|
| Status |
Public on Dec 12, 2023 |
| Title |
SRC93 |
| Sample type |
SRA |
| |
|
| Source name |
Undifferentiated pleomorphic sarcoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Undifferentiated pleomorphic sarcoma
cell type: Tumor
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Fresh sarcoma specimens were harvested and frozen in optimal cutting temperature compound (OCT). Sarcoma specimens were cryosectioned at -20 C onto gene expression slides and permeabilization time was optimized using 10 um sections with the Visium Spatial Tissue Optimization Slide & Reagents kit (10x Genomics).
Sequencing libraires were produced using the Visium Spatial Gene Expression Slide & Reagent kit (10x Genomics) according to the manufacturer’s instructions.
Spatial transcriptomics.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Spatial Gene Expression
|
| Data processing |
Sample demultiplexing, tissue and fiducial detection, read alignment, and generation of feature-barcode matrices was performed using Space Ranger v1.3.0 (10x Genomics).
Assembly: GRCh38.
Supplementary files format and content: Raw feature barcode matrix for downstream analysis.
|
| |
|
| Submission date |
Sep 01, 2022 |
| Last update date |
Mar 13, 2024 |
| Contact name |
Ajay Subramanian |
| E-mail(s) |
ajayss@stanford.edu
|
| Organization name |
Stanford University School of Medicine
|
| Department |
Radiation Oncology
|
| Lab |
Moding Lab
|
| Street address |
450 Serra Mall
|
| City |
Stanford |
| State/province |
CA |
| ZIP/Postal code |
94305 |
| Country |
USA |
| |
|
| Platform ID |
GPL24676 |
| Series (1) |
| GSE212526 |
Spatial transcriptomics analysis of soft tissue sarcomas. |
|
| Relations |
| BioSample |
SAMN30631404 |
| SRA |
SRX17394857 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6534009_SRC93_aligned_fiducials.jpg.gz |
1.3 Mb |
(ftp)(http) |
JPG |
| GSM6534009_SRC93_barcodes.tsv.gz |
25.1 Kb |
(ftp)(http) |
TSV |
| GSM6534009_SRC93_detected_tissue_image.jpg.gz |
1.6 Mb |
(ftp)(http) |
JPG |
| GSM6534009_SRC93_features.tsv.gz |
287.6 Kb |
(ftp)(http) |
TSV |
| GSM6534009_SRC93_matrix.mtx.gz |
15.5 Mb |
(ftp)(http) |
MTX |
| GSM6534009_SRC93_scalefactors_json.json.gz |
170 b |
(ftp)(http) |
JSON |
| GSM6534009_SRC93_tissue_hires_image.png.gz |
3.7 Mb |
(ftp)(http) |
PNG |
| GSM6534009_SRC93_tissue_lowres_image.png.gz |
368.6 Kb |
(ftp)(http) |
PNG |
| GSM6534009_SRC93_tissue_positions_list.csv.gz |
61.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
