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| Status |
Public on Feb 05, 2024 |
| Title |
D374Y mCherry-APOB |
| Sample type |
SRA |
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| Source name |
Liver
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| Organism |
Mus musculus |
| Characteristics |
tissue: Liver
genotype: D374Y mCherry-APOB
treatment: Day 10 after tamoxifen chow diet
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| 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
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| 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.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic single cell |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Description |
MM10
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| 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
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| Submission date |
Feb 02, 2024 |
| Last update date |
Feb 05, 2024 |
| Contact name |
Stephen Malin |
| E-mail(s) |
stephen.malin@ki.se
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| Organization name |
Karolinska Institutet
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| Street address |
Bioclinicum J8:20, Visionsgatan 4
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| City |
Stockholm |
| ZIP/Postal code |
17164 |
| Country |
Sweden |
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| Platform ID |
GPL24247 |
| Series (1) |
| GSE254971 |
Kupffer cells dictate hepatic responses to the atherogenic dyslipidemic insult (scRNA-Seq) |
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| 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 Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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