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Sample GSM5111239 Query DataSets for GSM5111239
Status Public on Feb 25, 2022
Title WT DMSO, 3xTg DMSO, WT SCDi, 3xTg SCDi
Sample type SRA
Source name Hippocampus
Organism Mus musculus
Characteristics strain: C57BL/6J x 129S1 and B6;129-Psen1tm1MpmTg(APPSwe,tauP301L)1Lfa/Mmjax
age: 10 months
treatment: 28 day ICV DMSO or SCDi
Treatment protocol For ICV infusions of SCDi or vehicle, mice were locally injected with buprivacaine (Hospira) and operated under isoflurane anesthesia (Baxter). Brain cannulae attached to Alzet osmotic pumps were stereotaxically implanted at 0.0mm antero-posterior and 0.9mm lateral to Bregma  and the pumps placed under the back skin according to manufacturer`s instructions. 28-day Alzet osmotic pumps were used in these experiments (0.11 μl/h infusion rate, model 1004; Durect). The SCD inhibitor (SCDi, ab142089, abcam) was dissolved in DMSO and infused at a final concentration of 80 µM in sterile aCSF. Vehicle pumps contained equal volumes as the SCDi pumps (0.8% DMSO/aCSF).
Extracted molecule total RNA
Extraction protocol Mice received a lethal dose of ketamine (Bimeda-MTC)/xylazine (Bayer Healthcare) and were then perfused transcardially with phosphate-buffered saline (PBS) followed by rapid dissected of the ipsilateral hippocampi from each mouse into ice cold HBSS. Hippocampi were dissociated into single cells and each sample was pooled to obtain 4 mice per group, then the cells were labeled with CD45 mouse immune multiplexing kit (BD Biosciences, USA), counted and 10 000 cells per sample were multiplexed, ready for single-cell capture. The viability of cells in all samples was 80-95%. Single-cell capture was performed on the BD Rhapsody Single-Cell Analysis System (BD, USA), the DNA from each cell attached to a barcoded bead was subsequently retrieved and libraries were prepared using the whole transcriptome analysis (WTA) amplification kit (BD Biosciences) according to the manufacturer’s recommendations.
Single cell RNA libraries were generated using the BD Rhapsody 3' WTA kit with sample multiplexing using the BD Mouse Immune Single-Cell Multiplexing Kit
Single cell RNAseq
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description Pooled multiplexed samples containing cells from WT DMSO, 3xTg DMSO, WT SCDi and 3xTg SCDi animals
Data processing Pooled mutliplexed library was sequenced on the NovaSeq 6000 platform
Resulting fastq files were processed using BD's Rhapsody WTA analysis pipeline on the Seven Bridges Platform using default parameters and the GRCm38 reference genome with gencodevM19-20181206 transcriptome annotation
Output Unfiltered MOI count matrices were processed on a Galaxy implementation of standard scanpy 1.4.3 processing pipeline.
Resulting .h5Anndata object was imported into R's Seurat package for further analysis
Genome_build: GRCm38
Supplementary_files_format_and_content: tab-delimited Unfiltered single cell MOI matrix
Supplementary_files_format_and_content: tab-delimited metadata table for all cells
Supplementary_files_format_and_content: processed .rds object with metadata
Supplementary_files_format_and_content: tab-delimited metadata table for microglial cells after reanalysis
Submission date Feb 26, 2021
Last update date Feb 25, 2022
Contact name Gaël Moquin-Beaudry
Organization name CRCHUM
Street address 900 Saint-Denis street
City Montréal
State/province QC
ZIP/Postal code H2X 0A9
Country Canada
Platform ID GPL24247
Series (2)
GSE167600 SCD inhibition reverses immune, synaptic and behavioral deficits in an animal model of Alzheimer’s disease [scRNA-Seq]
GSE167605 SCD inhibition reverses immune, synaptic and behavioral deficits in an animal model of Alzheimer’s disease
BioSample SAMN18064001
SRA SRX10175963

Supplementary file Size Download File type/resource
GSM5111239_Hamilton_scRNAseq_Microglia_metadata.tsv.gz 127.4 Kb (ftp)(http) TSV
GSM5111239_Hamilton_scRNAseq_matrix.tsv.gz 42.0 Mb (ftp)(http) TSV
GSM5111239_Hamilton_scRNAseq_metadata.tsv.gz 467.1 Kb (ftp)(http) TSV
GSM5111239_Hamilton_scRNAseq_unfiltered.rds.gz 548.3 Mb (ftp)(http) RDS
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Raw data are available in SRA
Processed data are available on Series record

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