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
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. Nucleic acid extraction was performed as part of the library construction. Libraries were generated using the Chromium Next GEM Single Cell 3' Kit v3.1 (10X Genomics), according to the manufacturer's instructions