|
| Status |
Public on Jan 13, 2025 |
| Title |
Brain, sham, biol rep 3 |
| Sample type |
SRA |
| |
|
| Source name |
Brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: Brain
strain: C57BL/6J
treatment: sham
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Freshly dissected right mouse brain hemisphere was flash frozen in OCT using a set-up of isopentane and liquid nitrogen (as per 10xGenomics Visium Spatial Gene Expression protocols). Fresh frozen tissue was directly sectioned onto Visium Spatial Gene Expression Slides at 10μm using a cryostat.
Spatial transcriptome sequencing libraries were prepared with 10xGenomics Visium Spatial Gene Expression Slides & Reagent kit according to manufacturer's instructions
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Fresh frozen spatial transcriptome sequencing
|
| Data processing |
Raw sequencing bcl files were processed using the 10x Genomics Space Ranger pipeline to generate FASTQ files.
Sequences were then aligned to the mm10 genome to obtain gene expression counts using the Space Ranger count pipeline
Assembly: mm10
Supplementary files format and content: barcodes.tsv.gz: list of all detected spatial barcodes (from raw_feature_bc_matrix/ spaceranger output folder)
Supplementary files format and content: features.tsv.gz: list of all detected gene IDs (from raw_feature_bc_matrix/ spaceranger output folder)
Supplementary files format and content: matrix.mtx.gz: gene expression count data in the Matrix Market Exchange format (from raw_feature_bc_matrix/ spaceranger output folder)
Supplementary files format and content: filtered_feature_bc_matrix.h5:
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: high resolution image of brain hemisphere tissue
Supplementary files format and content: tissue_lowres_image.png: low resolution image of brain hemisphere 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 |
Feb 27, 2024 |
| Last update date |
Jan 13, 2025 |
| Contact name |
Alexander Tang |
| E-mail(s) |
alex.tang@uwa.edu.au
|
| Phone |
(08) 6488 2245
|
| Organization name |
University of Western Australia
|
| Department |
School of Biomedical Science
|
| Lab |
Healthy Brain Ageing and Repair Lab
|
| Street address |
35 Stirling Highway, University of Western Australia
|
| City |
Perth |
| State/province |
Western Australia |
| ZIP/Postal code |
6009 |
| Country |
Australia |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE259405 |
Repetitive transcranial magnetic stimulation induces cortical layer, brain region, and protocol dependent neural plasticity [Spatial transcriptomics] |
|
| Relations |
| BioSample |
SAMN40177253 |
| SRA |
SRX23770357 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM8115653_sham3_aligned_fiducials.jpg.gz |
1.1 Mb |
(ftp)(http) |
JPG |
| GSM8115653_sham3_barcodes.tsv.gz |
28.2 Kb |
(ftp)(http) |
TSV |
| GSM8115653_sham3_detected_tissue_image.jpg.gz |
757.2 Kb |
(ftp)(http) |
JPG |
| GSM8115653_sham3_features.tsv.gz |
254.1 Kb |
(ftp)(http) |
TSV |
| GSM8115653_sham3_filtered_feature_bc_matrix.h5 |
10.2 Mb |
(ftp)(http) |
H5 |
| GSM8115653_sham3_matrix.mtx.gz |
31.1 Mb |
(ftp)(http) |
MTX |
| GSM8115653_sham3_scalefactors_json.json.gz |
162 b |
(ftp)(http) |
JSON |
| GSM8115653_sham3_tissue_hires_image.png.gz |
3.4 Mb |
(ftp)(http) |
PNG |
| GSM8115653_sham3_tissue_lowres_image.png.gz |
316.5 Kb |
(ftp)(http) |
PNG |
| GSM8115653_sham3_tissue_positions_list.csv.gz |
71.6 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
