High-resolution transcriptome analysis of mouse subventricular zone reveals features of stem cell lineage, anatomy, and aging

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UID: 10833

Author(s): Laks, Dan R.*, Poran, Asaf, Laughney, Ashley Marie*, Xie, Xuanhua P.* * MSK affiliated

Description: Summary from the GEO: "High-resolution transcriptome analysis of mouse subventricular zone reveals features of stem cell lineage, anatomy, and aging"

Overall design from the GEO: "Whole SVZ dissected, FACS sorted for GFPhi, Low, negative, and Unsorted Viable (6600 cells) or Aged SVZ samples, 2 weeks, 2 months, 6 months, 12 months, FACS sorted for viable cells, undergone Drop-seq single cell RNA sequencing."

Subject of Study

Subject(s)

Access via GEO
CSV files of expression profiling by high throughput sequencing
Accession #: GSE107220

Access via SRA
RNA sequencing of 8 samples.
Accession #: SRP125398

Access via BioProject
Additional information about the overall inititative.
Accession #: PRJNA419350
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.
Data Type: Genomic
Equipment Used: Illumina NextSeq 500
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, TAR, RAW
Data Tool(s): RNA Seq
Dataset Size: 22.5 (CSV), 12.2 (TAR of CSV), 28.7 (SRA)

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