Project description:Comparison between germline (blood) and microdissected bladder tumors to determine allelic imbalances. The GeneChip® Mapping 10K Early Access Array Affymetrix, Santa Clara, CA was used to determine the number of heterozygous SNPs in DNA from blood compared to the number of heterozygous SNPs in DNA from tumor in the same patient. Keywords: repeat sample
Project description:A 10K cDNA microarray was used to compare granulocyte RNA from one ATMDS patient to pooled granulocyte RNA from 7 healthy controls. Keywords: repeat sample
Project description:A 10K cDNA microarray was used to compare neutrophil RNA from 21 MDS patient and 2 AML patients to pooled neutrophil RNA from 7 healthy controls. Keywords: repeat sample
Project description:Labeled organ cDNA samples from six organs were hybridized on one glass slide with identical conditions. The hybridizations were repeated for 19 times with 4 biological replications each with 5 technical replications. Keywords: repeat sample
Project description:A particularly promising approach for engineering more precise TALE proteins is to better understand non-canonical RVDs. The RVD repertoire employed by Xanthomonas extends well beyond just the four canonical RVD types, and natural TALE repeat arrays often utilize serial combinations of both canonical and non-canonical RVDs in a manner which is not fully understood. Attempts to characterize these non-canonical RVDs have utilized various approaches, in terms of both TALE design and experimental method. Some studies have considered just TALEs of particular biological relevance, others have looked at large numbers of different RVDs within a fixed repeat-array-context, and still others have designed custom TALEs to address hypotheses about optimal RVD positioning within the repeat array. Methods for inferring the DNA binding activity of these TALEs have included sequencing of cleaved DNA fragments from TALE-nuclease fusions; ELISA assays for TALE-oligonucleotide binding; reporter assays for TALEs’ transcriptional-activating effects; and in silico modeling. In this study we employ a novel “wholesale swap-out” approach to characterize 3 non-canonical RVDs for thymine and 4 non-canonical RVDs for guanine.
Project description:Affymetrix 10K SNP mapping arrays were used to profile 14 basal cell carcinomas (BCCs) with matched blood DNA samples. Loss of heterozygosity (LOH) and copy number abnormality (CNA) profiles were derived from each tumour-blood pair. Keywords: Genomic DNA on Affymetrix 10K SNP array
Project description:Commercial Atlantic halibut (Hippoglossus hippoglossus) farming is restricted by variable oocyte quality, slow growth, and early maturation of male fish. Maternally transferred components regulate early developmental processes; therefore, they have an effect on the future development of an embryo. We profiled components of the transcriptome involved in immune defence as well as germline and muscle development during early developmental stages: 8-cell embryos, germ ring stage, 10-somite stage, and hatched embryos using a 10k oligonucleotide array and quantitative real-time PCR to specifically identify transcripts useful as molecular markers of embryo quality.