RNA-Seq Workshop 2015 Project Proposal Guidelines
Experiment and Dataset Specifications
RNA-Seq experimental projects will be considered for either differential gene expression (mRNA transcript abundance), or for transcriptome sequencing and genome annotation. All experiments must work with a genome with a published sequence and annotations. You may propose to develop a new dataset or use an existing one, for example available in SRA.
Funding for new datasets will include Illumina RNA-Seq library preparation and sequencing costs for 2 biological replicates of 2 control vs. experimental or over 2 time points (total of 4 RNA preparations) for differential expression or 2 biological replicates for transcriptome sequencing.
Existing datasets may be single or paired-end Illumina data in FASTQ format. You must own the data or have permission to use it and make it freely available.
Proposal Specifications
Narrative is limited to 5 pages, 12-point Times New Roman font, with 1-inch margins, single spaced text, and one line space between each paragraph.
Your proposal should be organized into the following sections and each section should include responses to the specific questions within each section:
- Proposed Experiment or Existing Dataset
What is your experiment or dataset? What is the importance and relevance? What are your research questions and hypotheses? What tissue(s) or experiment/control conditions or time points will be (were) used, and why?
- Personal and Institutional Context
How does the experiment/dataset relate to and build on your own research experience? What other faculty members will be involved in the project. How does the experiment/dataset relate to research interests and expertise at your institution? What resources are available at your institution to leverage student research with the dataset – such as follow up cloning or qRT-PCR experiments?
- Instructional Context and Pedagogy
In what setting(s) – independent or class-based – and what specific class(es) will the dataset be used during the 2015-16 school year? How many students will be involved and what will be the duration of their involvement? In what ways will students be involved with the project – such as analyzing the primary data or doing follow-up experiments? How will the data be partitioned between student researchers or teams? How will the RNA-Seq analysis be incorporated into a particular course or sequence to stimulate concept development and integration?
- Evaluation and Broader Impacts
How will the student research products and the impact of their experience be evaluated? What data products or publishable results are expected? What opportunities do you envision for student co-authorship and presentation? How will student research on NGS analysis be supported in the future at your institution? How will you share your expertise in RNA-Seq analysis with other faculty at your institution? How will participation in this project impact instructional pedagogy at your institution? How do you intend to disseminate the data and knowledge gained? How could other institutions collaborate to analyze your dataset?
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