Post-Xenium_IF_Rep1_homography.csv.gz |
135 b |
(ftp)(http) |
CSV |
| GSM7780153_Xenium_FFPE_Human_Breast_Cancer_Rep1_gene_groups.csv.gz |
1.7 Kb |
(ftp)(http) |
CSV |
| GSM7780153_Xenium_FFPE_Human_Breast_Cancer_Rep1_gene_panel.json.gz |
5.8 Kb |
(ftp)(http) |
JSON |
| GSM7780153_Xenium_FFPE_Human_Breast_Cancer_Rep1_if_image.tif.gz |
62.0 Mb |
(ftp)(http) |
TIFF |
| GSM7780153_Xenium_FFPE_Human_Breast_Cancer_Rep1_outs.zip |
9.2 Gb |
(ftp)(http) |
ZIP |
| GSM7780153_Xenium_FFPE_Human_Breast_Cancer_Rep1_panel.tsv.gz |
3.1 Kb |
(ftp)(http) |
TSV |
| GSM7780153_Xenium_R1_Fig1-5_supervised.csv.gz |
514.3 Kb |
(ftp)(http) |
CSV |
| GSM7780153_Xenium_R1_Fig_3_unsupervised.csv.gz |
501.2 Kb |
(ftp)(http) |
CSV |
