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| Status |
Public on Nov 02, 2023 |
| Title |
Aged NSC, scRNAseq |
| Sample type |
SRA |
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| Source name |
Brain SVZ
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| Organism |
Mus musculus |
| Characteristics |
cell type: Neural stem cells
tissue: Brain SVZ
strain: C57BL/6
age: 15-18 months old
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| Extracted molecule |
total RNA |
| Extraction protocol |
Primary NSCs were isolated from the brain SVZ of the young (2 months) and aged (15-18 months) mice, respectively (Nat Protoc. 2012 Nov; 7(11):2005-2012). Briefly, microdissection of the brain SVZ was performed on ice. The tissue pieces of SVZ from 5 mice were pooled and dissociated into single cells using Neural Tissue Dissociation kit. The isolated cells were maintained in the initial proliferation medium before used in scRNAseq library generation.
scRNAseq library was prepared according to the protocol of 10x Genomics (single cell 3’ v3 protocol). Briefly, the primary NSCs were resuspended in the master mix and loaded together with partitioning oil and gel beads into the chip to generate the gel bead-in-emulsion (GEM). The poly-A RNA from the cell lysate contained in every single GEM was retrotranscripted to cDNA, which contains an Ilumina R1 primer sequence, Unique Molecular Identifier (UMI) and the 10x Barcode. The pooled barcoded cDNA was then cleaned up with Silane DynaBeads, amplified by PCR and the apropiated sized fragments were selected with SPRIselect reagent for subsequent library construction. During the library construction Ilumina R2 primer sequence, paired-end constructs with P5 and P7 sequences and a sample index were added.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
10x Genomics
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| Data processing |
The demultiplexing, barcoded processing, gene counting and aggregation were made using the Cell Ranger software v3.0.2 (10x Genomics)
Assembly: mm10
Supplementary files format and content: Cell Ranger output files (barcodes.tsv, genes.tsv, matrix.mtx)
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| Submission date |
Sep 05, 2022 |
| Last update date |
Nov 02, 2023 |
| Contact name |
Chengyang Peter Huang |
| E-mail(s) |
chengyhuang@hotmail.com
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| Organization name |
Shantou University Medical College
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| Street address |
22 Xinling Street
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| City |
Shantou |
| ZIP/Postal code |
515041 |
| Country |
China |
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| Platform ID |
GPL24247 |
| Series (2) |
| GSE212723 |
Transcriptional dysregulation impairs efficacy of neural stem cell activation during aging [scRNA-seq] |
| GSE212725 |
Transcriptional and epigenetic dysregulation impairs generation of proliferative neural stem and progenitor cells during brain aging |
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| Relations |
| BioSample |
SAMN30677155 |
| SRA |
SRX17431028 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM6544096_AgedNSC_barcodes.tsv.gz |
21.0 Kb |
(ftp)(http) |
TSV |
| GSM6544096_AgedNSC_genes.tsv.gz |
218.8 Kb |
(ftp)(http) |
TSV |
| GSM6544096_AgedNSC_matrix.mtx.gz |
60.6 Mb |
(ftp)(http) |
MTX |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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