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Sample GSM3933590 Query DataSets for GSM3933590
Status Public on Dec 21, 2019
Title microglia, TREM2 -/-, old IL28_M
Sample type SRA
Source name Cd11b+ microglia isolated from whole brain
Organism Mus musculus
Characteristics genotype: TREM2 -/-
tissue: brain
cell_type: microglia
animal_id: IL28
age: 16
Sex: female
age_unit: months
rin: 10
Treatment protocol Trem2-WT and homozygous knockout mice were aged for 2 months (young) or 16-18 months (old), respectively.
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 astrocytes (ACSA-2+) 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 with the unique-molecular identifier add-on kit (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
Description microglia, TREM2 -/-, old
Data processing Sequencing adapters were trimmed using skewer (Jiang et al., 2014; version 0.2.2) with default parameters. Unique molecular identifiers (UMIs) were extracted from each read with the umi2index tool (Lexogen). Quality control of the trimmed reads was performed using FastQC (version 0.11.5:
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. Alignments sharing the same UMI and genomic coordinate were deduplicated using the collapse_UMI_bam tool (Lexogen). 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 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 counts results from deduplicated UMIs for each sample.
Submission date Jul 09, 2019
Last update date Dec 21, 2019
Contact name Thomas Sandmann
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)
GSE130627 TREM2 regulates microglial cholesterol metabolism upon chronic phagocytic challenge
GSE134031 TREM2 regulates microglial lipid metabolism during aging in mice [RNA-Seq]
BioSample SAMN12236938
SRA SRX6420572

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

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