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| Status |
Public on May 21, 2023 |
| Title |
mouse brain, Substantia Nigra, 6-OHDA, mouse4, FMP-10_iCTRL (V11T16-085_D1) |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: brain
age: 8 weeks
array id: V11T16-085_D1
protocol: FMP-10-iCTRL
section: coronal section at the Substantia Nigra level
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| 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)
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
NextSeq 2000 |
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| 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
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| Submission date |
May 19, 2023 |
| Last update date |
May 22, 2023 |
| Contact name |
Marco Vicari |
| E-mail(s) |
[email protected]
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| Organization name |
KTH, SciLifeLab
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| Department |
Gene Technology
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| Lab |
Joakim Lundeberg
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| Street address |
Tomtebodavägen 23
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| City |
Solna |
| ZIP/Postal code |
171 65 |
| Country |
Sweden |
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| Platform ID |
GPL30172 |
| Series (1) |
| GSE232910 |
Spatial Multimodal Analysis: MALDI-MSI and Spatial Transcriptomics within the same tissue section |
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| Relations |
| BioSample |
SAMN35215931 |
| SRA |
SRX20439564 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7392321_220620_MSi_SN_V11T16-085.D1-Spot000001.jpg.gz |
158.1 Mb |
(ftp)(http) |
JPG |
| GSM7392321_V11T16-085-D1.json.gz |
71.7 Kb |
(ftp)(http) |
JSON |
| GSM7392321_V11T16-085_D1_RegionLoupe.csv.gz |
22.0 Kb |
(ftp)(http) |
CSV |
| GSM7392321_V11T16-085_D1_filtered_feature_bc_matrix.h5 |
12.7 Mb |
(ftp)(http) |
H5 |
| GSM7392321_V11T16-085_D1_lesion.csv.gz |
20.2 Kb |
(ftp)(http) |
CSV |
| GSM7392321_V11T16-085_D1_raw_feature_bc_matrix.h5 |
15.0 Mb |
(ftp)(http) |
H5 |
| GSM7392321_V11T16-085_D1_region.csv.gz |
20.3 Kb |
(ftp)(http) |
CSV |
| GSM7392321_V11T16-085_D1_scalefactors_json.json.gz |
174 b |
(ftp)(http) |
JSON |
| GSM7392321_V11T16-085_D1_tissue_hires_image.png.gz |
12.0 Mb |
(ftp)(http) |
PNG |
| GSM7392321_V11T16-085_D1_tissue_positions_list.csv.gz |
61.7 Kb |
(ftp)(http) |
CSV |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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