Dear IDeA Institution Investigators,
We invite you to apply for an NM-INBRE SBC pilot project award valued at approximately $5k - $10k to drive your research, publications and grants!
APPLICATION INSTRUCTIONS: Please submit a ½ to 1 page proposal that includes the answers to these questions by deadline 11:59pm MST, April 30, 2017.
- Type of experimental design from the attached Appendix.
- NM-INBRE thematic area it applies to.
- Description and goals of your project.
- Biological relevance.
- ETA for your samples to arrive at NCGR.
- Download and fill in metadata accompaniment form and include with your submission.
- Proposals may require a co-contribution of funds to complete the experiment.
- The award expires if samples are not received within 3 months of award date.
- Please make sure your proposal is standalone. (Your email is not considered part of your proposal and will not be reviewed.)
- Past winners may apply, but new applicants have priority if all other factors are equal.
- To be efficient, NCGR will make the libraries for all awards.
- On any material presented or published based on this work, acknowledgement of:
- Funding provided by NM-INBRE through NIGMS IDe-Award P20GM103451.
- NM-INBRE SBC staff supporting the project to be included as co-authors.
Thank you and we look forward to working together!
Faye D. Schilkey
Director, Strategic Projects & NM-INBRE Sequencing & Bioinformatics Core
National Center for Genome Resources
2935 Rodeo Park Dr. East
Santa Fe, NM 87505
off: 505.995.4449 : fax: 505.995.4461 : www.nminbre.org : www.ncgr.org
Please fit your SBC pilot proposal into one of these experimental designs below.
1) Draft de novo genome or transcriptome assembly
- Pacbio only sequencing and assembly
- Illumina only assembly
- Pacbio/Illumina/454 hybrid assembly approaches
2) PacBio transcriptome or base modification detection.
- IsoSeq pilot: The Iso-Seq method provides reads that span entire transcript isoforms, from the 5' end to the 3' polyA-tail. It is now possible to directly sequence full-length transcripts ranging up to 10 kb. Determine a general survey your organisms transcript landscape with no assembly required!
- Base Modification Detection: Base modifications are important to the understanding of biological processes such as gene expression, host-pathogen interactions, DNA damage, and DNA repair. Find out more at http://www.pacificbiosciences.com/pdf/WP_Detecting_DNA_Base_Modifications_Using_SMRT_Sequencing.pdf
3) Illumina genomic sequencing and mutation detection.
Using a publically available reference (e.g. NCBI or Ensembl), this award provides DNA library prep, paired-end read coverage and mutation detection. Approximately 20-30x coverage of your genome is recommended.
4) Illumina RNA-seq or miRNA-seq and expression analysis.
Using a publically available reference (e.g. NCBI or Ensembl), this award provides RNA library preps, single-end reads, alignment, read-counts and differential expression analysis. For RNA-seq, an example would be 9 total RNA samples (a control and 2 treatments with 3 biological reps each) on one lane of 1x50nt to achieve approximately +/- 20M reads per sample. (Please indicate if non-coding RNA’s are of interest too.) For miRNA, an example would be 6 samples (2 conditions x 3 biological reps) on one lane of 1x50nt. Analysis includes annotating known miRNA sequences by aligning to miRBase and Rfam. Be clear on what your samples are and how they should be compared.
Customize your experiment based on one of the above with a de novo assembly, more samples, more sequencing, or another published technique. This may require co-financial contribution from the awardee but can evolve the award from a pilot to a robust experiment.