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Series GSE140009 Query DataSets for GSE140009
Status Public on Nov 07, 2019
Title RNA-seq of lipid droplet-low and lipid droplet-rich microglia isolated from the hippocampi of Progranulin KO mice
Organism Mus musculus
Experiment type Expression profiling by high throughput sequencing
Summary Sequencing data related to the manuscript entitled, "Lipid droplet accumulating microglia represent a dysfunctional and pro-inflammatory state in the aging brain".
Overall design 10-month old Progranulin knockout mice (GRN KO) were perfused and hippocampi were dissected (Hippocampi of 2 mice were pooled per sample). Primary microglia were isolated by gentle dounce homogenization of the brain, Percoll-based myelin removal, and FACS-purification of ~10,000 live CD11b+CD45lo cells. BODIPYlo (=lipid droplet-low) and BODIPYhi (=lipid droplet-high) microglia were sorted into RLT Plus buffer (Qiagen) containing beta-mercaptoethanol. RNA was extracted using a RNeasy Micro Plus kit (Qiagen) according to the manufacturer’s protocol. RNA integrity was assessed on a Bioanalyzer (Agilent), and high quality samples (RIN >9) 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). Sequencing of isolated microglia was carried out with Illumina Novogene 6000, paired end, 2x 100 bp. The quality of fastq files was assessed using FASTQC (v 0.11.4). Reads were mapped to mouse mm10 reference genome using STAR (v 2.5.3a). Raw read counts were generated with STAR using the GeneCounts function. Differential expression analysis was performed using DESeq2 with standard settings.
Contributor(s) Marschallinger J, Zardeneta M
Citation(s) 31959936
Submission date Nov 06, 2019
Last update date Feb 08, 2020
Contact name Julia Marschallinger
Phone 6502839032
Organization name Stanford University
Department Neurology
Lab Tony Wyss-Coray
Street address 1201 Welch Road
City Stanford
State/province CA
ZIP/Postal code 94305-5489
Country USA
Platforms (1)
GPL24247 Illumina NovaSeq 6000 (Mus musculus)
Samples (6)
GSM4151448 GRN1_lo
GSM4151449 GRN2_lo
GSM4151450 GRN3_lo
BioProject PRJNA588019
SRA SRP228776

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Supplementary file Size Download File type/resource
GSE140009_normalized_counts_GRN.txt.gz 380.9 Kb (ftp)(http) TXT
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Raw data are available in SRA
Processed data are available on Series record

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