|
| Status |
Public on Feb 07, 2025 |
| Title |
Hepatoblastoma sample 13 |
| Sample type |
SRA |
| |
|
| Source name |
Formalin-fixed paraffin-embedded hepatoblastoma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: Formalin-fixed paraffin-embedded hepatoblastoma
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Ten tissue sections with a maximum area of 6.5 x 6.5 mm2 were cut from ten distinct HB FFPE tissue bocks, placed on the mRNA capture areas of Visium Gene Expression slides for FFPE (10x Genomics), fixed in methanol, and H&E stained according to the respective user guide (CG000409 Rev C, 10x Genomics). Brightfield histology images were taken using a 4x or 10x objective on a Nikon Eclipse Ni. Raw images were stitched together using NIS-Elements (Nikon) and exported as TIFF files with high-resolution settings.
Libraries were prepared following the manufacturer’s user guide (G000407 Rev D, 10x Genomics).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Description |
H288
10x Genomics Visium FFPE spatial transcriptomics
|
| Data processing |
Raw sequencing data was demultiplexed and aligned to the human reference genome GRCh38-2020-A with Space Ranger 2.0.1 using spaceranger mkfastq and spaceranger count with default parameters.
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 Exchange Format
Supplementary files format and content: aligned_fiducials.jpg: aligned fiducials of the tissue image
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: scalefactors_json.json: scalefactors in json format
Supplementary files format and content: tissue_hires_image.png: hi-res image of tissue
Supplementary files format and content: tissue_lowres_image.png: low-res image of tissue
Supplementary files format and content: tissue_positions.csv: list of spatial barcodes and the coordinates specifying spots
Supplementary files format and content: spatial_enrichment.csv: list of genes and their spatial enrichment
Library strategy: spatial transcriptomics
|
| |
|
| Submission date |
Mar 19, 2024 |
| Last update date |
Feb 07, 2025 |
| Contact name |
Kornelius Kerl |
| Organization name |
University Children's Hospital Münster
|
| Department |
Department of Pediatric Hematology and Oncology
|
| Street address |
Albert-Schweitzer-Campus 1
|
| City |
Münster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL30173 |
| Series (2) |
| GSE261958 |
Multiomic analysis uncovers a continuous spectrum of differentiation and Wnt-MDK-driven immune evasion in hepatoblastoma [Spatial Transcriptomics] |
| GSE283207 |
Multiomic analysis uncovers a continuous spectrum of differentiation and Wnt-MDK-driven immune evasion in hepatoblastoma |
|
| Relations |
| BioSample |
SAMN40546946 |
| SRA |
SRX23994684 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8155171_H288_aligned_fiducials.jpg.gz |
1.7 Mb |
(ftp)(http) |
JPG |
| GSM8155171_H288_barcodes.tsv.gz |
21.1 Kb |
(ftp)(http) |
TSV |
| GSM8155171_H288_detected_tissue_image.jpg.gz |
768.1 Kb |
(ftp)(http) |
JPG |
| GSM8155171_H288_features.tsv.gz |
151.6 Kb |
(ftp)(http) |
TSV |
| GSM8155171_H288_matrix.mtx.gz |
21.8 Mb |
(ftp)(http) |
MTX |
| GSM8155171_H288_scalefactors_json.json.gz |
171 b |
(ftp)(http) |
JSON |
| GSM8155171_H288_spatial_enrichment.csv.gz |
783.2 Kb |
(ftp)(http) |
CSV |
| GSM8155171_H288_tissue_hires_image.png.gz |
5.6 Mb |
(ftp)(http) |
PNG |
| GSM8155171_H288_tissue_lowres_image.png.gz |
547.7 Kb |
(ftp)(http) |
PNG |
| GSM8155171_H288_tissue_positions.csv.gz |
62.3 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
