{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"submitter":["wangyf lab"],"instrument_platform":["BD Rhapsody system","not applicable","Illumina NovaSeq X","BD Rhapsody system; Qubit 4.0 Fluorometer"],"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-17139"],"description":["This experiment used single-cell RNA sequencing to characterize transcriptional heterogeneity and tumor-cell state dynamics in primary and metastatic lesions from a mouse B16 melanoma model. For each experimental group, small pieces of tumor tissues were collected from five mice and pooled to generate one sequencing sample. The pooled tumor tissues were dissociated into single-cell suspensions. Single-cell cDNA libraries were generated using the BD Rhapsody single-cell 3' whole transcriptome amplification (WTA) protocol. Briefly, single cells were washed, counted, loaded onto a cartridge, and lysed inside the wells, followed by mRNA capture on cell capture beads, reverse transcription, cDNA extension, amplification, and library construction according to the manufacturer's instructions. Lib"],"repository":["biostudies-arrayexpress"],"sample_protocol":["Sequencing - Single-cell libraries were prepared according to the manufacturer's instructions and sequenced on the Illumina NovaSeq X Plus system using 150 nt paired-end sequencing.","Library Construction - Single-cell cDNA libraries were generated using the BD Rhapsody single-cell 3' whole transcriptome amplification (WTA) protocol. Successfully prepared single-cell suspensions were washed three times, pooled, counted, and loaded onto a cartridge. Cells were lysed inside the wells, followed by mRNA capture on cell capture beads according to the manufacturer's instructions. Cell capture beads were retrieved and washed before reverse transcription and Exonuclease I treatment. cDNA was extended using WTA extension primers and purified using SPRIselect magnetic beads. WTA amplification primers and index primers were used for PCR amplification and library preparation. The quantity of PCR products was determined using Qubit 4.0 with the Qubit dsDNA HS Assay.","Sample Collection - For each experimental group, small pieces of tumor tissues were collected from five mice and pooled to generate one sequencing sample. The pooled tumor tissues were dissociated into single-cell suspensions for single-cell RNA sequencing.","Nucleic Acid Extraction - Single cells were loaded onto a cartridge and lysed inside the wells. mRNA was captured using cell capture beads according to the BD Rhapsody manufacturer's instructions. Cell capture beads were retrieved and washed before reverse transcription and Exonuclease I treatment."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","MAGE-TAB Files"],"pubmed_authors":["wangyf lab","Yufeng Wang"],"additional_accession":[]},"is_claimable":false,"name":"Single-cell RNA sequencing of primary and metastatic melanoma lesions in mice","description":"This experiment used single-cell RNA sequencing to characterize transcriptional heterogeneity and tumor-cell state dynamics in primary and metastatic lesions from a mouse B16 melanoma model. For each experimental group, small pieces of tumor tissues were collected from five mice and pooled to generate one sequencing sample. The pooled tumor tissues were dissociated into single-cell suspensions. Single-cell cDNA libraries were generated using the BD Rhapsody single-cell 3' whole transcriptome amplification (WTA) protocol. Briefly, single cells were washed, counted, loaded onto a cartridge, and lysed inside the wells, followed by mRNA capture on cell capture beads, reverse transcription, cDNA extension, amplification, and library construction according to the manufacturer's instructions. Lib","dates":{"release":"2026-08-20T00:00:00Z","modification":"2026-08-20T05:57:27.492Z","creation":"2026-06-19T17:36:31.468Z"},"accession":"E-MTAB-17139","cross_references":{"ENA":["ERP195396"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0005518","EFO_0004184"]}}