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Sample GSM5773456 Query DataSets for GSM5773456
Status Public on Feb 20, 2024
Title Young_mouse_brain_D1-1
Sample type SRA
Source name Brain
Organism Mus musculus
Characteristics tissue: Brain tissue
age: Young
region: cerebrum, brain stem and fiber tracts
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
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description Visium Spatial Gene Expression 
Data processing Illumina BCL files were converted to fastq files by using 10X Genomics Space Ranger pipeline spaceranger mkfastq function (
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
Submission date Jan 05, 2022
Last update date Feb 20, 2024
Contact name Cheng Wu
Phone 18846145680
Organization name Sun Yat-sen University
Street address No. 74, Zhongshan 2nd Road, Yuexiu District, Guangzhou
City Guangzhou
ZIP/Postal code 510600
Country China
Platform ID GPL24247
Series (1)
GSE193107 Spatial transcriptomic profiling of the aging mouse brain [spatial scRNA-seq]
BioSample SAMN24659873
SRA SRX13625975

Supplementary file Size Download File type/resource
GSM5773456_Young_mouse_brain_D1-1.tar.gz 50.2 Mb (ftp)(http) TAR
GSM5773456_Young_mouse_brain_D1-1.tif.gz 201.0 Mb (ftp)(http) TIFF
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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