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Additional Supporting information may be found in the online version of this article.

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DVDY_21989_sm_SuppFig1.tif3166KSupp. Fig. S1. Box plot analysis shows a five-number summary (the smallest observation, lower quartile, median, upper quartile, and largest observation) for the 584 significantly modulated mRNAs found either by SAM or t-test and harboring Stat92E TFBSs, based on five individual eye discs per group (R1 through R5).
DVDY_21989_sm_SuppFig2.tif20804KSupp. Fig. S2. Q-PCR results for 18 up-regulated genes. See the Experimental Procedures section for procedures. In all figures, gray bar is yw and black bar is GMR-upd. The Y-axis in the bar graphs represents relative mRNA abundance. Q-PCR, quantitative real-time polymerase chain reaction.
DVDY_21989_sm_SuppFig3.tif12279KSupp. Fig. S3. Q-PCR results for 9 down-regulated genes. See the Experimental Procedures section for procedures. In all figures, gray bar is yw and black bar is GMR-upd. The Y-axis in the bar graphs represents relative mRNA abundance. Q-PCR, quantitative real-time polymerase chain reaction.
DVDY_21989_sm_SuppFig4.tif4207KSupp. Fig. S4. Ser and wg expression in yw as compared to GMR-upd eye discs and repression of wg in hop-expressing clones. A,B: Single channel for Ser-lacZ expression (white) for Figure 3M,N. Brackets indicate the region where Ser expression is reduced in GMR-upd eye discs (B) as compared to yw controls (A). C,D: Merge of wg-lacZ (magenta) and Phalloidin (actin) for panels in Figure 3D,E. Brackets indicate region where wg expression is reduced in GMR-upd eye discs (D) as compared to yw controls (C). E–E″: Hop-expressing clones (green in E, white in E″) autonomously repress wg-lacZ (E′, arrowheads). wg-lacZ is magenta in E and white in E′. Furrow is marked by arrow in A–D. Ser-lacZ and wg-lacZ were detected with β-gal antibody.
DVDY_21989_sm_SuppFig5.tif4205KSupp. Fig. S5. Dl, but not fng, is ectopically expressed in cells lacking stat92E. A,B: In wild-type (WT) third-instar eye discs, Dl (brown) is expressed at low levels anterior to the furrow and in cone cells posterior to the furrow (A). In eye discs containing stat92E M+ clones, Dl expression is significantly increased in cells anterior to the furrow (B, arrow). C,D: In situ hybridization reveals that fng is expressed, as previously reported, in the ventral domain of a wild-type second-instar eye disc (C, bracket). In second-instar eye discs containing stat92E M+ clones, fng expression is still restricted to the ventral domain (D, bracket). In C and D, the eye discs are outlined with a dashed black line. E,F: In situ hybridization reveals that fng expression is not changed in third-instar wild-type (E) as compared to GMR-upd eye discs (F).
DVDY_21989_sm_SuppTableS1.xls544KSupp. Table S1. 584 differentially regulated genes in the GMR-upd micro-array. The table lists statistically significant mRNA transcripts detected by 584 Affymetrix probe sets (AFFY ID, column B) as described in the Experimental Procedures section and in Figure 2A,B. The Gene Symbol and Gene Titles (Columns C and D) were updated using Affymetrix NETAFFX Analysis Center, release of November 13, 2007. Column E lists the median value of fold change in GMR-upd samples that was baseline-normalized to median yw measurements set equal to 1. Column F lists either or both statistical algorithms applied to determine significant regulation of each gene (SAM, t-test, see Fig. 2A and the Experimental Procedures section). Column G indicates presence of Stat92E binding site in the target gene locus. Columns H through AA list the fold-change abundance (FC), raw intensities normalized by MBEI (Raw) and Present/Absent calls (Flags) of individual quintuple measurements in each genotype.
DVDY_21989_sm_SuppTableS2.xls340KSupp. Table S2. Genome-wide bioinformatics search for genes with Stat92E binding sites. See the Experimental Procedures section for procedures. Columns A and B list gene name and gene symbol, respectively, which were obtained from Flybase. Column C lists chromosomal location of the gene: X; 2L; 2R; 3L; 3R; 4; U, unmapped; Het, heterochromatin. Columns D and E list information for the first and second Stat92E binding site in the cluster, respectively. Specifically, they list the direction of the Stat92E binding site (for, forward; rev, reverse); the sequence identified by Target Explorer; its position on the chromosome (using Drosophila genome release 3.1, for which Target Explorer was designed (Sosinsky et al., 2003)); its binding site score (i.e., how similar it was to the consensus generated by matrix (minimum cutoff = 6.63)). Column F lists the location of the cluster in gene (i.e., 5′, 3′ or intronic regions). Column G lists the number of base pairs between the Stat92E binding site cluster and the start of the region of the gene (5′, 3′, intronic) in which the cluster was found.
DVDY_21989_sm_SuppTableS3.xls44KSupp. Table S3. Comprehensive functional annotation and pathway analysis of genes significantly modulated in GMR-upd samples. The table summarizes the results of functional annotation and pathway analysis (KEGG and Gene Ontologies). Genes that populate each Term in corresponding GO or KEGG Category are separated into either up-regulated or down-regulated sections (yellow field/up and blue field/down, respectively). Count = number of genes per Term whose symbols are listed to the right. All molecules with microarray expression profiles validated by independent techniques (see Experimental Procedures for details) are shown in red.

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