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| Status |
Public on Nov 18, 2024 |
| Title |
D1-D3 |
| Sample type |
SRA |
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| Source name |
brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: brain
model: pMCAO
strain: C57Black/6
age: 3 month
Sex: male
condition: 3 days
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| Treatment protocol |
Prior to the induction of MCAO, mice were anaesthetized with 3% isoflurane (Aerrane, Baxter) and amaintained in 2% isoflurane using a vaporizer (Tec-3, Cyprane Ltd.). A skin incision between the orbit and the external auditory meatus was made, and a 1-2 mm hole was drilled through the frontal bone 1 mm rostral to the fusion of the zygoma and the squamosal bone, about 3.5 mm ventrally to the dorsal surface of the brain. The middle cerebral artery (MCA) was exposed after the dura was opened and removed. The MCA was occluded by short coagulation with bipolar tweezers (SMT) at a proximal location, followed by transection of the vessel to ensure permanent occlusion. During the surgery, body temperature was maintained at 37 ± 1C using a heating pad. This MCAO model yields small infarct lesions in the parietal cortical region. Intact cortical tissue from 3 months old mice was used as control.
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| Extracted molecule |
total RNA |
| Extraction protocol |
Mice were deeply anesthetized with pentobarbital and perfused transcardially with cold (4–8C) isolation buffer.. The forebrain hemisphere was isolated by dissection of the olfactory lobes and the midbrain structure (bregma from ~ +3 to -4 mm). Dissected forebrains were embedded in optimal cutting temperature (OCT) medium, rapidly placed on dry ice to freeze, and then transferred to -80C for a maximum of six weeks of storage. The forebrains were sectioned coronally (10 um thickness) using Leica CM1950 cryostat (Leica Microsystems). Sections collected for 10X Visium Spatial Gene Expression processing were stored at -80C.
Sequencing libraries were prepared strictly according to the manufacturer’s manual “Visium Spatial Gene Expression Reagent Kits User Guide” (CG000239).
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| Library strategy |
OTHER |
| Library source |
transcriptomic |
| Library selection |
other |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
The raw sequencing data were processed using the recommended set of Spaceranger function (v1.2.2, 10X Genomics) for processing of fresh frozen samples. Binary base call files were demultiplexed using mkfastq function with default parameters, to generate FASTQ files.
The resulting fastq files were mapped separately to spaceranger reference (mm10/GRCm38) using count function, which takes a microscope slide image and fastq files, performs alignment, tissue detection, fiducial detection, and barcode/UMI counting.
Assembly: mm10/GRCm38
Supplementary files format and content: bardcodes.tsv: list of spatial barcodes
Supplementary files format and content: features.tsv: list of gene Ids
Supplementary files format and content: matrix.mtx: gene expression count data in Matrix Market Exchange Format
Supplementary files format and content: *.json: json file of tisue aligned to fiducial frame
Supplementary files format and content: *.tif: image of tissue
Library strategy: Spatial transcriptomics
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| Submission date |
May 31, 2023 |
| Last update date |
Nov 18, 2024 |
| Contact name |
Lukas Valihrach |
| Organization name |
Institute of Biotechnology, Czech Academy of Science
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| Lab |
Laboratory of Gene Expression
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| Street address |
Prumyslova 595
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| City |
Vestec |
| ZIP/Postal code |
25250 |
| Country |
Czech Republic |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE233814 |
Spatiotemporal transcriptomic map of glial cell response in a mouse model of acute brain ischemia [spatial transcriptomics] |
| GSE233815 |
Spatiotemporal transcriptomic map of glial cell response in a mouse model of acute brain ischemia |
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| Relations |
| BioSample |
SAMN35545333 |
| SRA |
SRX20555463 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7437223_D1-D3_barcodes.tsv.gz |
13.3 Kb |
(ftp)(http) |
TSV |
| GSM7437223_D1-D3_features.tsv.gz |
254.1 Kb |
(ftp)(http) |
TSV |
| GSM7437223_D1-D3_matrix.mtx.gz |
30.8 Mb |
(ftp)(http) |
MTX |
| GSM7437223_Mouse_3day_lesion_c1+2+3.tif.gz |
335.1 Mb |
(ftp)(http) |
TIFF |
| GSM7437223_V10M09-040-D1.json.gz |
91.0 Kb |
(ftp)(http) |
JSON |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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