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This SuperSeries is composed of the following subset Series: GSE29517: ChIP-chip from Drosophila egg chambers using ORC2 antibody GSE29518: ChIP-chip from dissected Drosophila egg chambers using antibody recognizing RNAPII GSE29520: ChIP-chip from Drosophila egg chambers using antibody recognizing tetra-acetylated histone H4 GSE29526: Expression profile of 16C ovarian follicle cells Refer to individual Series
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Transcription factors and their number of target genes in the D. melanogaster ChIP-chip gold standard network and in the predicted networks for six Drosophila species at the 10% recall level (in brackets for each TF the number of true positive predictions). The bottom two rows are the total number of interactions in each network and the overall precision (percentage of true positives) of the predicted networks.... We collected gene expression data for 3,610 genes in six Drosophila species measured at 9–13 time points during early embryonic development with 3–8 replicates per time point (200 samples in total) . To obtain a global view on the similarities and differences between samples, we performed multi-dimensional scaling using Sammon’s nonlinear mapping criterion on the 3,610-dimensional sample vectors (cf. Methods and Figure fig:sammona). The first (horizontal) axis of variation corresponded to developmental time, with samples ordered along this dimension according to increasing developmental time points, while the second (vertical) axis of variation corresponded to evolutionary distance, with samples ordered along this dimension according to species. By expanding these two axes of variation into principal components, we found that the “developmental” dimension explained 34% of the total variation in the data, while the “evolutionary” dimension explained 11% (cf. Methods). This result confirms that variations in gene expression levels across Drosophila species at the same developmental time point are not greater than variations across time points within the same species. In this study we were interested whether this additional layer of inter-species expression variation can be harnessed in the reconstruction of gene regulatory networks.... To quantitatively compare different methods across different gold standard networks we considered the area under the recall–precision curve (AUC) and the precision at 10% recall (PREC10) as performance measures and converted them to P -values by comparison to AUCs and PREC10s of networks generated by randomly assigning ranks to all possible edges in the corresponding gold standard network (cf. Methods and Figure fig:rec-prec-aggr for the recall vs. precision curves). While the AUC assesses the overall performance of a predicted network, PREC10 measures the quality of the top-ranked predictions, a property that may be of greater practical relevance. This analysis showed that no predicted network performs best for either measure across all gold standards (Figure fig:scorea-f). The single-species virilis networks performed best for 5 out of 12 AUC and PREC10 scores, albeit not for the ChIP-seq network measured in its own species. This overall good performance is consistent with virilis having the highest number of measured time points in the data (Supplementary Table tab:data). D. melanogaster also had more data points available than the other four species, but its time series were less complete (Supplementary Table tab:data). Among the integrative methods, the centroid and union methods both performed best for 5 out of 12 AUC and PREC10 scores (Figure fig:scorea-f). Both also had higher average AUC score than the best single-species network, but only the centroid method had higher average PREC10 score than the best single-species network (Figure fig:scoreg). The most important result however is the fact that the single-species network for the species were the gold standard network was measured never has the highest single-species AUC and only twice has the highest PREC10. In contrast, the centroid method always performs as good, and in most cases better, than the single-species network for the reference species (Figure fig:scorea-f). We conclude that the centroid method is the most robust network integration method achieving consistently high AUC and PREC10 scores, at least on this dataset.... Embryonic developmental time-course expression data in 6 Drosophila species (D. melanogaster (“amel”), D. ananassae (“ana”), D. persimilis (“per”), D. pseudoobscura (“pse”), D. simulans (“sim”) and D. virilis (“vir”)) was obtained from (ArrayExpress accession code E-MTAB-404). The data consists of 10 (amel), 13 (vir) or 9 (ana, per, pse, sim) developmental time points with several replicates per time point resulting in a total of 56 (amel), 36 (vir) or 27 (ana, per, pse, sim) arrays per species (Supplementary Table tab:data). The downloaded data was processed by averaging absolute expression levels over all reporters for a gene followed by taking the log 2 transform.... a. Number of interactions found in one to six species in the inferred gene regulatory networks at 10% recall level (red dots) and in 100 randomized networks with the same in- and out-degree distribution as the inferred networks (boxplots). b. Percentage of all predicted interactions (yellow) and of all true positive predictions (blue) in one to six species c. Precision of interactions found in one to six species. d. Recall of ChIP-seq gold standard interactions conserved in one to three species (green; data for BCD, KR, HB) and one to four species (red; data for TWI). e. Phylogenetic tree between six Drosophila species reconstructed from the inferred interactions at 10% recall level, with the total number of interactions in each species shown in brackets. The tree correctly splits the species in 3 groups – melanogaster (top), obscura (middle), virilis (bottom). Each branch, (numbered 1–9) represents a inferred network state transition. At each network state transition, the number of interactions inferred to be gained (red) or lost (blue) as well as the bootstrap value for each branch (in brackets) is indicated.... Although the gold standard network reconstructed from ChIP-chip data was in D. melanogaster, perhaps surprisingly the D. melanogaster predicted network did not perform better overall than the networks predicted for the other species (Figure fig:sammonb). To get confidence in this observation, we downloaded ChIP-sequencing data for three TFs (BCD, KR, HB) in three Drosophila species (melanogaster, pseudoobscura and virilis) and one TF (TWI) in four species (melanogaster, simulans, ananassae and pseudoobscura) , and created ChIP-seq gold standard networks for five species (cf. Methods). The recall-precision curves generated from the D. melanogaster ChIP-seq gold standard network (Supplementary Figure fig:rec-prec-singleb) were in good agreement with the ChIP-chip data, demonstrating again that the D. melanogaster predicted network performed no better than other Drosophila species. We also calculated recall-precision curves using the D. ananassae, D. pseudobscura, D. simulans and D. virilis ChIP-seq gold standard networks. Again, the regulatory network in that species did not perform better compared to the other species (Supplementary Figure fig:rec-prec-singlec–f).... Performance scores with respect to the gold standard ChIP-chip network for 14 TFs in D. melanogaster (a) and the ChIP-seq networks for D. melanogaster (b, 4 TFs), D. ananassae (c, 1 TF), D. pseudoobscura (d, 4 TFs), D. simulans (e, 1 TF), D. virilis (f, 4 TFs), and their averages over all gold standard networks (g). In each panel, the left, resp. right, figure shows - log 10 P A U C , resp. - log 10 P P R E C 10 for the six single-species predicted networks (green) and the five prediction aggregation methods (red). The dashed lines indicate the performance level of the single-species network for the gold standard species (a–f) or of the best performing single-species network (g). Values with a ∗ in panel a indicate numerical underflow values truncated to the smallest non-zero P -value ( 10 -324 ).... Recall vs. precision curves for predicted regulatory networks for five multi-species meta-analysis methods. The gold standard networks were the ChIP-chip network for 14 TFs in D. melanogaster (a) and the ChIP-seq networks for D. melanogaster (b, 4 TFs), D. ananassae (c, 1 TF), D. pseudoobscura (d, 4 TFs), D. simulans (e, 1 TF) and D. virilis (f, 4 TFs). The numbers in each legend are the area under the curve for each method.... Recall vs. precision curves for predicted regulatory networks in six Drosophila species. The gold standard networks were the ChIP-chip network for 14 TFs in D. melanogaster (a) and the ChIP-seq networks for D. melanogaster (b, 4 TFs), D. ananassae (c, 1 TF), D. pseudoobscura (d, 4 TFs), D. simulans (e, 1 TF) and D. virilis (f, 4 TFs). In panel a, the numbers in the legend are the area under the curve for each species. In panel b–f, the curve for the reference species is in red while the other species are in black.
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Supplementary figures: Fig. S1: Gene names for the data shown in Fig. 1aâ c, Fig. S2: Transcription factor motifs enriched in top ChIP-seq and ATAC-seq regions, Fig. S3: Differential H3K27ac analysis of ATAC-seq regions is an effective method to identify tissue-specific enhancers, Fig. S4: Genes near putative ATAC-seq derived enhancers are differentially regulated across tissues, Fig. S5: The identified putative DV enhancer regions derived from ATAC-seq are enriched for known DV transcription factor motifs, Fig. S6: Number of genes with one or multiple assigned enhancers, Fig. S7: Transcription factor ChIP-seq signal is preferentially found at the expected corresponding binding motifs present within putative MEs and DEEs. (PDF 2673 kb)
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We report genome-wide binding of the highly conserved TF Sine oculis (So), which is necessary for Drosophila eye development and has few previously known direct transcriptional targets. Our data identify novel putative targets of So-mediated regulation, including genes involved in multiple aspects of development. 2 biological replicates of ChIP-seq with anti-So antibody on chromatin from D. melanogaster third instar eye-antennal imaginal discs; negative control - same sample and ChIP-seq protocol without anti-So antibody
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Subcellular localization and genomic binding of BmCdp1 in BmN4 cells. (A) Western blotting. Flag-tagged BmCdp1 was detected using anti-Flag antibody. Actin was used as a control. N and C indicate nuclear and cytoplasmic fractions, respectively. (B) Immunohistostaining. BmN4 cells were probed with anti-Flag antibody, and visualized using Alexa Fluor 546-conjugated goat anti-mouse IgG. The cells were also counterstained with DAPI to visualize nuclear DNA. (C) ChIP-seq. Mapping patterns of ChIP-seq data from pIZ- and Flag-tagged BmCdp1-transfected cells were visualized using Genome studio (Illumina). A representative BmCdp1-enriched locus on chromosome 17 is shown. The primer sets used in Fig. 3D are indicated. (D) ChIP-qPCR. BmCdp1 enrichment on chromosome 17 was verified by ChIP-qPCR. ... ChIP-seq and ChIP-qPCR of BmCdp1-enriched locus on chromosome 10. (A) ChIP-seq. Mapping patterns, generated using ChIP-seq data, from pIZ- and Flag-tagged BmCdp1-transfected cells were visualized using Genome studio (Illumina). A representative BmCdp1-enriched locus on chromosome 10 is shown. The primer sets used in Fig. S2A were indicated. (B) ChIP-qPCR. BmCdp1 enrichment on chromosome 10 was verified by ChIP-qPCR. ... In this study, we discovered a novel gene with two CDs in the Bombyx genome. This gene, BmCdp1, encodes a nuclear protein that can bind to specific loci in the Bombyx genome. Phylogenetic analysis revealed that the Drosophila orthologs of BmCdp1 were CG8289 genes (Fig. 1C), but D. melanogaster CG8289 lacked one of the two CDs that were present in BmCdp1 (Fig. S1). In FlyBase, seven alleles have been found in D. melanogaster at this locus, three of which (CG8289d10824, CG8289GD13880, and CG8289GD16515) have been listed as viable and one (CG8289d1082) has been categorized as fertile. Similar to our observation in Bombyx (Fig. 2C), peak expression of CG8289 was observed within the 6–12hour embryonic stages. In addition, the FlyAtlas Anatomical Expression Data demonstrated that almost all larval and adult tissues express CG8289 at moderate levels, suggesting that Cdp1 expression profiles are conserved between these two insects. In the present study, no phenotypic abnormalities were observed in BmCdp1-knocked down embryos, suggesting that BmCdp1 is probably dispensable for silkworm embryogenesis. Further experiments, such as gene knockout studies using TALENs (Ma et al., 2012; Sajwan et al., 2013), will be necessary to understand the role of this gene at other developmental stages.... Domain structure of BmCdp1 orthologs in Drosophila species. BmCdp1 orthologs of Drosophila melanogaster and Drosophila persimilis have a single CD, whereas the others possess two CDs. ... Because BmCdp1 is a nuclear protein, it potentially interacts with modified histones via its CDs. To test this hypothesis, we investigated the BmCdp1-enriched genomic loci by ChIP-seq. We have recently constructed an epigenome map of BmN4 cell line (Kawaoka et al., 2013), allowing us to get information on gene expression and histone modifications at the interest genomic loci easily. Therefore, we used this cell line in ChIP-seq studies. We performed ChIP-seq analysis of control (pIZ vector-transfected) and Flag-tagged BmCdp1-transfected cells with anti-Flag antibody. First, we attempted to visually identify the BmCdp1-enriched loci using Genome studio, and detected a few distinct peaks (<10) after comparing the data from control cells (Figs. 3C, S2A). Similar results were obtained using the MACS program (data not shown). Consequently, we verified the observed enrichment at 8 loci by ChIP-qPCR, and identified two genomic loci on chromosomes 10 and 17, where BmCdp1 was reliably enriched (Figs. 3D, S2B). According to the Bombyx genome database, one of the two loci was localized upstream region of a putative gene, BGIBMGA007060 (Fig. 3C), suggesting that BmCdp1 occupancy at this locus affected BGIBMGA007060 transcription.
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ChIP-seq... The mouse and Drosophila PcG targets are associated with different sequence signatures. (A) The Pho and Yy1 motifs are similar. (B) ROC curves and corresponding AUC scores for cross-specifies prediction. ... The Hox clusters are targeted by PcG in both mouse and Drosophila but their promoter sequences show different properties. (A) The Drosophila ANT-C region. (B) The mouse Hoxb cluster. Each colored box represents a protein-coding gene, in the order of their chromosomal locations. The TSS coordinates of the genes are shown as vertical lines in the bottom of the figure. The color indicates either presence (red) or absence (blue) of a specific feature labeled on the left. The locations of the Hox genes are marked in the above. The label “:ChIP” after certain TFs is used to indicate that target information is based on ChIP-chip data. ... Enrichment analysis for overlaps between TF and PcG targets. (A) The 15 TFs probed by ChIP-chip/seq experiments in mouse ESCs. The statistically significant one are marked by asterisks (p<1.0E-7 from one-sided Fisher exact test with Bonferroni correction). (B) The most enriched or depleted TF motifs. ... Predicted propensity scores reflect the overall PcG target plasticity. (A) Comparison of the propensity score distribution among different gene groups with similar H3K27me3 profiles. The number of lineages in which the genes are marked by H3K27me3 is shown above the figure. The number of genes in each group is also shown (in parentheses). (B) Time course gene expression level analysis. The PcG target genes in ESCs are divided into 15 roughly equal-sized groups associated with similar propensity scores (mean values shown on the left). The heat map indicates the mean mRNA expression level within each group at different time points after LIF removal. (C) Comparison of the propensity score distributions for the Ezh2-/-, H3K27me3+ and Ezh2-/-, H3K27me3- genes, which correspond to the subset of PcG targets that either retain or lose the H3K27me3 mark in the Ezh2-/- mutant ESCs. (D) Enrichment score for overlap between the top 18 TF features and Ezh2-/-, H3K27me3+ or Ezh2-/-, H3K27me3- targets. The label “:ChIP” after certain TFs is used to indicate that target information is based on ChIP-chip/seq data. The enrichment score is defined as the ratio of the observed frequency of a TF feature among PcG targets over the frequency expected by chance. ... Predicted propensity scores and PcG status in Drosophila.
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JAK/STAT pathway plays important roles in controlling Drosophila intestinal homeostasis and regulating the ISC proliferation and differentiation. However,the downstream targets of its transcription factor-STAT92E remain largely unknown.To further identify the regualtory mechanisms of the JAK/STAT pathway in controlling intestinal homeostasis,we performed the ChIP-Seq assay with mouse raised STAT92E antibody using JAK/STAT signaling highly activated adult intestines.Through the ChIP assay, we have identified over 1000 significant peaks (p<0.01) around the putative targets.The well-characterized JAK/STAT downstream targets including Domeless,Socs36E,STAT92E and chinmo were identified in our ChIP assay,indicating that our experiment is workable to identify novel JAK/STAT downstream targets in adult intestines.This work will provide insights into our understanding of regulatory mechanisms of JAK/STAT signaling during Drosophila intestinal development. Identify the ChIP peaks of STAT92E antibody using JAK/STAT signaling highly actived Drosophila adult intestines, compared with input libaray as the control
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This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor H3K27me3 from D.sim_WPP generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Factors binding profiles are generated by using specific antibodies for the protein of interest. This submission represents the ChIP-seq component of the study
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This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Trl-D2 from D.sim_E0-4h generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Factors binding profiles are generated by using specific antibodies for the protein of interest. This submission represents the ChIP-seq component of the study
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This is a dataset generated by the Drosophila Regulatory Elements modENCODE Project led by Kevin P. White at the University of Chicago. It contains genome-wide binding profile of the factor KW3-Trl-D2 from D.yak_WPP generated by ChIP and analyzed on Illumina Genome Analyzer. For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf A validated dataset is comprised of three biological replicates for ChIP-chip experiments and two replicates for ChIP-seq and meet the modENCODE quality standards. The control sample is the chromatin Input used for ChIP. Factors binding profiles are generated by using specific antibodies for the protein of interest. This submission represents the ChIP-seq component of the study
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