| Experiment Id | GSE215418 | Name | Combined multidimensional single-cell protein and RNA profiling dissects the cellular and functional heterogeneity of thymic epithelial cells |
| Experiment Type | RNA-Seq | Study Type | Baseline |
| Source | GEO | Curation Date | 2024-12-20 |
| description | The network of thymic stromal cells provides essential niches with unique molecular cues controlling T-cell development and selection. Recent single-cell RNA-sequencing studies uncovered a large transcriptional heterogeneity among thymic epithelial cells (TEC) demonstrating a previously unappreciated complexity. However, there are only very few cell markers that allow a comparable phenotypic identification of TEC. Here we deconvoluted by massively parallel flow cytometry and machine learning known and novel TEC phenotypes into novel subpopulations and related these by CITEseq to the corresponding TEC subtypes defined by the cells' individual RNA profiles. This approach phenotypically identified perinatal cTEC, physically located these cells within the cortical stromal scaffold, displayed their dynamic change during the life course and revealed their exceptional efficiency in positively selecting immature thymocytes. Collectively, we have identified novel markers that allow for an unprecedented dissection of the thymus stromal complexity, the cells physical isolation and assignment of specific functions to individual TEC subpopulations. Cells were isolated from 1- and 16-week-old mice and depleted of CD45+ cells by autoMACS. Subsequently cells were stained for CD45, EpCAM1, Ly51, Ter119 and with PI. In addition cells were stained with antibodies coupled to oligonucleotides directed against CD9, CD40, CD49a, CD54, CD63, CD73, CD83, CD117, CD146 (human with cross reactivity to mouse), CD200, CD274, HVEM, Ly6D, Ly6C/Ly6G (Gr1), MadCAM1, Podoplanin, CD80, CD86, MHCII, Sca1, CD31, EpCAM1, CD36, CD133, CD157, CD300LG and the Ulex europaeus agglutinin I (UEA1) lectin labeled with biotin, followed by secondary staining with streptavidin-PE coupled to an oligonucleotid. CD45-Ter119-EpCAM1+ and CD45-Ter119-EpCAM1- cells were sorted in a 70% to 30% ratio into a 1.5 mL tube containing FACS buffer for the 1-week-old and 16-week-old samples, respectively. For both timepoints an estimate of 28000 total cells were loaded on two wells of a 10x Genomics Chromium Single Cell Controller. |
