Genetic variation and function of body axis determinants in midges and other flies

Scope of Work: The project entitled “Genetic variation and function of body axis determinants in midges and other flies” represents a collaboration between the Schmidt-Ott lab at the University of Chicago and the Blythe lab at Northwestern University. The scope of work that will be partly or entirely the responsibility of the Blythe lab will be: 1) To provide expertise, advice, and training in methodologies for sample preparation of insect embryos for high-throughput sequencing data generation using ChIP-seq and ATAC-seq approaches. Although the Blythe lab’s expertise on insect embryos is limited to the species Drosophila melanogaster, it is anticipated that the additional species described in the proposed research program will be similar in terms of the parameters critical for success of this program. Schmidt-Ott is a world expert in the biology of the additional insect species to be studied in this proposal and it is anticipated that through collaboration, suitable experimental conditions will be found. 2) To manage and coordinate sample submission and successful sequencing of samples generated to the NUSeq core facility. Samples generated in the Schmidt-Ott lab will be submitted to NUSeq for high throughput sequencing under the advisement of Dr. Blythe. The Blythe lab may further provide additional resources for monitoring quality of generated samples including quantification through the lab’s Qubit Fluorometer, or fragment size analysis by the lab’s Agilent TapeStation (pending purchase approval). The role of the Blythe lab will also include cost-benefit analysis for determining optimal library pooling and sequencing depth as determined empirically from pilot experiments. 3) To establish an analysis pipeline for sequenced samples to generate standard genomics datasets and to interpret biological effects of the experimental treatments. The Blythe lab has established pipelines for analysis of similar datatypes generated from Drosophila melanogaster. Unlike Drosophila, however, the additional species included in this proposal have relatively new genome assemblies and annotations. While the Blythe lab is not currently equipped to complete or advance genome assembly/annotation efforts (this is handled by Schmidt-Ott’s additional collaborators), the Blythe lab is capable of integrating alternative genome assemblies into existing analysis pipelines and adapting them as necessary to the differences between levels of refinement of current assemblies. 4) To train members of the Schmidt-Ott lab in the analysis of generated data. The Blythe Lab will provide training in the analysis of high-throughput sequencing data to the end of meeting the stated goals in the research proposal. It is anticipated that following the initial training, that members of the Schmidt-Ott lab will perform the majority of analysis themselves, although Dr. Blythe will enthusiastically consult with those in the Schmidt-Ott lab who perform the analysis. Budgeting is therefore limited to 1) sample preparation and sequencing costs, in addition to data storage. 2) Dr. Blythe’s effort for training and advising.