|
| Status |
Public on Sep 17, 2024 |
| Title |
APAP3h |
| Sample type |
SRA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
model: Acetaminophen induced liver injury model
treatment: Acetaminophen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Freshly harvested liver tissues were frozen using isopentane and liquid nitrogen, embedded in OCT, sectioned into 10 μm slices.
Spatial transcriptome sequencing libraries were prepared with 10x Genomics Visium Spatal Gene Expression Sides & Reagert kit acording to manlacturer's corstucion
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Fresh frozen Spatial transcriptome sequencing
|
| Data processing |
Raw sequencing data were processed with 10X Genomics Space Ranger pipleline to generate FASTQ files
Sequences were aligned to mm10 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: mm10
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: 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 |
Jul 18, 2024 |
| Last update date |
Sep 17, 2024 |
| Contact name |
Yaying Zhu |
| E-mail(s) |
zhuyaying@stu.ynu.edu.cn
|
| Phone |
15624985711
|
| Organization name |
yunnan university
|
| Street address |
Chenggong district of yunnan university in kunming, yunnan province
|
| City |
Kunming |
| State/province |
Yunnan |
| ZIP/Postal code |
650000 |
| Country |
China |
| |
|
| Platform ID |
GPL24247 |
| Series (2) |
| GSE272564 |
Mid-Lobular Hepatocytes Exhibit Transient Proliferation Pause and Stress Response through Atf4-Ddit3 axis in Early Acute Liver Injury (10x Visium) |
| GSE272566 |
Mid-Lobular Hepatocytes Exhibit Transient Proliferation Pause and Stress Response through Atf4-Ddit3 axis in Early Acute Liver Injury |
|
| Relations |
| BioSample |
SAMN42584843 |
| SRA |
SRX25377365 |
