characteristics.text: ERC000011
characteristics.characteristic: ENA-CHECKLIST
characteristics.text: 2017-04-14T17:01:30Z
characteristics.characteristic: ENA-FIRST-PUBLIC
characteristics.text: 2017-03-31T15:34:17Z
characteristics.characteristic: ENA-LAST-UPDATE
characteristics.text: SAMEA103954593
characteristics.characteristic: External Id
characteristics.text: Institute of Molecular Life Sciences, University of Zurich
characteristics.characteristic: INSDC center name
characteristics.text: 2017-04-14T17:01:30Z
characteristics.characteristic: INSDC first public
characteristics.text: 2017-03-31T15:34:17Z
characteristics.characteristic: INSDC last update
characteristics.text: public
characteristics.characteristic: INSDC status
characteristics.text: ERS1643761
characteristics.characteristic: SRA accession
characteristics.text: E-MTAB-5640:45_CD38+CD204+
characteristics.characteristic: Submitter Id
characteristics.text: ArrayExpress
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0009737
characteristics.characteristic: broker name
characteristics.text: macrophage
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/CL_0000235
characteristics.characteristic: cell type
characteristics.text: human
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: common name
characteristics.text: Protocols: Primary ccRCC tissue samples were obtained from the University Health Network (UHN) Biospecimen Sciences Program and from the Cooperative Health Tissue Network (CHTN) from generously consenting patients under University Health Network Research Ethics Board approval. Tumor samples were digested to generate single-cell suspensions as previously described (Gedye and Ailles, 2013). Cells were then viably frozen in 10% DMSO in D-SDCM complemented with 10% FBS. Viably frozen samples were resuscitated as previously described, incubated with the Zombie NIR dye (Biolegend) for dead cell exclusion for 15 min at room temperature, blocked with FcR blocking reagent (Miltenyi Biotech) for 10 min at 4 °C, and stained for 30 min at 4 °C with the antibodies indicated in Table S3. As shown in Figures S4C and S7B, cell subsets were sorted as CD14+/HLA-DR+/CD204-/CD38-/CD206- (Control) and CD14+/HLA-DR+/CD204+/CD38+/CD206- (M-5) , CD3+/CD8+/PD-1- (CD8+/PD-1- T cells) and CD3+/CD8+/PD-1+ (CD8+/ PD-1+ T cells) using a 100-μm nozzle on a FACS Aria III 5L Cell sorter. Cells were harvested in RPMI-FBS (10%) medium and immediately used for RNA purification using the PicoPure RNA Isolation Kit (ThermoFischer) according to manufacturer’s instructions 4 ng RNA was used to generate the sequencing libraries using the SMARTer Stranded Total RNA-Seq Kit - Pico Input Mammalian (Takara Bio) and Nextera XT (Illumina) according to manufacturer’s instructions
characteristics.characteristic: description
characteristics.text: clear cell renal carcinoma
characteristics.ontologyTerms: http://www.ebi.ac.uk/efo/EFO_0000349
characteristics.characteristic: disease
characteristics.text: 45
characteristics.characteristic: individual
characteristics.text: Homo sapiens
characteristics.characteristic: organism
characteristics.text: Homo sapiens
characteristics.ontologyTerms: http://purl.obolibrary.org/obo/NCBITaxon_9606
characteristics.characteristic: organism
characteristics.text: kidney
characteristics.characteristic: organism part
characteristics.text: CD204-positive, CD38-positive
characteristics.characteristic: phenotype
characteristics.text: Homo sapiens
characteristics.characteristic: scientific_name
characteristics.text: 45_CD38+CD204+
characteristics.characteristic: title