|
| Status |
Public on Nov 01, 2022 |
| Title |
SOR3 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Mus musculus |
| Characteristics |
tissue: brain
Sex: male
condition: spatial object recognition training
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mouse brain section per mouse was cut at 10 µm thickness and mounted onto each Visium slide capture area. After H&E staining, each bright-field image was taken as described in the Spatial Transcriptomics procedure. Tissue permeabilization was performed for 18 minutes, as established in the tissue optimization assay. The Visium Spatial Gene Expression Slide & Reagent kit (10X Genomics) was used to generate sequencing libraries for Visium samples.
Libraries were constructed according to the 10x Visium library construction protocol and sequenced by Illumina NovaSeq6000.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Data processing |
Raw files were processed with spaceranger-1.2.2.
Outputs for each samples are provided in tar.gz files.
Assembly: mm10
Supplementary files format and content: Compressed directory containing spaceranger output. _filtered_feature_bc.matrix.h5 contains expression data. Images are provided as low and high resolution PNG, and scaling information is provided in scalefactors_json.json. Mapping between image coordinates and spot identifiers are provided in tissue_positions_list.csv.
|
| |
|
| Submission date |
Apr 26, 2022 |
| Last update date |
Oct 10, 2024 |
| Contact name |
Ethan Bahl |
| E-mail(s) |
ethan-bahl@uiowa.edu
|
| Organization name |
University of Iowa
|
| Street address |
25 S Grand Ave
|
| City |
Iowa City |
| State/province |
IA |
| ZIP/Postal code |
52242 |
| Country |
USA |
| |
|
| Platform ID |
GPL24247 |
| Series (1) |
| GSE201610 |
Spatial RNA sequencing of mouses brain slices following spatial object recognition training |
|
| Relations |
| BioSample |
SAMN27784253 |
| SRA |
SRX15005003 |
