{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Aernout Luttun"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-9703"],"description":["Femoral artery segments from the ligated ('L') right side (downstream of the ligation site) as well as the corresponding segments from the unligated ('UL') left side were dissected out 3 days after femoral artery ligation in adult mice with or without a long-term (from post-natal day 1 onwards) endothelial-specific deletion of transcription factor Prdm16. Fragments from 4 donor mice were pooled to obtain sufficient cell numbers for sequencing. The experiment existed of 4 samples to be sequenced at single-cell resolution (Prdm16 wild-type L or 'Right_WT'; Prdm16 wild-type UL or 'Left_WT'; Prdm16 endothelial-specific knockout L or 'Right_KO'; Prdm16 endothelial-specific knockout UL or 'Left-KO'). The experiment was intended to identify in situ Prdm16 genotype-dependent genes and corresponding functional pathways in arterial endothelial cells that could be responsible for the observed endothelial dysfunction caused by endothelial-specific Prdm16 deletion in mice upon induction of hind limb ischemia."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - The barcoded library was sequenced on an Illumina Nextseq and NovaSeq6000 in 25-8-98 paired-end configuration up to a saturation over 60 %.","Nucleic Acid Extraction - Single cell suspensions were converted to barcoded Drop-seq libraries by using the Chromium Single Cell 3’  Library, Gel Bead & Multiplex Kit and Chip Kit (10X Genomics; Pleasanton, California, USA), aiming for an estimated 4,000 cells per library.","Sample Collection - Cell preparation, scRNA library preparation and sequencing. EC-Prdm16-/- or EC-Prdm16+/+ littermates (n=4 each) were treated with tamoxifen at P1 to P4 and were subjected to right FA ligation at 8 weeks of age. Three days later, FA segments downstream of the ligation and the corresponding segment on the unligated side were quickly dissected out and collected on ice. To obtain sufficient amounts of cells for sequencing, for each genotype and for each side, the segments from all 4 mice were pooled.","Library Construction - 4 mouse single cell libraries were prepared with the Chromium Single Cell 3’ V2 Chemistry Library Kit, Gel Bead & Multiplex Kit and Chip Kit from 10X Genomics."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Index1 files"],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_authors":["Aernout Luttun"],"additional_accession":[]},"is_claimable":false,"name":"scRNAseq of femoral artery segments in the context of hind limb ischemia in mice with or without an endothelial cell-specific deletion of transcription factor Prdm16","description":"Femoral artery segments from the ligated ('L') right side (downstream of the ligation site) as well as the corresponding segments from the unligated ('UL') left side were dissected out 3 days after femoral artery ligation in adult mice with or without a long-term (from post-natal day 1 onwards) endothelial-specific deletion of transcription factor Prdm16. Fragments from 4 donor mice were pooled to obtain sufficient cell numbers for sequencing. The experiment existed of 4 samples to be sequenced at single-cell resolution (Prdm16 wild-type L or 'Right_WT'; Prdm16 wild-type UL or 'Left_WT'; Prdm16 endothelial-specific knockout L or 'Right_KO'; Prdm16 endothelial-specific knockout UL or 'Left-KO'). The experiment was intended to identify in situ Prdm16 genotype-dependent genes and corresponding functional pathways in arterial endothelial cells that could be responsible for the observed endothelial dysfunction caused by endothelial-specific Prdm16 deletion in mice upon induction of hind limb ischemia.","dates":{"release":"2022-10-28T00:00:00Z","modification":"2025-05-09T17:36:07.991Z","creation":"2025-05-09T17:36:07.991Z"},"accession":"E-MTAB-9703","cross_references":{"ENA":["ERP124719"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184"]}}