|
| Status |
Public on Mar 06, 2024 |
| Title |
Healthy mouse liver-1 |
| Sample type |
SRA |
| |
|
| Source name |
liver
|
| Organism |
Mus musculus |
| Characteristics |
tissue: liver
genotype: Wild type
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Mouse liver slide gene expression were detected by 10x Visium Spatial Gene Expression Slide & Reagents Kit.
RNA libraries were prepared for sequencing using 10x Visium spatial protocols and standard Illumina protocols.
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Sequencing was performed on NovaSeq 6000 platform in a 28+120-base paired-end mode.
Illumina RTA v3.4.4 software was used for base calling.
Raw sequencing data for each sample were converted to matrices of expression using Space Ranger (version spaceranger-1.0.0, 10X Genomics).
Assembly: refdata-cellranger-mm10-3.0.0
Supplementary files format and content: filtered_barcodes.tsv.gz: list of spatial barcode. This file was in the "filtered_feature_bc_matrix" output folder of Space Ranger software.
Supplementary files format and content: filtered_features.tsv.gz: list of gene name and Ensembl ID. This file was in the "filtered_feature_bc_matrix" output folder of Space Ranger software.
Supplementary files format and content: filtered_matrix.mtx.gz: non-zero gene expresion count data in Matrix Market Exchange Formats. This file was in the "filtered_feature_bc_matrix" output folder of Space Ranger software.
Supplementary files format and content: raw_barcodes.tsv.gz: list of spatial barcode. This file was in the "raw_feature_bc_matrix" output folder of Space Ranger software.
Supplementary files format and content: raw_features.tsv.gz: list of gene name and Ensembl ID. This file was in the "raw_feature_bc_matrix" output folder of Space Ranger software.
Supplementary files format and content: raw_matrix.mtx.gz: non-zero gene expresion count data in Matrix Market Exchange Formats. This file was in the "raw_feature_bc_matrix" output folder of Space Ranger software.
Supplementary files format and content: tissue_positions_list.csv: list of spatial barcode and the cordinate specifying spot
Supplementary files format and content: detected_tissue_image.jpg: image of tissue and spots
Supplementary files format and content: tissue_hires_image.png: image of tissue
|
| |
|
| Submission date |
Sep 14, 2022 |
| Last update date |
Jul 01, 2024 |
| Contact name |
Daisuke Motooka |
| E-mail(s) |
dry_team@ngs.gen-info.osaka-u.ac.jp
|
| Organization name |
NGS core facility, Research Institute for Microbial Diseases, Osaka University
|
| Street address |
3-1, Yamadaoka
|
| City |
Suita |
| State/province |
Osaka |
| ZIP/Postal code |
5650871 |
| Country |
Japan |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE213388 |
Periportal macrophages protect against commensal-driven liver inflammation [spatial transcriptomics] |
|
| Relations |
| BioSample |
SAMN30861540 |
| SRA |
SRX17587153 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6585445_sample1_detected_tissue_image.jpg.gz |
1.5 Mb |
(ftp)(http) |
JPG |
| GSM6585445_sample1_filtered_barcodes.tsv.gz |
7.7 Kb |
(ftp)(http) |
TSV |
| GSM6585445_sample1_filtered_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM6585445_sample1_filtered_matrix.mtx.gz |
21.2 Mb |
(ftp)(http) |
MTX |
| GSM6585445_sample1_raw_barcodes.tsv.gz |
27.7 Kb |
(ftp)(http) |
TSV |
| GSM6585445_sample1_raw_features.tsv.gz |
272.8 Kb |
(ftp)(http) |
TSV |
| GSM6585445_sample1_raw_matrix.mtx.gz |
31.9 Mb |
(ftp)(http) |
MTX |
| GSM6585445_sample1_tissue_hires_image.png.gz |
3.7 Mb |
(ftp)(http) |
PNG |
| GSM6585445_sample1_tissue_positions_list.csv.gz |
61.5 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
