Dataset: Spatial mapping of thymic stromal microenvironments reveals unique features influencing T lymphoid differentiation
Interaction of hematopoietic progenitors with the thymic stromal microenvironment induces them to proliferate, adopt the T cell fate, and...
Interaction of hematopoietic progenitors with the thymic stromal microenvironment induces them to proliferate, adopt the T cell fate, and asymmetrically diverge into multiple T lineages. Progenitors at various developmental stages are stratified among different regions of the thymus, implying that the corresponding microenvironments differ from one another, and provide unique sets of signals to progenitors migrating between them. The nature of these differences remains undefined. Here we use novel physical and computational approaches to characterize these stromal subregions, distinguishing gene expression in microdissected tissues from that of their lymphoid constituents. Using this approach, we comprehensively map gene expression in functionally distinct stromal microenvironments, and identify clusters of genes that define each region. Quite unexpectedly, we find that the central cortex lacks distinctive features of its own, and instead appears to function by sequestering unique microenvironments found at the cortical extremities, and modulating the relative proximity of progenitors moving between them. 4 to 6 weeks old male C57bl6/J were used for microdissection of 3 thymic cortical subregions and thymic medulla or for sorting cortical and medullary thymocytes. These samples were used for subsequent RNA purification, labeling and hybridization to Affymetrix arrays
- Species:
- mouse
- Samples:
- 33
- Source:
- E-GEOD-18281
- PubMed:
- 20064453
- Updated:
- Dec.12, 2014
- Registered:
- Nov.11, 2014
Sample | TISSUE | CELL TYPE | CELL PHENOTYPE |
---|---|---|---|
GSM45650 | n/a | cortical thymocyte | CD3-/lo AND CD45+ AND (CD90+ OR CD117+) |
GSM45650 | n/a | cortical thymocyte | CD3-/lo AND CD45+ AND (CD90+ OR CD117+) |
GSM45650 | n/a | cortical thymocyte | CD3-/lo AND CD45+ AND (CD90+ OR CD117+) |
GSM45650 | n/a | cortical thymocyte | CD3-/lo AND CD45+ AND (CD90+ OR CD117+) |
GSM45650 | n/a | cortical thymocyte | CD3-/lo AND CD45+ AND (CD90+ OR CD117+) |
GSM456506 | n/a | medullary thymocyte | CD3hi AND CD45+ |
GSM456506 | n/a | medullary thymocyte | CD3hi AND CD45+ |
GSM456506 | n/a | medullary thymocyte | CD3hi AND CD45+ |
GSM456506 | n/a | medullary thymocyte | CD3hi AND CD45+ |
GSM456506 | n/a | medullary thymocyte | CD3hi AND CD45+ |
GSM456512 | Sub-capsular cortex | n/a | n/a |
GSM456512 | Sub-capsular cortex | n/a | n/a |
GSM456512 | Sub-capsular cortex | n/a | n/a |
GSM456517 | Central cortex | n/a | n/a |
GSM456517 | Central cortex | n/a | n/a |
GSM456517 | Central cortex | n/a | n/a |
GSM45652 | Peri-medullary cortex | n/a | n/a |
GSM45652 | Peri-medullary cortex | n/a | n/a |
GSM45652 | Peri-medullary cortex | n/a | n/a |
GSM456524 | Whole cortex | n/a | n/a |
GSM456524 | Whole cortex | n/a | n/a |
GSM456524 | Whole cortex | n/a | n/a |
GSM456524 | Whole cortex | n/a | n/a |
GSM456524 | Whole cortex | n/a | n/a |
GSM456524 | Whole cortex | n/a | n/a |
GSM456524 | Whole cortex | n/a | n/a |
GSM45653 | Whole medulla | n/a | n/a |
GSM45653 | Whole medulla | n/a | n/a |
GSM45653 | Whole medulla | n/a | n/a |
GSM45653 | Whole medulla | n/a | n/a |
GSM45653 | Whole medulla | n/a | n/a |
GSM45653 | Whole medulla | n/a | n/a |
GSM45653 | Whole medulla | n/a | n/a |