{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Line Moesgaard Strauss"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-13634"],"description":["Single cell RNA sequencing of monocytes and macrophages harvested from a YUMM1.7 tumor of mice 21 weeks after subcutaneous inoculation."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Single cell transcriptomes were generated from roughly 4000 cells per mouse using 10x Genomics Chromium Next GEM Single Cell 3’ GEM kit v2.","Sequencing - Samples were sequenced to an average depth of 45000 reads per cell using a NovaSeq S2 flow cell.","Sample Treatment - Mice were injected s.c. with 1x10^6 cells from YUMM1.7.","Library Construction - Sequencing libraries were generated using 10x Genomics Chromium Next GEM Single Cell 3’ GEM kit v2.","Sample Collection - Single cell suspensions were prepared from YUMM1.7 tumors in 8 week-old wild-type male C57BL6/J, Junf/f, Il4f/f, JunDCsf1r and IL4RaDcsf1R mice. Monocytes/macrophages were isolated by flow cytometry gating on CD11b+, Lin-(CD3, CD19, Ly6G, NK1.1, Siglec F). Prior to cell sorting, tumor cell suspensions from Junf/f, Il4f/f, JunDCsf1r and IL4RaDcsf1R mice were labelled with barcoded hashtag antibodies for MHCI/CD45 (Biolegend) and CiteSeq antibodies for CD169 and Ly6C. Single-cell transcriptomes were generated from individual samples (Y1,Y3,Y4) or pools of oligo-labelled cells (S1,S2,S3,S4) with roughly 4,000 cells per sample using Chromium Next GEM Single Cell 3ʹ GEM kit v2 and sequenced to a depth that averaged ∼1,800 genes per cell. After sequencing, samples were processed with 10x Genomics CellRanger pipeline (version 2.1.0) using mm10 (v2.1.0) reference genome."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Filtered gene counts were generated with 10x Genomics CellRanger pipeline (version 2.1.0) using mm10 (v2.1.0) reference genome."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["CellRanger v2.1.0","10x Genomics Chromium","Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_authors":["Line Moesgaard Strauss","Anders Etzerodt"],"additional_accession":[]},"is_claimable":false,"name":"Single cell RNA sequencing of murine subcutaneous tumor after inoculation with YUMM1.7","description":"Single cell RNA sequencing of monocytes and macrophages harvested from a YUMM1.7 tumor of mice 21 weeks after subcutaneous inoculation.","dates":{"release":"2026-05-14T00:00:00Z","modification":"2026-05-14T01:01:44.48Z","creation":"2024-01-05T17:18:54.593Z"},"accession":"E-MTAB-13634","cross_references":{"ENA":["ERP156490"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0003816","EFO_0004184","EFO_0003969"]}}