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Sample GSM8279112 Query DataSets for GSM8279112
Status Public on May 22, 2024
Title GR11_site1, 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
GSM8279112_GR11_site1_aligned_fiducials.jpg.gz 1.9 Mb (ftp)(http) JPG
GSM8279112_GR11_site1_barcodes.tsv.gz 20.6 Kb (ftp)(http) TSV
GSM8279112_GR11_site1_detected_tissue_image.jpg.gz 2.0 Mb (ftp)(http) JPG
GSM8279112_GR11_site1_features.tsv.gz 151.6 Kb (ftp)(http) TSV
GSM8279112_GR11_site1_matrix.mtx.gz 56.3 Mb (ftp)(http) MTX
GSM8279112_GR11_site1_scalefactors_json.json.gz 177 b (ftp)(http) JSON
GSM8279112_GR11_site1_tissue_hires_image.png.gz 5.7 Mb (ftp)(http) PNG
GSM8279112_GR11_site1_tissue_lowres_image.png.gz 510.3 Kb (ftp)(http) PNG
GSM8279112_GR11_site1_tissue_positions_list.csv.gz 62.8 Kb (ftp)(http) CSV
Raw data not provided for this record

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