|
| Status |
Public on Dec 21, 2019 |
| Title |
Microglia cells from Trem2 +/- animal 944 after 12 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: 944
diet: control
Sex: female
timepoint: 12
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 |
SAMN10625294 |
| SRA |
SRX5173927 |
