NCBI Logo
GEO Logo
   NCBI > GEO > Accession DisplayHelp Not logged in | LoginHelp
GEO help: Mouse over screen elements for information.
          Go
Sample GSM8215031 Query DataSets for GSM8215031
Status Public on May 06, 2024
Title IgG_CD45
Sample type SRA
 
Source name Atherosclerosis plaques
Organism Mus musculus
Characteristics tissue: Atherosclerosis plaques
cell type: CD45 Sorted cells
genotype: Apoe-/-
Treatment protocol Animals were maintened in a Western Diet for 18 weeks
Extracted molecule total RNA
Extraction protocol Individual atherosclerotic plaques from the brachiocephalic artery were removed from underlying media with forceps and deposited into FACS buffer (1% BSA in PBS) plus 1 ug/mL Actinomycin D,(Gibco, #11805017). Samples were then minced and digested with 1mL Liberase (Roche, #355374) plus 1ug/mL ActinomycinD for 1 hour at 37 degrees, then resuspended in PBS plus 0.04% UltraPure non-Acetylated BSA (ThermoFisher #AM2616) and filtered through 30um filters on ice. Samples were then either counted and submitted directly for scRNAseq or sorted by flow cytometry. Samples for flow were stained with Sytox Blue viability dye and sorted with a BD FACSAria Fusion cell sorter with gating on live, single cells that were eYFP+. Cells were collected into LoBind tubes containing 0.04% non-acetylated BSA.
2,000 cells in each group were targeted in Chromium 10X genomics libraries, which after barcoding, were pooled and sequenced on the Illumina NextSeqTM, 150 cycle high-output.
single-cell RNA-seq (10x genomics, 3')
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina MiSeq
 
Data processing Basecalls performed using CASAVA
Reads were aligned against mouse genome mm10 using the CellRanger software (10x Genomics).
Gene-barcode matrices were analyzed in R using Seurat v3. Cells were filtered for 200-5000 reads per UMI, 10% or less mitochondrial and less than 5% hemoglobin gene content.
Significant principal components of variation (PCs) were calculated using JackStraw test with 10000 repetitions, and clusters were calculated as described in the manuscript
Differential expression analysis was done using MAST
Assembly: mm10
Supplementary files format and content: Cell-gene-barcode matrices
 
Submission date Apr 17, 2024
Last update date May 06, 2024
Contact name Gary K Owens
Organization name University of Virginia
Street address 415 Lane Road MR5 Building Room 1322
City Charlottesville
State/province VA
ZIP/Postal code 22908
Country USA
 
Platform ID GPL16417
Series (1)
GSE264253 IL-1β inhibition partially negates the beneficial effects of diet-induced lipid lowering
Relations
BioSample SAMN40996593
SRA SRX24290867

Supplementary file Size Download File type/resource
GSM8215031_IgG_CD45_filtered_feature_bc_matrix.tar.gz 2.5 Mb (ftp)(http) TAR
SRA Run SelectorHelp
Raw data are available in SRA

| NLM | NIH | GEO Help | Disclaimer | Accessibility |
NCBI Home NCBI Search NCBI SiteMap