Supplementary Materials

Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion

Marta Florio, Mareike Albert, Elena Taverna, Takashi Namba, Holger Brandl, Eric Lewitus, Christiane Haffner, Alex Sykes, Fong Kuan Wong, Jula Peters, Elaine Guhr, Sylvia Klemroth, Kay Prüfer, Janet Kelso, Ronald Naumann, Ina Nüsslein, Andreas Dahl, Robert Lachmann, Svante Pääbo, Wieland B. Huttner

Materials/Methods, Supplementary Text, Tables, Figures, and/or References

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  • Materials and Methods
  • Figs. S1 to S14
  • Table S3
  • Captions for Tables S1, S2, and S4
  • Full Reference List
Table S1
'aRG>bRG>neurons' gene set and step-wise filtering analysis. Dataset including the human genes contained in the 'aRG>bRG>neurons' gene set, which has been used as input for the gene expression analysis shown in Figure 3A and described in Figure legend 3. The first spreadsheet (aRG>bRG>N (190)) lists the 190 genes significantly upregulated (p<0.01) in aRG relative to bRG and neurons (N), and in bRG relative to N (Fig. 3A). First column: Ensemble Gene ID. Second column: gene set (aRG>bRG & bRG>N). Third and fourth columns: gene name and description, respectively. Fifth column: gene biotype (protein coding). Sixth column: FPKM values relative to human aRG, bRG and N. The second spreadsheet (filtered msNPC+GZs, hCP (17)) shows the stepwise exclusion of genes in the aRG>bRG>N gene set, and reads as follows. First column (aRG>bRG>N): names of the 190 genes contained in the aRG>bRG>N set. Second column (mNPC filtered): names of the 22 genes in the aRG>bRG>N list, which are not expressed (FPKM≤1) in none of the mouse neural progenitor cells (mNPCs), i.e. aRG, bRG or bIP, isolated in this study. Third column (mGZ filtered): names of the 18 genes in the 'mNPC filtered' list, which are not expressed (FPKM≤1) in none of the mouse germinal zones (mGZs), i.e. VZ or SVZ, isolated by Fietz et al. (13). Fourth column (hCP filtered): names of the 17 genes in the 'mGZ filtered' list, which are not expressed (FPKM≤1) in the human cortical plate (hCP), isolated by Fietz et al. (13). Fifth and sixth columns: Ensemble Gene ID and gene description, respectively. Seventh column, FPKM values relative to human aRG, bRG and N. The fourth spreadsheet (with ms ortholog (13)) lists the 13 genes in the 'hCP filtered' set, which have a mouse ortholog. First column: Ensemble Gene ID. Second column: gene set (aRG>bRG & bRG>N). Third and fourth columns: gene name and description, respectively. Fifth column: gene biotype (protein coding). Sixth column: FPKM values relative to human aRG, bRG and N. The fifth spreadsheet (without ms ortholog (4)) lists the 4 genes in the 'hCP filtered' set, which have no mouse ortholog. Columns read as indicated above.
Table S2
'bRG≥aRG>neurons' gene set and step-wise filtering analysis. Dataset including the human genes contained in the 'bRG≥aRG>neurons' gene set, which has been used as input for the gene expression analysis shown in Figure 3B and described in Figure legend 3. The first spreadsheet (bRG≥aRG>N (394)) lists the 394 genes significantly upregulated (p<0.01), or equally expressed, in bRG relative to aRG, and up-regulated in both aRG and bRG, relative to N (Fig. 3B). Columns read as indicated in the legend to Table S1. The second, third and fourth spreadsheets show the stepwise exclusion of genes in the bRG≥aRG>N gene set, and columns read as described in the legend to Table S1.
Table S4
List of primers used for gene expression analysis by qPCR. Lists of primers used for RT-qPCR on mouse (first spreadsheet) and human (second spreadsheet) isolated cells. Gene name, primer names, primer sequence, and references to previously published work (if any) are listed in the first, second, third and fourth column, respectively.