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Status |
Public on Dec 21, 2019 |
Title |
Non-microglia cells from Trem2 +/- animal 9463 after 12 weeks on control diet |
Sample type |
SRA |
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Source name |
Non-microglia isolated from whole brain
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Organism |
Mus musculus |
Characteristics |
genotype: Trem2 +/- tissue: brain cell_type: other animal_id: 9463 diet: control Sex: female timepoint: 12 timepoint_unit: weeks
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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.
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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.
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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.
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Library strategy |
RNA-Seq |
Library source |
transcriptomic |
Library selection |
cDNA |
Instrument model |
Illumina HiSeq 4000 |
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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.
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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 |
SAMN10625289 |
SRA |
SRX5173932 |