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| Status |
Public on Feb 20, 2024 |
| Title |
Young_mouse_brain_A1-1 |
| Sample type |
SRA |
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| Source name |
Brain
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| Organism |
Mus musculus |
| Characteristics |
tissue: Brain tissue
age: Young
region: cerebrum, brain stem and fiber tracts
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| Extracted molecule |
total RNA |
| Extraction protocol |
Young (2 months old) and old mice (28 months old) (strain C57BL/6J) were euthanized with an overdose of isoflurane. The brains were rapidly extracted from the cranial cavity, and immediately submerged in ice-cold artificial cerebrospinal fluid. The brains were then blotted to remove excess liquid and were subsequently embedded in optimal cutting temperature (OCT) compound (SAKURA). The brains with OCT compound were quick-frozen on dry ice immediately and stored at -80℃ until cryosectioning process. The cryosectioning placed in a cryostat (Leica, CM1950) to cryosection the OCT embedded tissue blocks into appropriately sized sections for Visium Spatial slides while keeping the samples frozen. Brain sections were 10 μm thick each
10x Genomics Visium Spatial protocols
Spatial scRNA-seq
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Visium Spatial Gene Expression
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| Data processing |
Illumina BCL files were converted to fastq files by using 10X Genomics Space Ranger pipeline spaceranger mkfastq function (https://support.10xgenomics.com/).
Fastq files were aligned to mm10 reference, manually aligned to respective H&E stain images using spaceranger count (spaceranger v 1.2.0) to obtain the spatial transcription profiles.
Genome_build: mm10
Supplementary_files_format_and_content: Matrix table with raw and fittered gene-cell counts for every sample, tissue hires image, tissue position list, scale factors and Hematoxylin & H&E stain images
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| Submission date |
Jan 05, 2022 |
| Last update date |
Feb 20, 2024 |
| Contact name |
Cheng Wu |
| E-mail(s) |
wuch55@mail2.sysu.edu.cn
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| Phone |
18846145680
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| Organization name |
Sun Yat-sen University
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| Street address |
No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou
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| City |
Guangzhou |
| ZIP/Postal code |
510600 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE193107 |
Spatial transcriptomic profiling of the aging mouse brain [spatial scRNA-seq] |
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| Relations |
| BioSample |
SAMN24659876 |
| SRA |
SRX13625972 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM5773453_Young_mouse_brain_A1-1.tar.gz |
50.3 Mb |
(ftp)(http) |
TAR |
| GSM5773453_Young_mouse_brain_A1-1.tif.gz |
232.8 Mb |
(ftp)(http) |
TIFF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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