|
| Status |
Public on Nov 17, 2023 |
| Title |
SS1960050 |
| Sample type |
SRA |
| |
|
| Source name |
pancreatic cancer tissue
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: pancreatic cancer tissue
|
| Extracted molecule |
total RNA |
| Extraction protocol |
FFPE block were sectioned for 10X Genomics Visium Spatial Gene Expresssion Slides according to manufacturer's instruction
Spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expression Slides & Reagent kit
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
10X visium
|
| Data processing |
Raw sequencing data were processed with 10X Genomics Space Ranger (v1.3.1) pipleline to generate FASTQ files
Sequences were aligned to GRCh38 genome to gene expression count using Space Ranger's default settings
Gene expression level of coding genes were quantifiied using Space Ranger's default settings
Assembly: hg38
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 expresssion count data in Matrix Market Exchange Format
Supplementary files format and content: filtered_feature_bc_matrix.h5: gene expression count data in HDF5 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_list.csv: list of spatial barcodes and the coordinates specifying spots
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
Jun 20, 2023 |
| Last update date |
Nov 17, 2023 |
| Contact name |
Jong-Eun Park |
| Organization name |
Korea Advanced Institute of Science and Technology
|
| Street address |
291, Daehak-ro, Yuseong-gu
|
| City |
Daejeon |
| ZIP/Postal code |
34141 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL24676 |
| Series (2) |
| GSE235315 |
Integrative single-cell transcriptome analysis of human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis [Spatial] |
| GSE235452 |
Integrative single-cell transcriptome analysis of human pancreatic cancer reveals an intermediate cancer cell population associated with poor prognosis |
|
| Relations |
| BioSample |
SAMN35811194 |
| SRA |
SRX20731451 |
