|
| Status |
Public on May 22, 2024 |
| Title |
GR2_site4, Visium |
| Sample type |
SRA |
| |
|
| Source name |
Desmoplastic Small Round Cell Tumor
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Desmoplastic Small Round Cell Tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
We used five-mm sections of selected areas from scRNA-seq-matched FFPE samples. Extraction, whole transcriptome probe hybridization, release, and capture were performed according to Visium Spatial Gene expression for FFPE samples standard protocol.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's protocol
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
FFPE Spatial transcriptome sequencing
Patient raw data cannot be provided due to privacy concerns
|
| Data processing |
Raw sequencing data were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files
Sequences were aligned to GRCh38 using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: GRCh38
Supplementary files format and content: barcodes.tsv.gz: list of spatial barcodes
Supplementary files format and content: features.tsv.gz: list of gene IDs
Supplementary files format and content: matrix.mtx.gz: gene expression count data in Matrix Market Echange Format
Supplementary files format and content: aligned_fiducials.jpg.gz: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg.gz: image of tissue and spots
Supplementary files format and content: scalefactors_json.json.gz: scale factors in json format
Supplementary files format and content: tissue_hires_image.png.gz: high-resolution image of tissue
Supplementary files format and content: tissue_lowres_image.png.gz: low-resolution image of tissue
Supplementary files format and content: tissue_positions_list.csv.gz: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial transcriptomics
|
| |
|
| Submission date |
May 18, 2024 |
| Last update date |
May 22, 2024 |
| Contact name |
Clémence Henon |
| E-mail(s) |
clemence.henon@gustaveroussy.fr
|
| Organization name |
Gustave Roussy
|
| Street address |
114 rue Edouard Vaillant
|
| City |
Villejuif |
| ZIP/Postal code |
94800 |
| Country |
France |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE263523 |
Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors |
| GSE267806 |
Single-cell multiomics profiling reveals heterogeneous transcriptional programs and microenvironment in Desmoplastic Small Round Cell Tumors [Visium: Spatial transcriptomics] |
|
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8279107_GR2_site4_aligned_fiducials.jpg.gz |
2.1 Mb |
(ftp)(http) |
JPG |
| GSM8279107_GR2_site4_barcodes.tsv.gz |
23.6 Kb |
(ftp)(http) |
TSV |
| GSM8279107_GR2_site4_detected_tissue_image.jpg.gz |
2.2 Mb |
(ftp)(http) |
JPG |
| GSM8279107_GR2_site4_features.tsv.gz |
151.6 Kb |
(ftp)(http) |
TSV |
| GSM8279107_GR2_site4_matrix.mtx.gz |
41.8 Mb |
(ftp)(http) |
MTX |
| GSM8279107_GR2_site4_scalefactors_json.json.gz |
175 b |
(ftp)(http) |
JSON |
| GSM8279107_GR2_site4_tissue_hires_image.png.gz |
6.1 Mb |
(ftp)(http) |
PNG |
| GSM8279107_GR2_site4_tissue_lowres_image.png.gz |
511.9 Kb |
(ftp)(http) |
PNG |
| GSM8279107_GR2_site4_tissue_positions_list.csv.gz |
67.4 Kb |
(ftp)(http) |
CSV |
| Raw data not provided for this record |
