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Sample GSM3526595 Query DataSets for GSM3526595
Status Public on Dec 21, 2019
Title Microglia cells from Trem2 -/- animal 1104 after 5 weeks on control diet
Sample type SRA
 
Source name Microglia isolated from whole brain
Organism Mus musculus
Characteristics genotype: Trem2 -/-
tissue: brain
cell_type: microglia
animal_id: 1104
diet: control
Sex: female
timepoint: 5
timepoint_unit: weeks
Treatment protocol Trem2-WT, heterozyogus knockout, and homozygous knockout mice were fed a control or 0.2% cuprizone diet for 5 weeks or 12 weeks.
Growth protocol Mice were housed on a 12hr/12hr light dark cycle. All mouse husbandry and experimental procedures were approved by Denali's Institutional Animal Care and Use Committee.
Extracted molecule total RNA
Extraction protocol Mice were perfused with PBS, brain were removed and dissociated with the Adult Brain Dissociation Kit (Miltenyi). Cells were fluorescence-activated cell sorted for viability, then microglia (Cd11b+) and all other cells were collected for RNA extaction using the RNeasy Plus Micro kit (Qiagen)
Libraries were prepared using the QuantSeq 3’ mRNA-Seq Library Prep Kit FWD for Illumina (Lexogen), following the ‘low-input’ procedure defined by the manufacturer.
 
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina HiSeq 4000
 
Data processing Sequencing adapters were trimmed using skewer (Jiang et al., 2014; version 0.2.2) with default parameters. Quality control of the trimmed reads was performed using FastQC (version 0.11.5: www.bioinformatics.babraham.ac.uk/projects/fastqc).
Reads were aligned to an index of the mouse genome (version GRCm38_p6) A STAR index (Dobin et al., 2013; version 2.5.3a) was built with the --sjdbOverhang=50 argument. Splice junctions from Gencode gene models (release M17) were provided via the --sjdbGTFfile argument. STAR alignments were generated with the following parameters: --outFilterType BySJout --quantMode TranscriptomeSAM --outFilterIntronMotifs RemoveNoncanonicalUnannotated --outSAMstrandField intronMotif --outSAMattributes NH HI AS nM MD XS --outSAMunmapped Within. Post-alignment quality control reports were generated using MultiQC (Ewels et al., 2016; version 1.0).
The raw gene expression matrix was constructed from the 'forward' column of STAR's ReadsPerGene.out.tab output files using R (version 3.4.3). Gene symbols and Entrez gene identifiers were mapped using Ensembl (version 91) via the biomaRt R package (Durinck et al, 2009; version 2.34.0).
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited, gzip-compressed text file with matrix of raw quantitation results for each sample.
 
Submission date Dec 21, 2018
Last update date Dec 21, 2019
Contact name Thomas Sandmann
E-mail(s) genomics@dnli.com, sandmann@dnli.com
Organization name Denali Therapeutics
Street address 161 Oyster Point Blvd
City South San Francisco
State/province California
ZIP/Postal code 94080
Country USA
 
Platform ID GPL21103
Series (2)
GSE124266 TREM2 regulates microglial cholesterol metabolism upon chronic phagocytic challenge [bulk RNA-seq]
GSE130627 TREM2 regulates microglial cholesterol metabolism upon chronic phagocytic challenge
Relations
BioSample SAMN10625286
SRA SRX5173873

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

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