Transcription Factor 4 loss-of-function is associated with deficits in progenitor proliferation and cortical neuron content

Supplementary Data 2: Gene expression datasets for neural progenitor cells and neurons and lists of DE genes between PTHS and parents.

Tab ‘neural progenitors’: Gene expression abundance values for RNA sequencing libraries from NPCs of subjects PTHS #1 to PTHS #4 and respective parents. Gene expression is quantified in transcripts per million reads (TPM) aggregated to gene level (see Methods for details). Gene names follow nomenclature in GRCh38 (GENCODE 32) human genome build. Independent replicates are denoted as A, B, and C.

Tab ‘DE gene neural progenitors’: Metrics of differential expression (DE) analysis for pairwise comparisons (each parent versus respective PTHS child) obtained using DESeq2 (see Methods for details). For each comparison, ‘baseMean’ indicates across-sample average of normalized counts aggregated at the gene level, ‘log2FoldChange’ is the apeglm-shrunken log2 fold change (effect size), ‘lfcSE’ is the standard error of log2 fold change, and ‘s-value’ indicates the estimated rate of false sign among genes with equal or smaller s-values. The last two columns indicate whether the difference in expression between the parent and respective PTHS child is statistically significant (genes with s-values smaller than 0.005) and the direction of change.

Tab ‘Common DE – progenitors’: Lists and numbers of DE genes in comparisons between 2 and 4 parent-PTHS subject pairs. Cells marked in yellow indicate WNT, cadherin, and protocadherin DE genes in ‘Cadherin’ and ‘Wnt signaling’ pathway analysis categories.

Tab ‘neurons’: Gene expression abundance values for RNA sequencing libraries from neurons of PTHS #1 through #4 patients and parents #1, #2, and #4.

Tab ‘DE gene neurons’: Metrics of differential expression analysis for pairwise comparisons (parent versus PTHS).

Tab ‘Common DE – neurons: List and number of DE genes in comparison between 3 parent-PTHS subject pairs. Genes coding for ion channels are highlighted.

Tab ‘neural progenitors-low passage’: Gene expression abundance values for RNA sequencing libraries from NPCs of low passage (P5) from subjects PTHS #1 and PTHS #4 and respective parents.

Supplementary Data 3: List of DE genes in organoids.

Each tab contains information on each subpopulation type being compared. The first column in each tab is a list of all genes. The second and third columns indicate the average log-transformed values of expression for each gene across all cells in the parent and PTHS groups (see Methods for details on log-transformation). The fourth and fifth columns indicate the average values of expression (calculated in the non-log space) for each gene across all cells in the parent and PTHS subpopulations being contrasted. ‘avg_log2FC’ column shows the average log2 fold-change between parent and PTHS across all cells in the subpopulations being contrasted (negative values indicate lower expression in the PTHS group). ‘corrected avg_log2FC’ is the log2FC corrected by adding 0.0001 to the expression values in each group, to eliminate the issue of dividing by null values in the parent group. The last two columns show the p-value (p_value) and adjusted p-value (adj p_value) for multiple comparisons, according to the DESeq2 method.