Project description:Sex chromosomes and more particularely the X chromosomes are known to have a major effect on hybrid male sterility. In this experiment by making use of the reciprocal hybrids between D. simulans and D. sechellia, we are showing the effect of these chromosomes on gene expression in male hybrids Keywords: X chromosome, hybrid Testes from for days old individuals (D. simulans, D. sechellia, hybrid D. simulans female x D. sechellia male, hybrid D. sechellia female x D. simulans male) were dissected and RNA was extracted and hybridized along with a reference RNA from the whole body of 4 days old D. melanogaster male. Gene expression in hybrids were compared to parental gene expression in order to isolate misexpressed genes in each hybrids. In order to reveal the cross effect misexpressed genes in hybrids were compared to identify genes commonly misexpressed and genes genes misexpressed in only one hybrid.
Project description:Sex chromosomes and more particularely the X chromosomes are known to have a major effect on hybrid male sterility. In this experiment by making use of the reciprocal hybrids between D. simulans and D. sechellia, we are showing the effect of these chromosomes on gene expression in male hybrids Keywords: X chromosome, hybrid
Project description:Data from the VLA lyssavirus genotyping microarray. The array platform for this data is GEO accession GPL8066, and consists of 624 oligos representing two viral families. The data set itself consists of 14 arrays, 7 hybridised with RNA from mice brains infected with 7 genotypes of lyssaviruses, 1 hybridised with RNA from normal mouse brain, and 6 hybridised with RNA from coded samples consisting of infected mouse brains or control mouse brains. Keywords: Lyssavirus genotyping microarray
Project description:477 spring-type Brassica napus (canola) lines from a hybrid breeding programme were genotyped using the Brassica Infinium™ 60k genotyping array.
Project description:We adapted the widely used digestion of chromatin with micrococcal nuclease (MNase) followed by deep sequencing to the parasite Trypanosoma cruzi, which presents numerous singularities. In this work, we use the hybrid CL Brener strain carrying two set of chromosomes from two substantially different parental strains. The hybrid strain CL Brener is composed of the Esmeraldo-like and non Esmeraldo-like haplotypes. Additionally, part of the genome was not assembled into any of the haplotypes. Sometimes the community working in the field uses just one haplotype as reference genome for simplicity. In this work, we emphasize the importance of using its whole genome as a reference. Moreover, we extended our analysis to a clonal strain, Sylvio-X10.
Project description:By hybridizing mRNA to oligonucleotide arrays and searching for probes that are outliers in their probe set, we identify and genotype polymorhisms in two strains of yeast (BY, isogenic to S288C, and RM, a wild vineyard strain) and segregants from a cross between the two strains. We then use this mRNA based genotyping approach to study allele-specific expression in diploid hybrids from a cross between BY and RM. A 1:1 mixture of BY and RM parental mRNA is created and hybridized to arrays as a control in these allele-specific expression experiments. The S. cerevisiae strains BY4716, an S288C derivative, and RM11-1a, a haploid Bb32(3) derivative, are described elsewhere (Brem et al. 2002, Yvert et al. 2003). We grew cultures to 10e7 cells/mL in shake flasks at 175 rpm at 300 C in synthetic C medium. We followed the standard Affymetrix protocol for preparation of RNA samples and for hybridization of the samples to Affymetrix YGS98 expression arrays. In total, three cultures of the BY strain, three cultures of the RM strain, one culture of each of the two haploid segregants and the two diploid segregants hybrids, three cultures of the BY-BY hybrid, three cultures of the RM-RM hybrid, and six cultures of the BY-RM hybrid were analyzed. Values calculated using the method described by Zhang et al. (Nat Biotechnol. 21, 818-821). The results are part of Ronald et al. (2005) describing a novel use of oligonucleotide expression arrays to perform genotyping. This method requires the use of individual probe signals, rather than the overall probeset value as is produced by analysis programs such as MAS or RMA.