|
| Status |
Public on May 24, 2024 |
| Title |
spatial transcriptomics of normal tissue of patient 1 |
| Sample type |
SRA |
| |
|
| Source name |
colon
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: colon
patient diagnosis: mucinous colorectal adenocarinoma
disease state: normal
|
| Extracted molecule |
total RNA |
| Extraction protocol |
fresh frozen tissue were OCT embedded, and 10μm frozen sections were cut with cryostat
spatial transcriptome sequencing libraries were prepared with 10X Genomics Visium Spatial Gene Expresssion Slides & Reagent kit according to manufacture's instruction
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Description |
fresh frozen spatial transcriptome sequencing
|
| Data processing |
raw sequencing data were processed using the 10X Genomics Space Ranger pipeline to generate fastq files
sequences were aligned to GRCh 38 genome for gene experssion counting using Space Ranger's default settings
Gene expression level of Refseq coding genes were quantified using Space Ranger's default settings
Assembly: GRCh 38
Supplementary files format and content: p1_N.barcodes.tsv.gz list of spatial barcodes
Supplementary files format and content: p1_N.features.tsv.gz list of gene IDs
Supplementary files format and content: p1_N.matrix.mtx.gz gene expression count data in matrix market exchange format
Supplementary files format and content: p1_N.aligned_fiducials.jpg aligned fiducials of the tissue image
Supplementary files format and content: p1_N.detected_tissue_image.jpg image of tissue and spots
Supplementary files format and content: p1_N.scalefactors_json.json scalefactors in json format
Supplementary files format and content: p1.tissue_hires_images.png hi-res image of tissue
Supplementary files format and content: p1.tissue_lowres_image.png low-res image of tissue
Supplementary files format and content: p1_N.tissue_position_list.csv list of spatial barcodes and the coordinates sepecifying spots
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
May 22, 2024 |
| Last update date |
May 24, 2024 |
| Contact name |
guangyong zheng |
| E-mail(s) |
zhenggy@sibs.ac.cn
|
| Organization name |
shutcm
|
| Street address |
cailun road 1200
|
| City |
Shanghai |
| ZIP/Postal code |
201203 |
| Country |
China |
| |
|
| Platform ID |
GPL16791 |
| Series (2) |
| GSE236697 |
Spatial transcriptomics reveals functional compartmentalization of mucinous colorectal adenocarcinoma |
| GSE236698 |
Mucinous colorectal adenocarcinoma |
|
| Relations |
| BioSample |
SAMN41494578 |
| SRA |
SRX24654770 |
