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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Feb 25, 2022 |
| Title |
WT DMSO, 3xTg DMSO, WT SCDi, 3xTg SCDi |
| Sample type |
SRA |
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| Source name |
Hippocampus
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| 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
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| 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).
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| 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
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
Pooled multiplexed samples containing cells from WT DMSO, 3xTg DMSO, WT SCDi and 3xTg SCDi animals
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| 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
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| Submission date |
Feb 26, 2021 |
| Last update date |
Feb 25, 2022 |
| Contact name |
Gaël Moquin-Beaudry |
| E-mail(s) |
gael.moquin-beaudry@umontreal.ca
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| Organization name |
CRCHUM
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| Street address |
900 Saint-Denis street
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| City |
Montréal |
| State/province |
QC |
| ZIP/Postal code |
H2X 0A9 |
| Country |
Canada |
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| 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 |
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| Relations |
| 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 |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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