Project description:Raw data of TMT-labeled proteome of Chinese breast cancers. Uploaded by Zhi-Ming Shao Lab, Fudan University Shanghai Cancer Center (FUSCC)
Project description:A High Density Rice Array (HDRA) was developed as an Affymetrix Custom GeneChip Array by the McCouch Rice Lab at Cornell University. The HDRA assays 700,000 SNPs, or approximately one SNP every 0.54 Kb across the rice genome (genome size = 380 Mb). It was designed to capture most of the haplotype variation observed in a discovery panel consisting of 16M SNPs (generated by sequencing 125 rice genomes at ~7X genome coverage) and to maximize the inclusion of non-synonymous SNPs. Six probes per SNP target were designed as 3 A-allele and 3 B-allele probes at offsets from center ranging from -6 to +6. A small fraction of SNPs have only 4 probes (2-A, 2-B). For all SNPs, the “A” allele is the reference allele (Os-Nipponbare-Reference-IRGSP-1.0 assembly). Additionally, we designed 23,656 x 25-bp probes complimentary to invariant regions of the genome that were used to normalize systematic differences between samples. An estimated 45% of HDRA SNPs map within genes, hitting all 39,045 unique, non-TE rice gene models (MSUv7 rice genome annotation, GFF3 file, Feb. 7, 2012, http://rice.plantbiology.msu.edu/), while 55% of SNPs map to intergenic regions. Non-synonymous are found in 91% of unique, non-TE gene models, and 57% of genic SNPs are distributed within exons, 36% within introns, 5% within 5’ UTRs and 2% within 3’ UTRs. Of the intergenic SNPs, 40% are located in putative regulatory regions within 2 Kb of a transcriptional start site.
Project description:Understanding gene function through forward genetic screens remains foundational to microbial genetics. Here, we describe the design and implementation of a multi-week course-based undergraduate research experience (CURE) embedded within a third-year Microbial Genetics course. In this CURE, students construct a high-density Tn5 transposon insertion library in Escherichia coli, challenge the library with bacteriophage P1, and use Transposon-Directed Insertion-site Sequencing (TraDIS) coupled with statistical analysis (edgeR) to identify genes required for phage propagation. Students perform transposome electroporation, phage infection assays, genomic DNA extraction, high-throughput sequencing data processing in Galaxy, differential insertion analysis, visualization in Artemis, and Gene Ontology enrichment analysis. The project integrates wet-lab microbiology, molecular genetics, and bioinformatics while modeling an authentic forward genetic screen. This CURE emphasizes experimental design, genome-wide functional analysis, statistical reasoning, and interpretation of large-scale sequencing data. The curriculum is adaptable to other bacterial species, phage systems, or selective pressures and provides a scalable framework for integrating authentic genomics research into upper-level microbiology courses.
Project description:After extraction with mild non-denaturing detergents, we affinity-purified 785 endogenously-tagged CEPs and then identified stably-associated polypeptides by precision mass spectrometry. The resulting high-quality physical interaction network, comprising most (77%) of all targeted CEPs, revealed hundreds of previously unknown heteromeric complexes. Lab Heads: Andrew Emili; andrew.emili@utoronto.ca ;Donnelly CCBR, University of Toronto, Toronto ON M5S 3E1, Canada Mohan Babu; mohan.babu@uregina.ca ;Research and Innovation Centre, University of Regina, SK S4S OA2, Canada