VERMONT IMMUNOBIOL/INFECTIOUS DIS CTR: MICROARRAY & BIOINFORMATIC ANALYSIS CORE

这个子项目是众多研究子项目之一

This subproject is one of many research subprojects utilizing the resources provided by a Center grant funded by NIH/NCRR. The subproject and investigator (PI) may have received primary funding from another NIH source, and thus could be represented in other CRISP entries. The institution listed is for the Center, which is not necessarily the institution for the investigator. Summary (Table I) During the reporting period Core B provided substantive support for four VCII investigators and consulted with three others. Core B service was associated a publication, three manuscripts in preparation, and a submitted grant application. VCII projects discussed during our previous report have moved forward, new projects have begun, and conversations about potential projects have taken place. Table I: Core B Utilization. Chips refers to the number of GeneChips scanned by Core B. Hours refers to bioinformatics support. indicates that additional detail is provided below. Matrajt From our last progress report: "Nine arrays were processed for Dr. Matrajt, who was able to demonstrate that arrays provide an appropriate technique for a series of proposed experiments. Bioinformatics support (16.5 hours) included six meetings with Dr. Matrajt or her student, Ms. Pamela Lescault." The experiment was expanded to include a time series and six additional genotypes (a total of 54 chips). The analysis was expanded to include 5 chips from a time series made available by a colleague and a mixture model was developed (required to accommodate an association between genotype and the distribution of cells in samples between differentiated and undifferentiated states). The results have been presented at a conference and constituted a chapter of an MS thesis (Pamela Lescault). A manuscript is in preparation and a follow-up experiment is in progress. Delaney Preliminary analysis of a two-way design (genotype X treatment, 36 chips) was completed. Core B met twice with Dr. Delaney and his technician, Rodrigo Olarte, to discuss next steps. Rincon From our previous progress report: "Six arrays were processed for Dr. Rincon, which resulted in a submitted manuscript. Bioinformatics support (17 hours) included three meetings with Dr. Rincon or Dr. Dienz, her postdoctoral fellow." Dr. Dienz' manuscript is undergoing revision for resubmission. In the context of preliminary results for of an NIH grant application (now submitted) Core B consulted on use of publicly available (GEO) data and analyzed data made available by a colleague (laser capture microscopy samples from human samples, 66 chips). Teuscher From our previous progress report: "Thirty-eight arrays were processed for Dr. Teuscher and a manuscript is in preparation. Bioinformatics support (10.25 hours) included five meetings with Dr. Teuscher or his postdoctoral associate, Dr. Changming Lu." Dr. Lu's manuscript was accepted for publication. Core B is involved in analysis of protein concentration data (23 proteins, 42 samples, genotype X time X treatment design) that will be submitted for publication during April. Core B met three times regarding analysis of a tissue source X genotype X treatment design; a follow-up 6 chip experiment was performed and being analyzed. A 10 chip comparison in expression among genotypes is nearing the end of the analysis stage and is expected to be included in a manuscript. Services Core B supports: -Gene Expression Profiling -target preparation -eukaryotic and prokaryotic -single and double amplification -Nugen based target preps for low RNA targets, i.e., LCM , cell sorting -Hybridization and scanning -DNA Mapping target preparation -Exon Array target preparation -RNA Integrity assessment -Nucleic Acid quantification -RNA extraction assistance and training -SOP's established for all services offered -Analysis using -linear modeling -GO annotation -Permutation tests Scientific or technical changes include: -Purchased AB 7500 Fast Sequence Detection System allowing fast cycling real-time PCR for microarray target validation while increasing throughput -Optimized methods and developed protocols to quantify low recovery RNA from fluorescence- activated cell sorting -Development and optimization of methods for homogenization of challenging tissues for downstream molecular analysis ***Please see paper copy for figures and tables (would not reproduce here).***