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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Jul 02, 2024 |
| Title |
Old, 1, spatial transcriptomics |
| Sample type |
SRA |
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| Source name |
Whole brain
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| Organism |
Mus musculus |
| Characteristics |
cell type: Brain cells
tissue: Whole brain
strain: C57Bl/JRj
age: 16-21 month old
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| Extracted molecule |
total RNA |
| Extraction protocol |
For scRNA-seq, freshly collected brain cells from dentate gyrus of C57Bl6/JRj mice were dissociated using Neural Tissue Dissociation Kit (P) and Myelin Removal Beads II (Miltenyi Biotec). For spatial transcriptomics, mouse brains were collected and embedded in OCT.
Library was performed according to the manufacter’s instructions (single cell 3’ v3.1 protocol, spatial gene expression protocol, 10x Genomics).
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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 |
Raw data was processed using the Cell Ranger (v6) and Space Ranger (v2) softwares.
Assembly: mm10
Supplementary files format and content: Tab-separated values files and matrix files
Library strategy: Spatial Transcriptomics
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| Submission date |
May 24, 2023 |
| Last update date |
Jul 02, 2024 |
| Contact name |
Yicheng Wu |
| E-mail(s) |
yicheng.wu1987@gmail.com
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| Organization name |
University of Zurich
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| Department |
Brain Research Institute
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| Street address |
Winterthurerstrasse 190
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| City |
Zurich |
| ZIP/Postal code |
8057 |
| Country |
Switzerland |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE233363 |
Multimodal transcriptomic analysis of aging neurogenic niche in the mouse hippocampus |
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| Relations |
| BioSample |
SAMN35354666 |
| SRA |
SRX20509339 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM7426328_P23360_1013_S13_barcodes.tsv.gz |
14.7 Kb |
(ftp)(http) |
TSV |
| GSM7426328_P23360_1013_S13_features.tsv.gz |
284.1 Kb |
(ftp)(http) |
TSV |
| GSM7426328_P23360_1013_S13_matrix.mtx.gz |
37.9 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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