Additional file 1:

SLY1 is expressed in all major thymocyte subsets. Semi-quantitative RT-PCR. Thymocytes were sorted according to their surface expression of CD4 and CD8. Subsequently, RNA was isolated and transcribed into cDNA. A serial 1:3 dilution of cDNA was used to amplify SLY1 or GAPDH transcripts with SLY1- or GAPDH-specific primers, respectively. Zipped folder containing EPS file.

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Additional file 2:

Proliferation and differentiation defect of sorted SLY1^-/- and SLY1^Δ/Δ DN3 thymocytes cannot be rescued by adding IL-7. A. Fold expansion of sorted DN3 thymocytes after six days of culture on OP9 DL-1 cells. If indicated, 1 ng/ml mIL-7 was included in the cultures. B. Differentiation rate of sorted DN3 thymocytes after six days of culture on OP9 DL-1 cells without IL7. C. Differentiation rate of sorted DN3 thymocytes after six days of culture on OP9 DL-1 cells with 1 ng/ml murine IL7. Data are based on triplicate analyses. The differentiation rate corresponds to the percentage of DP cells divided by the percentage of remaining DN cells. The expansion rate was determined by comparing the obtained cell number on day six to initial seeding numbers on day 0. Representative data of two independently performed experiments is shown. Zipped folder containing EPS file.

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Additional file 3:

Notch- and preTCR-dependent activation of mTOR results in cell size increase and is diminished in sorted DN SLY1^-/- and SLY1^Δ/Δ thymocytes. A. mTOR activation is strictly dependent on a combined preTCR- and Notch receptor-derived signal. Cell size of DN thymocytes was analysed after 12 h culture on OP9 GFP or OP DL-1 cells. Cells were gated on intracellular TCRβ-positive or -negative. B. Cell size overlay of DN SLY1^+/+, SLY1^-/- and SLY1^Δ/Δ preTCR-positive thymocytes cultured on OP9 DL-1 cells. As a control, 20 nM Rapamycin was added during the cultivation period to inhibit mTOR activation. Zipped folder containing EPS file.

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Additional file 4:

γ-Secretase-inhibitor (GSI) titration of OP9-cultured DN3 cells. Sorted SLY1^+/+, SLY1^-/- and SLY1^Δ/Δ DN3 thymocytes were cultured on OP9 DL-1 or OP9 GFP cells for six days before analysis. Then, CD4- and CD8-expression was assessed by FACS (left panel). The expansion rate based on initial seeding numbers was determined (right panel). *p <0.01; **p <0.001; *** p <0.0001. Zipped folder containing EPS file.

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