Drosophila melanogaster
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA298537 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Chromosomal instability which involves deletion and duplication of chromosomes or chromosome parts is a common feature of cancers, and deficiency screens are commonly used as a method to find genes involved in different biological pathways. Still, how gene expression from whole chromosomes or large chromosomal domains is affected by deficiencies, duplications or chromosome loss is largely unknown. Using expression microarrays of deficiency hemizygotes and a duplication hemizygote we show that expressed genes are significantly buffered when present in a deficiency hemizygote and that the buffering effect is general and not mainly caused by feedback regulation of individual genes. Differentially expressed genes are in general better buffered than ubiquitously expressed genes when present in one copy. When present in three copies, differentially expressed genes are in general less buffered than ubiquitously expressed genes. Furthermore, we show that the 4th chromosome is compensated in response to dose differences. Our results suggest that general mechanisms exist to stimulate and to repress gene expression of aneuploidy regions and on the 4th chromosome this compensation is mediated by POF (Painting of Fourth). Experiment Overall Design: We prepared total RNA from flies heterozygous for three different deletions, Df(2L)J-H, Df (2L)ED4470, Df(2L)ED4651, flies heterozygous for the duplication Dp(2;2)Cam3 and flies with only one chromosome 4, or three copies of the 4th chromosome, as well as from wild type control flies. Three biological replicates of all genotypes were prepared.
2009-04-03 | E-GEOD-14517 | biostudies-arrayexpress
Project description:We performed mRNA transcriptional profiling on 99 hemizygotic lines (Df/+) from the DrosDel project covering 68% of chromosome 2L, in order to understand how changes in gene copy number affect overall transcriptome.
2016-01-31 | GSE61509 | GEO
Project description:Expression profiling pooled Drosophila melanogaster heterozygous for deletions on Chromosome 2L
| PRJNA261333 | ENA
Project description:Aneuploidy, i.e., variation in the number of individual chromosomes (chromosomal aneuploidy) or chromosome segment (segmental aneuploidy) is associated with developmental abnormalities and reduced fitness in all species examined, is the leading cause of miscarriages and mental retardations and a hallmark of cancer. Despite their documented importance in disease the effects of aneuploidies on the transcriptome remains largely unknown. Here we have examined the expression output in seven deficiency heterozygotes as single deficiencies and in all pairwise combinations. The results show that genes in one copy are buffered, i.e., are expressed above the expected 50% expression level compared to wild type and the buffering is general and not influenced by additional haploid regions. Long genes are significantly better buffered than short genes and our analysis suggests that gene length is the primary determinant for the degree of buffering. For short genes the degree of buffering depends on expression level and expression pattern. Furthermore, the results show that in deficiency heterozygotes the expression of genes involved in proteolysis is enhanced and negatively correlates with the degree of buffering. Our results suggest that proteolysis is a general response induced by aneuploidy. We prepared total RNA from flies heterozygous for seven different deletions, Df(3R)ED10953, Df(2L)ED4559, Df(2R)ED1770, Df(2R)ED1612, Df(2L)ED3, Df(3R)ED5071 or Df(3R)ED7665 in two or three single biological replicates or in pairwise combinations, as well as from six biological replicates of wild type control flies.
2012-04-04 | E-GEOD-34400 | biostudies-arrayexpress
Project description:Many protein complexes are involved in gene regulation during Drosophila spermatogenesis. tplus3a and tplus3b code for Plus3 domain proteins and are enriched in spermatocytes. Male flies ∆tplus3a/b carrying deletions of both genes in trans to deficiency Df(2L)BSC151 show severely reduced fertility. tbrd-1 is known to regulate hundreds of genes during spermatogenesis in cooperation with tTAFs. To gain more insight into the regulatory mechanisms during spermatogenesis we used RNA from testes of ∆tplus3a/b/Df(2L)BSC151 and tbrd-11 mutant flies for RNAseq in comparison to w1118 wild-typic control. RNA was isolated with Trizol from 200 Testes dissected from w1118, homozygous tbrd-11 mutants or ∆tplus3a/b/Df(2L)BSC151. After DNAse I digestion RNA was purified and RNAseq was performed in three replicates. Genotype Description: w1118: wild-typic control tbrd-11: homozygous tbrd-11 mutants (knock-out through P{EPgy2}tbrd-11, as described in Leser et al., 2012) ∆tplus3a/b/Df(2L)BSC151: CRISPR/Cas9 deletion mutants, representing knock-out of both tplus3 and tplus3b. Male flies y1cho2v1;∆tplus3a/b/CyO were crossed with virgin females w1118;Df(2L)BSC151/CyO. Male offspring with w1118;∆tplus3a/b/Df(2L)BSC151 were used for RNAseq.
2019-11-04 | E-MTAB-7013 | biostudies-arrayexpress
Project description:GSE31386: Microarray expression analysis of Drosophila DrosDel deficiency lines GSE31401:RNA-Seq on SOLiD platform of DrosDel deficiency and w1118 flies GSE31549: RNA-Seq on Illumnia platform of DrosDel deficiency and w1118 lines GSE31550: DNA-Seq of Drosophila DrosDel deficiency and w1118 lines Refer to individual Series
2012-04-02 | E-GEOD-31407 | biostudies-arrayexpress
Project description:RNA-Seq of female, male, and sex-transformed Drosophila melanogaster heads from flies heterozygous for deletions on chromosome X and 3L
| PRJNA258556 | ENA
Project description:In order to understand the effect of genetic background on the response to gene dose perturbation, we performed mRNA transcriptional profiling on 99 hemizygotic lines (Df/+) from the DrosDel project, which have hybrid genetic background of OregonR/w1118.
2016-01-31 | GSE73920 | GEO
Project description:Euchromatic chromatin modifications on chromosome 2L
| PRJNA103149 | ENA
Project description:To measure the response to gene dose, we performed mRNA-Seq of fly heads with molecularly defined deletions constructed from DrosDel deficiency lines (Ryder et al. Genetics 2007, 177(1):615-29) on the Illumina HiSeq 2000 platform.
2015-03-26 | GSE60571 | GEO