{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Azusa Terasaki"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-16050"],"description":["Analysis of total RNA of B16 melanoma cell line after co-culture with mitochondria-tagged (Dendra2 PhAMexcised mitochondria reporter - also known as mtD2, strain no. 018397mtD2) leukocytes. The cells were sorted to two groups: mtD2+ B16 and mtD2- B16 cells."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Nucleic Acid Extraction - Total RNA was isolated using Qiagen RNEasy Plus isolation kit.","Sequencing - Bulk RNAseq was performed using the DNBSEQ platform.","Sample Collection - After tumor-immune co-cultures, cells were resuspended in FACS buffer (PBS in 0.5% BSA) and stained with DAPI and CD45. Live tumor cells (TdTomato+CD45-DAPI-) were sorted into Dendra2+ and Dendra2- subpopulations and pelleted immediately.","Library Construction - 1) mRNA enrichment and purification: Oligo dT Selection (mRNA enrichment): Use oligo dT beads to enrich mRNA with poly A tail. 2) RNA fragment and reverse transcription Fragment the RNA and first-strand cDNA was generated using random N6-primed reverse transcription, followed by a second-strand cDNA synthesis with dUTP instead of dTTP. 3) End repair, add A and adaptor ligation The synthesized cDNA was subjected to end-repair and then was 3' adenylated. Adaptors were ligated to the ends of these 3' adenylated cDNA fragments; 4) PCR amplification Prior to PCR amplification, the dUTP-marked strand is selectively degraded by Uracil-DNA-Glycosylase(UDG). The remaining strand is amplified to generate a cDNA library suitable for sequencing. Many rounds of PCR amplification were performed to enrich the purified cDNA template using PCR primer; 5) Single strand separation and cyclization Denature the PCR product by heat and the single strand DNA is cyclized by splint oligo and DNA ligase; 6) DNA nanoball synthesis"],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - The raw RNA sequencing data was mapped to mouse reference genome hg38 using the STAR aligner, and genes annotated in Gencode v3664 was quantified using featurecounts in the subread package."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["DNBSEQ-T7"],"study_type":["RNA-seq of coding RNA"],"species":["Mus musculus"],"pubmed_authors":["Azusa Terasaki"],"additional_accession":[]},"is_claimable":false,"name":"Mitochondria transfer from immune cells enables lymph node metastasis","description":"Analysis of total RNA of B16 melanoma cell line after co-culture with mitochondria-tagged (Dendra2 PhAMexcised mitochondria reporter - also known as mtD2, strain no. 018397mtD2) leukocytes. The cells were sorted to two groups: mtD2+ B16 and mtD2- B16 cells.","dates":{"release":"2025-12-25T00:00:00Z","modification":"2026-05-30T16:00:21.016Z","creation":"2025-11-13T15:17:19.756Z"},"accession":"E-MTAB-16050","cross_references":{"ENA":["ERP183980"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005518","EFO_0003816","EFO_0003738","EFO_0004184"]}}