Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury

UID: 10834

Author(s): Llorens-Bobadilla, Enric, Zhao, Sheng, Martin-Villalba, Ana

Description: Summary from the GEO: "Heterogeneous pools of adult neural stem cells (NSCs) contribute to brain maintenance and regeneration after injury. The balance of NSC activation and quiescence, as well as the induction of lineage-specific transcription factors, may contribute to diversity of neuronal and glial fates. To identify molecular hallmarks governing these characteristics, we performed single-cell sequencing of an unbiased pool of adult subventricular zone NSCs. This analysis identified a discrete, dormant NSC subpopulation that already expresses distinct combinations of lineage-specific transcription factors during homeostasis. Dormant NSCs enter a primed-quiescent state before activation, which is accompanied by downregulation of glycolytic metabolism, Notch, and BMP signaling and a concomitant upregulation of lineage-specific transcription factors and protein synthesis. In response to brain ischemia, interferon gamma signaling induces dormant NSC subpopulations to enter the primed-quiescent state. This study unveils general principles underlying NSC activation and lineage priming and opens potential avenues for regenerative medicine in the brain."

Overall design from the GEO: " Single cell RNAseq of cells isolated from their in vivo niche in the subventricular zone, Striatum and Cortex during homeostasis as well as following ischemic injury.
In total 272 single cells. (: homeostasis samples; and : samples following ischemic injuried)."

Subject of Study

Subject(s)

Access via GEO
CSV file of expression profiling by high throughput sequencing
Accession #: GSE67833

Access via SRA
RNA sequencing of 272 samples.
Accession #: SRP057125

Access via BioProject
Additional information about the overall inititative.
Accession #: PRJNA281015
Access Restrictions: Free to All
Access Instructions: The NCBI Gene Expression Omnibus, SRA, and BioProject databases provide open access to these files. The SRA Run Selector link at the bottom of the page is a processing tool for raw data.
Associated Publications: Xie X, Laks D, Sun D, et al. High-resolution mouse subventricular zone stem-cell niche transcriptome reveals features of lineage, anatomy, and aging. Proceedings of the National Academy of Sciences of the United States of America. 2020; 117(49):31448-31458.

Llorens-Bobadilla E, Zhao S, Baser A, Saiz-Castro G, Zwadlo K, Martin-Villalba A. Single-Cell Transcriptomics Reveals a Population of Dormant Neural Stem Cells that Become Activated upon Brain Injury. Cell Stem Cell. 2015;17(3):329-340.
Data Type: Genomic
Equipment Used: Illumina HiSeq 2000
High throughput gene sequencing system
Software Used: SRA Toolkit
The NCBI SRA Toolkit enables reading ("dumping") of sequencing files from the SRA database and writing ("loading") files into the .sra format.
Dataset Format(s): CSV, SRA
Data Tool(s): RNA Seq
Dataset Size: 6.3 MB (CSV), 282.4 Gb (SRA)

Do you have or know of a dataset that should be added to the catalog? Let us know!