Array CGH of Drosophila polytene chromosomes on heterochromatin custom array.
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ABSTRACT:
ORGANISM(S): Drosophila melanogaster
SUBMITTER: Bing He
PROVIDER: E-GEOD-36264 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
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Project description:Mapping the Drosophila melanogaster centromeric heterochromatin by CGH analysis of embryos lacking specific chromosomes or chromosome arms. Nine chromosome or chromosome arm deletions were tested: embryos lacking the entire second chromosome (2En-), 2L (2L-), 2R (2R-), the entire third chromosome (3En-), 3L (3L-), 3R (3R-), the entire fourth chromosome (4En-), the X chromosome (X-), or both X and Y chromosomes (XY-). Control: Blastoderm stage wild type Oregon R embryos. For each experiment 100-150 embryos of the appropriate genotype were collected. DNA from randomly staged 0-8 hr wild type Oregon R embryos was used as reference for all experiments. Embryos with no X chromosome were obtained by crossing attached-X/Y females (C(1)DX, y f) to X/Y males. Embryos with no X and Y chromosomes were obtained by crossing attached-X/Y females (C(1)RM, y2suwawa) to attached-XY males (YSX YL, In(1)EN, y B). The compound II chromosomes RM(2L); RM(2R)=C(2)v and the compound III chromosomes RM(3L); RM(3R)=C(3)se were used to generate 2L- and 2R-, and 3L- and 3R- embryos, respectively. The compound II C(2)EN and compound III C(3)EN st1 cu1es stocks were used to generate embryos deficient for the entire second and third chromosome, respectively. The compound IV C(4)RM, ci1eyR/0 were used to generate embryos deficient for the fourth chromosome. Embryos deficient for chromosome 4 were identified by their defects in denticle belt patterning during late embryogenesis, whereas embryos deficient for other chromosome/chromosome arm were recognized based on their specific phenotypic defects during early embryonic development. All embryos were collected at room temperature.
2012-03-06 | E-GEOD-36260 | biostudies-arrayexpress
Project description:The transcription profiles of newly mapped Drosophila heterochromatic sequences during early embryonic stages were investigated by microarray. cDNA were prepared from manually staged wild type Oregon R embryos at various developmental stages (0-1 hr, 2-2.5 hr/cycle 13-early cycle 14, 2.5-3 hr/mid- to late cycle 14, 3-4 hr, 4-5 hr, 19-22 hr) and analyzed by microarray. cDNA prepared from Oregon R embryos with mixed developmental stages (0-16 hrs) were used as reference for hybridization. Each stage has two biological repeats. 100-150 embryos were collected for each experiment. All embryos were collected at room temperature.
2012-03-06 | E-GEOD-36265 | biostudies-arrayexpress
Project description:Chemical cross-linking and high-throughput sequencing have revealed regions of intra-chromosomal interaction, referred to as topologically associating domains (TADs), interspersed with regions of little or no such interaction, in interphase nuclei. We find that TADs and the regions between them correspond with the bands and interbands of polytene chromosomes of Drosophila. We further establish the conservation of TADs between polytene and diploid cells of Drosophila. From direct measurements on light micrographs of polytene chromosomes, we then deduce the states of chromatin folding in the diploid cell nucleus. Two states of chromatin folding, fully extended fibers containing regulatory regions and promoters, and fibers condensed up to ten-fold containing coding regions of active genes, constitute the euchromatin of the nuclear interior. Chromatin fibers condensed up to 30-fold, containing coding regions of inactive genes, represent the heterochromatin of the nuclear periphery. A convergence of molecular analysis with direct observation thus reveals the architecture of interphase chromosomes. Hi-C experiments where ligation is performed on beads (tethered) on male Drosophila salivary glands from three independent biological replicates. Also one Hi-C experiment where the ligation is performed in solution (conventional).
2015-11-05 | E-GEOD-72510 | biostudies-arrayexpress
Project description:modENCODE_submission_722 This submission comes from a modENCODE project of David MacAlpine. For full list of modENCODE projects, see http://www.genome.gov/26524648 Project Goal: Most terminally differentiated Drosophila tissues are either polyploid or polytene. Unlike normal chromosomes, where the entire chromosome must be replicated exactly once, polytene chromosomes are often differentially replicated with many regions underreplicated and some overreplicated. We will characterize five different polytene tissues using comparative genomic hybridization (CGH) to identify differentially replicated regions of each chromosome. These studies will also identify tissue specific amplicons, where the replication mediated amplification of specific loci is essential for up-regulation of mRNA levels encoding proteins critical for development. The differential replication of polytene chromosomes in Drosophila will provide a unique opportunity to understand how developmental cues and chromosomal domains influence replication initiation. Keywords: CGH For data usage terms and conditions, please refer to http://www.genome.gov/27528022 and http://www.genome.gov/Pages/Research/ENCODE/ENCODEDataReleasePolicyFinal2008.pdf EXPERIMENT TYPE: CGH. BIOLOGICAL SOURCE 1: Strain: Oregon-R Orr-Weaver; Developmental Stage: Embryo 0-4h; Genotype: TBA; Sex: Unknown; BIOLOGICAL SOURCE 2: Strain: Oregon-R Orr-Weaver; Tissue: larval salivary gland; Genotype: TBA; Sex: Unknown; NUMBER OF REPLICATES: 2; EXPERIMENTAL FACTORS: Tissue larval salivary gland
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Project description:Mapping the Drosophila melanogaster X heterochromatin by CGH analysis of embryos lacking specific regions of the X chromosome. Eight ChrX deficiencies and duplications were tested: 168 (Dp(1;Y)y[2]67g), 175 (Dp(1;Y)y[2]sc), 114n (Dp(1;Y)y[+]mal[126]), 114f (Df(1)fog[114]), 186n (Dp(1;Y)y[+]mal), 186f (Df(1)mal12), B2580 (Dp(1;Y)ct y[+]), B5280 (Dp(1;Y)ct[+]y[+]). To generate embryos lacking different portions of the X heterochromatin, two types of stocks were used: (1) males carrying a deficient X chromosome missing part of the heterochromatin (generally fog-) and a duplication on the Y chromosome that complements the deficiency, and (2) males carrying a duplication of X on the Y chromosome which covers part of the X heterochromatin. In both cases males were crossed to attached X females. In the first case, one quarter of embryos lack most of the X chromosome except the duplication of X on Y. These embryos were identified according to their defects during cellularization. Another quarter of the embryos carry the deficient X chromosome as their sole X chromosome. These embryos were identified according to their defects in posterior midgut formation during early gastrulation. In the second case, one quarter of embryos that lack most of the X chromosome except the duplication of X on Y were identified according to their defects in cellularization or posterior midgut formation. All embryos were collected at room temperature.
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Project description:Mapping the Drosophila melanogaster 2R heterochromatin by CGH analysis of embryos lacking specific regions of 2R. Seven translocations with breakpoints in 2R heterochromatin were tested: 2219 (T(2;3)ftz[Rpl]), 130058 (T(Y;2)B[SV5]), 130093 (T(Y;2)B63), 130112 (T(Y;2)B238), 101579 (T(2;3)bxd[68]), 101988 (T(Y;2)G10), and 107387 (T(2;3)E(da)). To generate embryos deficient for smaller regions of 2R heterochromatin, T(2;Y) or T(2;3) translocation males were crossed to C(2)EN females. One eighth of the embryos that lack 2R were identified according to their failure in forming the ventral furrow during early gastrulation. All embryos were collected at room temperature.
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Project description:A major goal of biology is the construction of networks that predict complex system behavior. We combine multiple types of molecular data, including genotypic, expression, transcription factor binding site (TFBS), and protein-protein interaction (PPI) data previously generated from a number of yeast experiments in order to reconstruct causal gene networks. Networks based on different types of data are compared using metrics devised to assess the predictive power of a network. A network reconstructed by integrating genotypic, TFBS and PPI data is shown to be the most predictive. This network is used to predict causal regulators responsible for hot spots of gene expression activity in a segregating yeast population. The network is also shown to elucidate the mechanisms by which causal regulators give rise to larger-scale changes in gene expression activity. Predictions are prospectively validated to provide direct experimental evidence that predictive networks can be constructed by integrating multiple, appropriate data types. Keywords: allele replacement Allele replacement strains were created in two backgrounds: BY (BY4724 and BY4742), and RM11-1a, and compared to the parental type (BY4716 and RM11-1a). BY7g, BY9g, BY11g are BY4716, while RM7g, RM9g, and RM11g are RM11-1a. YAD350 is a MKT1 D30G replacement strain in BY4742 background. YLK804 is a SAL1-RM allele in BY4724 and YLK806 is a SAL1-BY allele in RM11-1a. All strains were grown in YNB + 2% glucose, with leucine, lysine, and uracil. YAD350 was also grown with histidine.
2008-06-15 | E-GEOD-11111 | biostudies-arrayexpress
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Project description:This study is a quantitative trait linkage mapping study targeted at gene-environment interaction. A family of yeast derived from BY4716 and RM11-1a was grown in two carbon sources (glucose and ethanol) and expression profiled. The analysis revealed how the influence of genetic factors changes in different conditions. Abstract: The effects of genetic variants on phenotypic traits often depend on environmental and physiological conditions, but such gene–environment interactions are poorly understood. Recently developed approaches that treat transcript abundances of thousands of genes as quantitative traits offer the opportunity to broadly characterize the architecture of gene–environment interactions. We examined the genetic and molecular basis of variation in gene expression between two yeast strains (BY and RM) grown in two different conditions (glucose and ethanol carbon sources). We observed that most transcripts vary by strain and condition, with 2,996, 3,448, and 2,037 transcripts showing significant strain, condition, and strain–condition interaction effects, respectively. We expression profiled over 100 segregants derived from a cross between RM and BY in both growth conditions, and identified 1,555 linkages for 1,382 transcripts that show significant gene–environment interaction. At the locus level, local linkages, which usually correspond to polymorphisms in cis-regulatory elements, tend to be more stable across conditions, such that they are more likely to show the same effect or the same direction of effect across conditions. Distant linkages, which usually correspond to polymorphisms influencing trans-acting factors, are more condition-dependent, and often show effects in different directions in the two conditions. We characterized a locus that influences expression of many growth- related transcripts, and showed that the majority of the variation is explained by polymorphism in the gene IRA2. The RM allele of IRA2 appears to inhibit Ras/PKA signaling more strongly than the BY allele, and has undergone a change in selective pressure. Our results provide a broad overview of the genetic architecture of gene–environment interactions, as well as a detailed molecular example, and lead to key insights into how the effects of different classes of regulatory variants are modulated by the environment. These observations will guide the design of studies aimed at understanding the genetic basis of complex traits. Keywords: QTL This data set includes 24 parental arrays (6 of each parent in each condition, 218 segregant arrays (109 in both conditions), and 4 allele replacement arrays (IRA2 replacements in both backgrounds in both conditions). All arrays are from an unique biological sample, and many are randomized for dye (no dye-swaps on the same RNA sample). For the 24 parental arrays, there are three of each strain*condition*dye combination. The segregant arrays were randomized for dye. The replacement arrays are all of the Cy5 = experimental, Cy3 = reference type. All arrays are hybridized to a common reference consisting of an equal portions of RNA samples. from BY and RM grown in glucose and ethanol. Analysis was performed using default settings in Agilent Feature Extractor software versions 8.0-9.5. Spots were excluded if their intensity was below 350 or if they were flagged as non-uniformity outliers. Transcripts were considered good if they were present in all parental arrays (for the parental analysis) or 80% of all arrays in each condition for the segregant analysis.
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