 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on May 21, 2023 |
| Title |
human post-mortem brain, Striatum, PD, FMP-10 (V11T17-102_C1) |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: brain
age: 94 years
array id: V11T17-102_C1
protocol: SMA_RRST
section: section of human post-mortem caudate nucleus
|
| Extracted molecule |
total RNA |
| Extraction protocol |
snap-frozen un-embedded tissue specimens were cryo-sectioned at 10-12um thickeness, placed onto Visium gene expression array, imaged with MALDI-MSI and then processed with the Visium protocol (10x Genomics) or RRST protocol (https://doi.org/10.1038/s41467-023-36071-5)
spatial gene expression libraries were generated following 10X Genomic Visium Spatial Gene Expression protocol (User Guide, CG000239 Rev F) for the standard Visium, iCTRL, iCTRL_FMP-10 and SMA_Visium samples (ref. protocol column above) or The Visium Spatial Gene Expression for FFPE reagent kit (10x Genomics, User Guide CG000407 Rev C, mouse transcriptome, human transcriptome) for the SMA_RRST samples
Visium spatial gene expression (RNA)
|
| |
|
| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
| |
|
| Data processing |
A pre-built reference (refdata-gex-mm10-2020-A for the mouse samples and refdata-gex-GRCh38-2020-A for the human samples) was downloaded from 10x Genomics website and used as a reference for data processing with Space Ranger v1.3.1 (SMA_RRST samples) or Space Ranger v1.2.1 (rest of the samples)
Raw fastq files and H&E images were processed with the Space Ranger v1.3.1 or Space Ranger v1.2.1 command line tool to produce the following processed data files: expression matrices (h5 files), scaled H&E images (png files), spot coordinate tables (csv files) and scale factors (json files). Loupe Browser 6 (10x Genomics) was used to manually annotate the tissue sections and produced the following processed data files: csv tables ending with _RegionLoupe.csv, _filter.csv, _dopamine.csv, _lesion.csv, _region.csv
Assembly: mm10, GRCh38
Supplementary files format and content: Space Ranger processed data files: expression matrices (h5 files), scaled H&E images (png files), spot coordinate tables (csv files) and scale factors (json files). Loupe Browser 6 processed data files: csv tables ending with _RegionLoupe.csv, _filter.csv, _dopamine.csv, _lesion.csv, _region.csv
Library strategy: Spatial Transcriptomics
|
| |
|
| Submission date |
May 19, 2023 |
| Last update date |
May 22, 2023 |
| Contact name |
Marco Vicari |
| E-mail(s) |
marcovicari3@gmail.com
|
| Organization name |
KTH, SciLifeLab
|
| Department |
Gene Technology
|
| Lab |
Joakim Lundeberg
|
| Street address |
Tomtebodavägen 23
|
| City |
Solna |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL30173 |
| Series (1) |
| GSE232910 |
Spatial Multimodal Analysis: MALDI-MSI and Spatial Transcriptomics within the same tissue section |
|
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7392327_220512_MSI_hStriatum_V11T17-102_MVRM.C1-Spot000002.jpg.gz |
402.6 Mb |
(ftp)(http) |
JPG |
| GSM7392327_V11T17-102_C1_RNA_RegionLoupe.csv.gz |
27.6 Kb |
(ftp)(http) |
CSV |
| GSM7392327_V11T17-102_C1_RNA_dopamine.csv.gz |
28.6 Kb |
(ftp)(http) |
CSV |
| GSM7392327_V11T17-102_C1_RNA_filtered_feature_bc_matrix.h5 |
3.7 Mb |
(ftp)(http) |
H5 |
| GSM7392327_V11T17-102_C1_RNA_raw_feature_bc_matrix.h5 |
5.3 Mb |
(ftp)(http) |
H5 |
| GSM7392327_V11T17-102_C1_RNA_scalefactors_json.json.gz |
179 b |
(ftp)(http) |
JSON |
| GSM7392327_V11T17-102_C1_RNA_tissue_hires_image.png.gz |
16.9 Mb |
(ftp)(http) |
PNG |
| GSM7392327_V11T17-102_C1_RNA_tissue_positions_list.csv.gz |
69.8 Kb |
(ftp)(http) |
CSV |
| Processed data provided as supplementary file |
| Raw data not provided for this record |
|
|
|
|
 |
