{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["Mingxia Li"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"organism":["Mus musculus"],"species":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-10610"],"description":["Here, we used single cell RNA-sequencing (scRNA-seq) to profile the difference of the CD45 positive cells subgroups infiltrating in  MC38-Bap1-Wildtype and MC38-Bap1-Knockout  tumor microenvironment on the 10th day of tumor growth in C57BL/6 mice. Additionally, we used scRNA-seq to profile differential gene expression of CD8 T cells and the difference of related signal."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Sequencing library was constructed according to the instructions of Chromium Single Cell 3ʹ Reagent kits v3 (10×Genomics).","Nucleic Acid Extraction - The cell suspension was loaded into Chromium microfluidic chips with 30v3 chemistry and barcoded with a 10× Chromium Controller (10X Genomics). mRNA from the barcoded cells was reverse-transcribed into cDNA according to the manufacturer's instructions .","Sample Collection - Tumor cells were separated from the C57BL/6 mice on the 10th of tumor growth, Tumor Dissociation Kit (Miltenyi,130-096-730) was used to dissociate the tumor tissues into single cells as the manufacturer’s instructions. ACK lysis buffer (Gibco,492-01) was used to remove the red blood cell. Then Dead Cell Removal kit (Miltenyi,130-090-101) was used to remove dead cells by column in MACS Separator, and CD45+ cells were enriched from tumor tissues according to CD45(TIL) MicroBeads (Miltenyi,130-110-618).The cells were resuspended with 1×PBS containing 0.04% BSA, and cell viability was detected with 0.4% trypan blue staining solution and counted with Countess II (Invitrogen) cell counter, and the cell viability was over 90%.","Sequencing - Sequencing was performed with NovaSeq according to Illumina instructions ."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["Mingxia Li"],"additional_accession":[]},"is_claimable":false,"name":"Single cell analysis of CD45 positive cells isolated from MC38 colon carcinoma tumor-bearing C57BL/6 mice","description":"Here, we used single cell RNA-sequencing (scRNA-seq) to profile the difference of the CD45 positive cells subgroups infiltrating in  MC38-Bap1-Wildtype and MC38-Bap1-Knockout  tumor microenvironment on the 10th day of tumor growth in C57BL/6 mice. Additionally, we used scRNA-seq to profile differential gene expression of CD8 T cells and the difference of related signal.","dates":{"release":"2025-06-29T00:00:00Z","modification":"2023-07-07T11:00:20.845Z","creation":"2022-03-10T04:33:16.715Z"},"accession":"E-MTAB-10610","cross_references":{"ENA":["ERP129735"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0004184"]}}