GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
Series GSE127542 Query DataSets for GSE127542
Status Public on Mar 01, 2019
Title RNA-seq of microglia isolated from the hippocampi of young and aged mice
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Sequencing data related to the manuscript entitled, "CD22 blockade restores homeostatic microglial phagocytosis in the aging brain."
Overall design Hippocampi from young (3 month old) and aged (20 month old) mice were microdissected following perfusion. Primary microglia were isolated by gentle dounce homogenization of the brain, magentic myelin removal, and FACS-purification of ~20,000 live CD11b+CD45lo cells. Microglia were sorted into RLT Plus buffer (Qiagen) containing beta-mercaptoethanol. RNA was extracted using a RNeasy Micro Plus kit (Qiagen) according the manufacturer’s protocol. RNA integrity was assessed on a Bioanalyzer (Agilent), and high quality samples were used for library preparation. cDNA synthesis and amplification was performed using the SmartSeq v4 Ultra-low input kit (Takara), and libraries were tagmented, adaptor ligated, and indexed using the Nextera XT kit (Illumina). After normalization and pooling, libraries were sequenced on a Novaseq 6000 (Illumina) using paired-end 150bp reads. Raw sequencing files were demultiplexed with bcl2fastq, trimmed with fastx_trimmer, reads were aligned using STAR, the count matrix was generated using samtools, and differential expression analysis was performed using DESeq2 with standard settings.
Contributor(s) Pluvinage J, Bonanno L
Citation(s) 30944478
Submission date Feb 28, 2019
Last update date Apr 06, 2019
Contact name John Pluvinage
Organization name Stanford
Street address 3801 Miranda Ave Rm D3-131
City palo alto
State/province California
ZIP/Postal code 94304
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (16)
GSM3635990 YH1
GSM3635991 YH2 technical replicate 1
GSM3635992 YH2 technical replicate 2
BioProject PRJNA524906
SRA SRP187108

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE127542_normalized_counts_aging.csv.gz 1.0 Mb (ftp)(http) CSV
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