GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Sample GSM5061724 Query DataSets for GSM5061724
Status Public on Feb 04, 2021
Title ElimSVZ_4 [SVZ9_S9]
Sample type SRA
Source name ElimSVZ
Organism Mus musculus
Characteristics strain: C57BL/6
treatment: PLX
tissue/cell type: subventricular zone
Extracted molecule total RNA
Extraction protocol Brains were removed, microdissected into cortex, hippocampus, and thalamus/striatum, and flash frozen on dry ice. RNA was extracted using Rneasy Mini Kit (Qiagen). cDNA synthesis, amplification, library construction and sequencing were performed by Novogene Inc. using Illumina NovaSeq and HiSeq platforms with paired-end 150 bp (PE 150) sequencing strategy.
RNA libraries were prepared for sequencing using standard Illumina protocols
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
Data processing Illumina HiSeq 4000 was used to produce 50bp single-end reads.
Sequenced reads mapped to mm10 whole genome using STAR aligner.
featureCounts were calculated using function of the Rsubread package in R.
After filtering out low-count genes, count distributions were scaled using the calcNormFactors function of the edgeR package.
plotMDS function of the limma package in R was used to perform principal component analysis. Reads Per Kilobase of exon per Megabase of library size (RPKM) were prepared and fitted to linear models using the voom and lmfit functions.
Genome_build: mm10
Supplementary_files_format_and_content: FPKM values for all Samples
Submission date Feb 03, 2021
Last update date Feb 05, 2021
Contact name Kim Green
Phone 9498243859
Organization name University of California, Irvine
Department Neurobiology and Behavior
Street address 3208 Biological Sciences 3
City Irvine
State/province CA
ZIP/Postal code 92617
Country USA
Platform ID GPL21103
Series (1)
GSE166092 Subventricular zone/white matter microglia reconstitute the empty adult microglial niche in a dynamic wave
BioSample SAMN17769152
SRA SRX10012769

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap