E-GEOD-7875 - Transcription profiling of mouse PKBalpha-/-thymus reveals deletion of PKBalpha/Akt1 affects thymic development

Submitted on 23 May 2007, released on 15 June 2008, last updated on 2 May 2014
Mus musculus
Samples (16)
Array (1)
Protocols (8)
The thymus constitutes the primary lymphoid organ for the majority of T cells. The phosphatidyl-inositol 3 kinase (PI3K) signaling pathway is involved in lymphoid development. Defects in single components of this pathway prevent thymocytes from progressing beyond early T cell developmental stages. Protein kinase B (PKB) is the main effector of the PI3K pathway. To determine whether PKB mediates PI3K signaling in early T cell development, we characterized PKB knockout thymi. Our results reveal a significant thymic hypocellularity in PKBalpha-/- neonates and an accumulation of early thymocyte subsets in PKBalpha-/- adult mice. The latter finding is specifically attributed to the lack of PKBalpha within the lymphoid component of the thymus. Microarray analyses show that the absence of PKBalpha in early thymocyte subsets modifies the expression of genes known to be involved in pre-TCR signaling, in T cell activation, and in the transduction of interferon-mediated signals. This report highlights the specific requirements of PKBalpha for thymic development. Experiment Overall Design: Early thymocyte subsets (DN3 and ISP8) were sorted by FACS from 4 PKBalpha-/- / PKBalpha+/+ mouse littermate pairs. The same number of DN3 or ISP8 cells was sorted (7 000 to 25 000 cells) within a PKBalpha-/- / PKBalpha+/+ pair. Four replicates per condition were then analysed (4xPKBalpha-/- DN3, 4xPKBalpha+/+ DN3, 4xPKBalpha-/- ISP8, 4xPKBalpha+/+ ISP8). Total RNA was extracted using PicoPureTM RNA isolation kit (Arcturus, Sunnyvale, CA, USA) and RNA quality was controlled using the 2100 Bioanalyser (Agilent Technologies, Santa Clara, CA, USA). Total RNA was amplified and labeled using the Affymetrix 2-cycle 3’ labelling kit according to manufacturer’s instructions. After fragmentation, 10 ug cRNA was hybridised to mouse genome 430 2.0 GeneChips (Affymetrix, Santa Clara, CA). The supplementary file represents the expression values estimated using the GC-RMA function provided by Refiner 3.1 (Genedata, Basel, Switzerland) for each of the samples.
Experiment types
transcription profiling by array, unknown experiment type
Brian A. Hemmings
Deletion of PKBalpha/Akt1 Affects Thymic Development. Elisabeth Fayard, Jason Gill, Magdalena Paolino, Debby Hynx, Georg A Holländer, Brian A Hemmings. PLoS ONE 2(10):e992 (2007)
Investigation descriptionE-GEOD-7875.idf.txt
Sample and data relationshipE-GEOD-7875.sdrf.txt
Raw data (1)E-GEOD-7875.raw.1.zip
Processed data (1)E-GEOD-7875.processed.1.zip
Array designA-AFFY-45.adf.txt
R ExpressionSetE-GEOD-7875.eSet.r