organism: Mus musculus
description: Protocols: Whole organs were dissected, followed by dissociation using tissue-specific digestion protocols. Samples were then enriched for endothelial cells (ECs) by magnetic bead sorting using the MACS system (Miltenyi Biotec). Next, positive selection of ECs was performed using CD31 MicroBeads (Miltenyi Biotec), followed by staining with various antibody combinations for multi-parameter flow acquisition. FACS-purification of ECs was then performed, and single cell suspensions of freshly isolated ECs were then resuspended in PBS containing 0.04% ultra-pure BSA. scRNA-seq libraries were prepared using the Chromium Single Cell 3′ Reagent Kits v2 (10x Genomics; Pleasanton, CA, USA) according to the manufacturer's instructions. The aimed target cell recovery for each library was 5000 (except for soleus, aimed recovery of 3000 cells). Generated libraries were sequenced on an Illumina HiSeq4000, followed by de-multiplexing and mapping to the mouse genome (build mm10) using CellRanger (10x Genomics, version 2.1.1). Samples were processed using V2 barcoding chemistry kits (10x Genomics). Single samples were always processed in a single well of a PCR plate, allowing all cells from a sample to be treated similarly. All samples were processed in parallel in the same thermal cycler.
attributes.tag: ENA-FIRST-PUBLIC
attributes.value: 2020-01-05T04:03:12Z
attributes.tag: ENA-LAST-UPDATE
attributes.value: 2019-06-19T16:04:32Z
attributes.tag: External Id
attributes.value: SAMEA5723230
attributes.tag: INSDC center name
attributes.value: Laboratory of Angiogenesis and Vascular Metabolism VIB-KU Leuven Center for Cancer Biology (CCB)
attributes.tag: INSDC first public
attributes.value: 2020-01-05T04:03:12Z
attributes.tag: INSDC last update
attributes.value: 2019-06-19T16:04:32Z
attributes.tag: INSDC status
attributes.value: public
attributes.tag: Submitter Id
attributes.value: E-MTAB-8077:Small Intestine
attributes.tag: age
attributes.value: 8
attributes.tag: broker name
attributes.value: ArrayExpress
attributes.tag: cell type
attributes.value: endothelial cell
attributes.tag: common name
attributes.value: house mouse
attributes.tag: developmental stage
attributes.value: adult
attributes.tag: genotype
attributes.value: wild type genotype
attributes.tag: organism part
attributes.value: small intestine
attributes.tag: sample name
attributes.value: E-MTAB-8077:Small Intestine
attributes.tag: scientific_name
attributes.value: Mus musculus
attributes.tag: sex
attributes.value: male
attributes.tag: strain
attributes.value: C57BL/6J