{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Yumeng Pei"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15770"],"description":["We subcutaneous injected MC38 tumors in Mg53tg-fl;Lyz2cre mice and their littermate controls Mg53tg-fl mice, the tumors were excised 15 days after and digested into single-cell suspensions, and CD45+ cells were sorted using flow cytometry in order to obtain single-cell sequencing data."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - After quality control, the viable cells were washed, resuspended, and prepared as a single-cell suspension at an appropriate concentration. The cell suspension was then loaded according to the target cell recovery count. Following loading, the formation of GEMs (Gel Bead-In-Emulsions) was monitored. If GEMs formed successfully, they were transferred to a PCR tube for subsequent reverse transcription and library construction. Once the constructed library passed quality control, it was subjected to sequencing.","Nucleic Acid Extraction - The single-cell suspension was subjected to quality control with the following criteria: cell viability must meet the requirements (>80% by AO/PI fluorescent staining or >75% by trypan blue exclusion), cell concentration between 700-1,200 cells/μL, cell diameter ranging from 5 to 30 μm, total cell count up to 100,000, clean suspension background with no significant debris or impurities.","Sample Collection - We sorted live, CD45+ cells from single-cell suspensions of tumors from 3 mice using a FACS (BD Biosciences).","Sequencing - The 10x single-cell transcriptome libraries were sequenced using the Illumina NovaSeq PE150 strategy. It is recommended to obtain 50,000-100,000 reads per cell (minimum of 20,000 read pairs per cell), which corresponds to a sequencing depth of 15-30 million reads per cell. Since sequencing has a certain saturation point, appropriately increasing the sequencing depth can improve the gene detection rate within a certain range."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - Cell Ranger first defines an expected number of cells (N, default 3000). It then sorts all barcodes by their total UMI counts in descending order. The 99th percentile of the UMI counts from the top N barcodes is calculated as the estimated maximum UMI count (m). Finally, barcodes with UMI counts exceeding m/10 are classified as successfully captured cells."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq X"],"study_type":["single nucleus RNA sequencing"],"species":["Mus musculus"],"pubmed_authors":["Yumeng Pei"],"additional_accession":[]},"is_claimable":false,"name":"scRNA seq of MG53high and MG53low TAMs","description":"We subcutaneous injected MC38 tumors in Mg53tg-fl;Lyz2cre mice and their littermate controls Mg53tg-fl mice, the tumors were excised 15 days after and digested into single-cell suspensions, and CD45+ cells were sorted using flow cytometry in order to obtain single-cell sequencing data.","dates":{"release":"2025-10-30T00:00:00Z","modification":"2026-05-27T15:12:29.509Z","creation":"2025-10-17T15:17:17.693Z"},"accession":"E-MTAB-15770","cross_references":{"ENA":["ERP182429"],"EFO":["EFO_0002944","EFO_0004170","EFO_0009809","EFO_0005518","EFO_0003816","EFO_0004184"]}}