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ABSTRACT:
PROVIDER: PRJNA623115 | ENA |
REPOSITORIES: ENA
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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:CGH analysis of translocations with breakpoints at the euchromatin/heterochromatin boundary. Three translocations with breakpoint at the euchromatin/heterochromatin boundary of 2L, 3L and X, respectively, were analyzed by CGH to distinguish heterochromatic sequences from euchromatic sequences. X: 101042(T(1;Y)B91); 2L: 130186 (T(Y;2)R146); and 3L: 102004(T(2;3)H31). To obtain embryos lacking the euchromatin portion of the chromosome arms, translocation males bearing breakpoint at the euchromatin/heterochromatin boundary of 2L, 3L and X were crossed to C(2)EN, C(3)EN or attached X females, respectively. All embryos were collected at room temperature.
2012-03-06 | E-GEOD-36261 | biostudies-arrayexpress
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:A man was referred to our lab for peripheral blood karyotyping because of infertility. A deletion in 8p was observed. Further characterization was needed in order to determine the exact breakpoints and what genes have been deleted.
2023-11-11 | E-MTAB-13528 | biostudies-arrayexpress
Project description:Characterization of copy number alterations and unbalanced breakpoints in human esophageal squamous cell carcinoma cell lines by array-based comparative genomic hybridization.
2013-02-28 | GSE36115 | GEO
Project description:Whole genome sequencing (WGS) of tongue cancer samples and cell line was performed to identify the fusion gene translocation breakpoint. WGS raw data was aligned to human reference genome (GRCh38.p12) using BWA-MEM (v0.7.17). The BAM files generated were further analysed using SvABA (v1.1.3) tool to identify translocation breakpoints. The translocation breakpoints were annotated using custom scripts, using the reference GENCODE GTF (v30). The fusion breakpoints identified in the SvABA analysis were additionally confirmed using MANTA tool (v1.6.0).
2024-02-17 | E-MTAB-12534 | biostudies-arrayexpress
Project description:We used a Drosophila melanogaster line (a "double balancer") carrying balancer chromosomes for both the second (CyO) and third (TM3) chromosomes. We crossed the double balancer to an isogenic wild-type "virginizer" line to obtain trans-heterozygous adults from the F1 generation. Whole-genome sequencing and mate pair sequencing were used to identify Single Nucleotide Variants (SNVs) and Structural Variants (SVs) on both chromosomes.
2019-05-02 | E-MTAB-7510 | biostudies-arrayexpress
Project description:Characterization of copy number alterations and unbalanced breakpoints in human esophageal squamous cell carcinoma cell lines by array-based comparative genomic hybridization. Six cell lines
2013-02-28 | E-GEOD-36115 | biostudies-arrayexpress
Project description:In Drosophila, X chromosome dosage compensation requires the male-specific lethal (MSL) complex, which associates with actively transcribed genes on the single male X chromosome to upregulate transcription approximately 2-fold. We found that on the male X chromosome, or when MSL complex is ectopically localized to an autosome, histone H3K36 trimethylation (H3K36me3) is a strong predictor of MSL binding. We isolated mutants lacking Set2, the H3K36me3 methyltransferase, and found that Set2 is an essential gene in both sexes of Drosophila. In set2 mutant males, MSL complex maintains X specificity but exhibits reduced binding to target genes. Furthermore, recombinant MSL3 protein preferentially binds nucleosomes marked by H3K36me3 in vitro. Our results support a model in which MSL complex uses high-affinity sites to initially recognize the X chromosome and then associates with many of its targets through sequence-independent features of transcribed genes. Keywords: ChIP-chip ChIP-chip experiments were performed on custom Nimblegen arrays (GPL5636). Each array contained 388,000 oligonucleotide probes covering all of the X and the 2L chromosomes, with a 100 bp resolution (50mer probes with 50 bp gaps). The design was based on FlyBase 3.2. For the superspreading experiments, an additional array was used that contains the entire X chromosome and 3R (GPL5660). MSL complex binding sites on both arrays are the same and signal on the 3R chromosome was at background level.
2007-09-20 | E-GEOD-8557 | biostudies-arrayexpress
Project description:We used a Drosophila melanogaster line (a "double balancer") carrying balancer chromosomes for both the second (CyO) and third (TM3) chromosomes, and crossed it to an isogenic wild-type "virginizer" line. Trans-heterozygous adults from the F1 generation were further crossed to the wild-type parental line to obtain the pool of N1 embryos. Allele-specific RNA-seq was used to measure changes in gene expression from both chromosomes.
2019-04-24 | E-MTAB-7511 | biostudies-arrayexpress