 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Mar 03, 2022 |
| Title |
Spatial Htra3KO sham |
| Sample type |
SRA |
| |
|
| Source name |
heart
|
| Organism |
Mus musculus |
| Characteristics |
cell type: heart
strain: C57BL/6N
operation: sham
tissue: heart
name in supplementary file: N/A
molecule subtype: Spatial
protocol: Visium
|
| Treatment protocol |
Sham surgery was performed in mice randomly selected from among those weighing 20–23 g at the age of 9–11 weeks.
|
| Growth protocol |
C57BL/6N mice were purchased from CLEA Japan, Inc. Female and male mice were housed in separate cages at a maximum of 6 mice per cage in a specific-pathogen–free, temperature-controlled vivarium under a 19-h light/dark cycle with ad libitum access to food and water. All experiments were approved by the University of Tokyo Ethics Committee for Animal Experiments and strictly adhered to the guidelines of the University of Tokyo for animal experiments.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen samples were embedded in OCT (TissueTek Sakura) and cryosectioned at −14℃ (Leica CM1860). Sections were placed on chilled Visium Spatial Gene Expression Slides (2000233, 10X Genomics), and adhered by warming the back of the slide. Tissue sections were then fixed in chilled methanol and stained according to the Visium Spatial Gene Expression User Guide (CG000239 Rev D, 10X Genomics). For gene expression samples, tissue was permeabilized for 15 minutes, which was selected as the optimal time based on tissue optimization time course experiments (CG000238 Rev D, 10X Genomics). Brightfield histology images were taken using a 10X objective on a BZ-X700 microscope (Keyence Corporation, Itasca, Illinois). Raw images were stitched together using BZ-X analyzer software (Keyence Corporation) and exported as TIFF files.
Libraries were prepared according to the Visium Spatial Gene Expression User Guide (CG000239 Rev D, 10X Genomics).
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Library strategy: Spatial transcriptomics
Differentially expressed genes were detected by using FindMarkers in Seurat (log2fc.threshold > 0.25, p_val_adj < 0.05).
Genome_build: mm10
|
| |
|
| Submission date |
Mar 11, 2021 |
| Last update date |
Mar 04, 2022 |
| Contact name |
Seitaro Nomura |
| E-mail(s) |
senomura-cib@umin.ac.jp
|
| Phone |
81338155411
|
| Organization name |
The University of Tokyo
|
| Department |
Department of Cardiovascular Medicine
|
| Street address |
7-3-1, Hongo, Bunkyo-ku
|
| City |
Tokyo |
| State/province |
Select a State or Province |
| ZIP/Postal code |
113-8655 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE168742 |
Cardiac fibroblasts regulate the development of heart failure via Htra3-TGF-β-IGFBP7 axis |
|
| Relations |
| BioSample |
SAMN18270747 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5164952_HtrA3KO_Sham.tif.gz |
16.0 Mb |
(ftp)(http) |
TIFF |
| GSM5164952_HtrA3KO_Sham_filtered_feature_bc_matrix.tar.gz |
19.5 Mb |
(ftp)(http) |
TAR |
| GSM5164952_HtrA3KO_Sham_raw_feature_bc_matrix.tar.gz |
30.3 Mb |
(ftp)(http) |
TAR |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
