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Sample GSM8061586 Query DataSets for GSM8061586
Status Public on Feb 05, 2024
Title D374Y mCherry-APOB
Sample type SRA
 
Source name Liver
Organism Mus musculus
Characteristics tissue: Liver
genotype: D374Y mCherry-APOB
treatment: Day 10 after tamoxifen chow diet
Growth protocol mice were housed in a specific pathogen-free vivarium at the Karolinska Institute. The light/dark period was 12h/12h, and mice were kept under standard temperature and humidity conditions (20-22 °C, 45-55% RH). All mice had ad libitum access to food and water. Breeding mice were fed chow diet R36 (12.6 MJ/kg, 18% protein, 4% fat; Lantmännen, Sweden). Experimental mice received chow diet (R70, Lantmännen, Sweden, 12.5 MJ/kg, 14% protein, 4.5% fat) or HFD (R638, Lantmännen, Sweden, 15.6 MJ/kg, 17.2% protein, 21% fat, 0.15% cholesterol) as stated in each experiment
Extracted molecule polyA RNA
Extraction protocol live CD45+ mCherry+ cells were sorted from the liver. A small sample from one lobe was cut into small pieces and digested in 0.2 mg/mL collagenase IV for 30 min at 37 °C in RPMI 1640. The cell suspension was passed through an 18 g syringe 10 times to remove any clumps and then a 70uM cell strainer. The cell suspension was then washed with FACS buffer before being sorted by a Sony SH800S cell sorter. Cells were additionlay stained with Total-seq cell hashing antibodies from Biolegend. A0301 defines this liver sample
Cells were processed immediately for GEM generation and barcoding on a 10X Chromium using Next GEM 3’ v3.1 reagents (10X Genomics) followed by sequencing and processing on Cellranger. equenced on a NovaSeq 6000 on an SP flow cell with the following run set up: Run setup 28-8-0-91 , 1% Phix.
 
Library strategy RNA-Seq
Library source transcriptomic single cell
Library selection cDNA
Instrument model Illumina NovaSeq 6000
 
Description MM10
Data processing Data analysis was performed in R using Seurat v4 (45) with the gene Gm42418 removed from the data set. Liver cells were identified with Total-seq cell hashing antibodies from Biolegend. A0301 defines this liver sample
Assembly: MM10
Supplementary files format and content: H5ad file format of 10x count matrix
 
Submission date Feb 02, 2024
Last update date Feb 05, 2024
Contact name Stephen Malin
E-mail(s) stephen.malin@ki.se
Organization name Karolinska Institutet
Street address Bioclinicum J8:20, Visionsgatan 4
City Stockholm
ZIP/Postal code 17164
Country Sweden
 
Platform ID GPL24247
Series (1)
GSE254971 Kupffer cells dictate hepatic responses to the atherogenic dyslipidemic insult (scRNA-Seq)
Relations
BioSample SAMN39751659
SRA SRX23511318

Supplementary file Size Download File type/resource
GSM8061586_seurat-liver-filtered-aorta-clustered.h5ad.gz 50.8 Mb (ftp)(http) H5AD
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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