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| Status |
Public on Sep 16, 2022 |
| Title |
NSC-B23 pE |
| Sample type |
SRA |
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| Source name |
striatum & ventricular-subventricular zone
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| Organism |
Mus musculus |
| Characteristics |
tissue: striatum & ventricular-subventricular zone
cell type: TAP
genotype: WT
treatment: naive
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| Treatment protocol |
Two months old TiCY mice were intraperitoneally injected with tamoxifen. In these mice, tamoxifen-induced Cre recombination takes place in neural stem cells in the vSVZ, which express Tlx (Nr2e1) and will stably activate the production of enhanced YFP, labeling NSCs and their progeny. Two weeks after injection, an injury by bilateral carotid artery occlusion (BCCAO) was performed as described (Llorens-Bobadilla et al., 2015). The animals were sacrificed for single cell sorting either 48 h or 3 weeks after ischemia. WT mice were not subjected to tamoxifen or ischemia.
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| Extracted molecule |
total RNA |
| Extraction protocol |
For the ischemia experiment, the vSVZ and striatum were isolated. For the naïve experiments, vSVZ, striatum, and olfactory bulb were isolated. Depending on the plate, individual or pooled mice were used to sort cells on plate. Tissues were processed and sorted in a BD FACSAria II at the DKFZ Flow Cytometry Facility. Cells were stained with the following antibodies (all conditions and tissues together): O4-APC and O4-APC-Vio770 (Miltenyi; diluted 1:50), Ter119-APC-Cy7 (Biolegend; 1:100), CD45-APC-Cy7 (BD; 1:200), GLAST (ACSA-1)-PE (Miltenyi: 1:20), PSA-NCAM-PE-Vio770 (Miltenyi; 1:75), Prominin1-A488 (eBioscience; 1:75), and Sytox Blue (Life Technologies, 1:1000), CD9-eFluo450 (eBioscience, 1:300).
For profiling the transcriptome and epigenome of single cells we developed and implemented a miniaturized and higher throughput version of the scNMT-seq protocol (Clark et al., 2018). On this new version, the Smart-seq3 (Hagemann-Jensen et al., 2020) method and specific normalization steps were implemented. A detailed version of the protocol is described in Cerrizuela et al., (2022). The samples listed here represent the transcriptomic portion of this multi-omic data set.
Single-cell RNA-seq (Smart-seq3)
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
NextSeq 550 |
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| Description |
single-cell RNA-seq
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| Data processing |
mapping with STAR via zUMIs
transcript quantification with featureCounts via zUMIs
Assembly: GRCm38 (mm10)
Supplementary files format and content: Single-cell RNA-seq count matrix in gzip-compressed csv (comma-separated values) format. Values are not normalized, decimals are due to distribution of multimapping reads.
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| Submission date |
Jul 25, 2022 |
| Last update date |
Sep 16, 2022 |
| Contact name |
Ana Martin-Villalba |
| Organization name |
German Cancer Research Center
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| Department |
Molecular Neurobiology
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| Street address |
Im Neuenheimer Feld 280
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| City |
Heidelberg |
| ZIP/Postal code |
69121 |
| Country |
Germany |
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| Platform ID |
GPL21626 |
| Series (2) |
| GSE209656 |
scNMT-seq of the adult NSC lineage - RNA |
| GSE210806 |
Single-cell triple-omics uncovers DNA methylation as key feature of stemness in the healthy and ischemic adult brain |
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| Relations |
| BioSample |
SAMN29937735 |
| SRA |
SRX16651941 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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