|
| Status |
Public on Feb 07, 2025 |
| Title |
Hepatoblastoma sample 24 |
| 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, Visium v1), deparaffinized, and H&E stained according to the respective user guide (CG000409 Rev C, 10x Genomics). Twelve additional samples were processed using a CytAssist machine (10x Genomics, Visium v2), which transfers the transcriptomic probes from standard glass slides to spatially barcoded Visium slides, enabling more efficient capture of whole gene expression. For all samples, 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 |
Library name: H1157
10x Genomics Visium CytAssist FFPE spatial transcriptomics (v2)
|
| Data processing |
Raw sequencing data was demultiplexed and aligned to the human reference genome GRCh38-2020-A with Space Ranger 2.0.1 (Visium v1) and Space Ranger 2.1.1 (Visium v2) using spaceranger mkfastq and spaceranger count with default parameters. Fiducial alignment was repeated manually for samples H1156, H1190, H1192, and H1225 using Loupe Browser (10x Genomics).
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
Supplementary files format and content: cytassist_image.tif: hi-res image of tissue from CytAssist machine
Supplementary files format and content: loupe_alignment.json: manual fiducial alignment in json format
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
Nov 29, 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 |
SAMN45106083 |
| SRA |
SRX26922234 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8657780_H1157_aligned_fiducials.jpg.gz |
3.2 Mb |
(ftp)(http) |
JPG |
| GSM8657780_H1157_barcodes.tsv.gz |
25.7 Kb |
(ftp)(http) |
TSV |
| GSM8657780_H1157_cytassist_image.tiff.gz |
26.5 Mb |
(ftp)(http) |
TIFF |
| GSM8657780_H1157_detected_tissue_image.jpg.gz |
1.2 Mb |
(ftp)(http) |
JPG |
| GSM8657780_H1157_features.tsv.gz |
152.8 Kb |
(ftp)(http) |
TSV |
| GSM8657780_H1157_matrix.mtx.gz |
36.1 Mb |
(ftp)(http) |
MTX |
| GSM8657780_H1157_scalefactors_json.json.gz |
183 b |
(ftp)(http) |
JSON |
| GSM8657780_H1157_spatial_enrichment.csv.gz |
854.8 Kb |
(ftp)(http) |
CSV |
| GSM8657780_H1157_tissue_hires_image.png.gz |
6.4 Mb |
(ftp)(http) |
PNG |
| GSM8657780_H1157_tissue_lowres_image.png.gz |
607.2 Kb |
(ftp)(http) |
PNG |
| GSM8657780_H1157_tissue_positions.csv.gz |
57.1 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
