Transcriptional Profiling of Doxycycline-Inducible Cells

Integrity of total RNA was verified using the Agilent 2100 Bioanalyzer (Agilent Technologies). Copy RNA synthesis, hybridization to HG U133 plus 2.0 microarrays (Affymetrix), and subsequent steps were performed according to the manufacturers’ protocol. Data analysis was performed in R version 3.6.3. The Affy package (93 (link)), version 1.64.0, was used for Robust Multichip Average (RMA) normalization. All +dox samples (n = 9) were compared with the –dox samples (n = 9), using the Limma package (94 (link)), version 3.42.2. Upregulated (log₂ fold change > 0.6, P < 0.05, and q < 0.1) and downregulated (log₂ fold change < –0.6, P < 0.05, and q < 0.1) probe sets were collapsed to genes. The gene names were used for GO term analysis in the web version of PANTHER (released 20200407, ref. 95 (link)), using the human data set with default settings. Heatmaps were created using Pheatmap package in R.

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Canté-Barrett K., Meijer M.T., Cordo’ V., Hagelaar R., Yang W., Yu J., Smits W.K., Nulle M.E., Jansen J.P., Pieters R., Yang J.J., Haigh J.J., Goossens S, & Meijerink J.P. (2022). MEF2C opposes Notch in lymphoid lineage decision and drives leukemia in the thymus. JCI Insight, 7(13), e150363.

Publication 2022

Agilent 2100 Bioanalyzer HG U133 plus 2.0 microarrays

Gene Human Hybridization Microarrays Synthesis

Corresponding Organization : Princess Máxima Center

Other organizations : St. Jude Children's Research Hospital, Research Institute in Oncology and Hematology, CancerCare Manitoba, University of Manitoba, Ghent University

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Variable analysis

independent variables

Treatment with dox (+dox vs -dox)

dependent variables

Gene expression levels

control variables

Integrity of total RNA verified using Agilent 2100 Bioanalyzer
Copy RNA synthesis, hybridization to HG U133 plus 2.0 microarrays, and subsequent steps performed according to manufacturers' protocol

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