{"database":"biostudies-arrayexpress","file_versions":[],"scores":null,"additional":{"submitter":["Thorsten Klampfl"],"organism":["Mus musculus"],"full_dataset_link":["https://www.ebi.ac.uk/biostudies/studies/E-MTAB-15478"],"description":["To examine transcriptional differences in thymic double negative (DN) T cells between wildtype (WT), NPM-ALK(Tg/+) and NPM-ALK(Tg/+)Cdk6-/-Stat5b-/- mice, single-cell RNA sequencing (scRNA-seq) was performed on fluorescence-activated cell sorted (FACS) DN T cells. The aim was to understand how genetic alterations in the NPM-ALK(Tg/+) and NPM-ALK(Tg/+)Cdk6-/-Stat5b-/- backgrounds influence early T cell development and oncogenic transformation at the transcriptional level."],"repository":["biostudies-arrayexpress"],"sample_protocol":["Library Construction - Libraries were generated using the Chromium Next GEM Single Cell 3' Kit v3.1 (10X Genomics), according to the manufacturer’s instructions","Nucleic Acid Extraction - Nucleic acid extraction was performed as part of the library construction.","Sequencing - Libraries were sequenced on an Illumina NovaSeq 6000 instrument using a 150 bp paired end configuration.","Sample Collection - Thymic cells were isolated from three female C57BL/6 mice. The thymuses were dissected and processed through a 40 μm filter to obtain single-cell suspensions. Cells were stained and sorted by flow cytometry, excluding CD19⁺ (B cells), Ter119⁺ (erythroid cells), Ly6G/C⁺ (granulocytes), CD11b⁺ (myeloid cells), CD4⁺ and CD8⁺ (mature T cells), while selecting for Thy1.2⁺ cells. This strategy ensured enrichment for early thymic progenitors in the double negative stage."],"figure_sub":["Organization","MINSEQE Score","Assays and Data","Processed Data","MAGE-TAB Files"],"data_protocol":["Data Transformation - raw_feature_bc_matrix files (*matrix.mtx.gz) as well as corresponding *features.tsv.gz and *barcodes.tsv.gz were generated using the default Cell Ranger v7.0.0 (10x Genomics) workflow.","Sequence Alignment - Raw sequencing reads were processed with the Cell Ranger v7.0.0 software (10x Genomics) for demultiplexing and counting using the mm10 version 3.0.0 reference data and default parameters."],"omics_type":["Metabolomics","Unknown","Transcriptomics","Genomics","Proteomics"],"instrument_platform":["Illumina NovaSeq 6000"],"study_type":["RNA-seq of coding RNA from single cells"],"species":["Mus musculus"],"pubmed_authors":["Karoline Kollmann","Thorsten Klampfl","Jonatan Kendler"],"additional_accession":[]},"is_claimable":false,"name":"Single cell RNA-seq to investigate transcriptional profiles of thymic double negative T cells in WT, NPM-ALK(Tg/+) and NPM-ALK(Tg/+)Cdk6-/-Stat5b-/-  mice","description":"To examine transcriptional differences in thymic double negative (DN) T cells between wildtype (WT), NPM-ALK(Tg/+) and NPM-ALK(Tg/+)Cdk6-/-Stat5b-/- mice, single-cell RNA sequencing (scRNA-seq) was performed on fluorescence-activated cell sorted (FACS) DN T cells. The aim was to understand how genetic alterations in the NPM-ALK(Tg/+) and NPM-ALK(Tg/+)Cdk6-/-Stat5b-/- backgrounds influence early T cell development and oncogenic transformation at the transcriptional level.","dates":{"release":"2026-07-24T00:00:00Z","modification":"2026-07-24T11:08:49.594Z","creation":"2025-08-12T21:40:55.775Z"},"accession":"E-MTAB-15478","cross_references":{"ENA":["ERP178702"],"EFO":["EFO_0002944","EFO_0004170","EFO_0005684","EFO_0004917","EFO_0005518","EFO_0003816","EFO_0004184"]}}