RNA-seq analysis of PAX9-depleted MCF10A cells relative to siNT control.

Tab 1. Cufflinks [89] results from the RNA-seq analysis. See Materials and Methods for further details. Tab 2. Comparison of the RNA-seq hits to genome-wide siRNA screens for ribosome biogenesis factors (Farley-Barnes et al [34], Badertscher et al [57], and Neumüller Yeast and Neumüller Drosophila referring to the siRNA screens in yeast and Drosophila, respectively [58]). A 1 denotes a mRNA that was included as a hit in that siRNA screen, while a 0 indicates that the mRNA was not considered a hit in that screen. For the second column, a 1 denotes that the mRNA had decreased expression (fold change ≤ - 2) in the RNA-seq dataset, while a 0 indicates denotes that the mRNA had increased expression (fold change ≥ - 2) in the RNA-seq dataset. Tab 3. Comparison of all RNA-seq differentially expressed mRNAs to 3 databases of nucleolar proteins: the Human Protein Atlas [52], the NOPdb [51], and nucleolar proteins in human T-cells from the Gautier laboratory [50]. A 1 denotes a mRNA that was included in the indicated database, while a 0 indicates that the mRNA was not included in the indicated database. For the second column, a 1 denotes that the mRNA had decreased expression (fold change ≤ - 2) in the RNA-seq dataset, while a 0 indicates denotes that the mRNA had increased expression (fold change ≥ - 2) in the RNA-seq dataset. Tab 4. Comparison of all RNA-seq differentially expressed mRNAs to genes differentially occupied by PAX9 in the vertebral columns of E12.5 mice by PAX9 ChIP-seq (Sivakamasundari et al. [54]). A 1 denotes a mRNA that was regulated in the ChIP-seq experiment, while a 0 indicates that the mRNA was not regulated in the ChIP-seq experiment. For the second column, a 1 denotes that the mRNA had decreased expression (fold change ≤ - 2) in the RNA-seq dataset, while a 0 indicates denotes that the mRNA had increased expression (fold change ≥ - 2) in the RNA-seq dataset.
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