Pilot Award RFP

Dear INBRE & IDeA institution investigators,

We invite you to apply for an NM-INBRE Sequencing and Bioinformatics Core (SBC) pilot project award valued at approximately $5k – $10k to drive your research, publications and grants!

DEADLINE: Every 2nd Sunday of the month by 11:59pm.

  • Email proposal to inbre@ncgr.org with “Proposal for NM-INBRE SBC Pilot Award RFP” in the subject line.
  • You will be notified once your proposal has been received within 3-business days. If not, please inquire.

APPLICATION INSTRUCTIONS: Please submit a ½ to 1 page proposal that includes the answers to these questions below. Please ensure your proposal is standalone.  (Your email is not considered part of your proposal and may not be reviewed.)

  1. experimental design
  2. NM-INBRE thematic area it applies to.
  3. Description and goals of your project.
  4. Biological relevance.
  5. Download and fill in the fillable metadata form, save and include with your submission. This is a fillable PDF form.


  1. Proposals from ‘non’ NM-INBRE investigators will require a co-contribution to foster state, regional and national INBRE collaborations.
  2. The award expires if data are not received within 3 months of award date.
  3. Past winners may apply, but new applicants have priority if all other factors are equal.
  4. On any material presented or published based on this work, acknowledgement of:
    • Funding provided by the NM-INBRE Sequencing and Bioinformatics Core (SBC) at NCGR through NIGMS IDe-Award P20GM103451.
    • NM-INBRE SBC staff supporting the project and inclusion as co-authors. We will review and write sections of posters and papers.

Please let us know if you have any questions. 

We look forward to your proposal!


Faye D. Schilkey

Director, Strategic Projects & NM-INBRE Sequencing & Bioinformatics Core

Advanced Bioinformatics Center

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


All sequencing and/or bioinformatics projects are eligible.  Suggestions are provided below.

1) Bioinformatics only

  • BYOD: Bring your own next generation sequencing data and we will provide bioinformatics. 

2) Draft de novo genome or transcriptome assembly

  • Pacbio only sequencing and assembly
  • Illumina only assembly
  • Pacbio/Illumina/etc hybrid assembly approaches

3) 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

4) 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.

5) 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.

6) Custom 

An experiment that falls out of the above categories is fine and welcome.  This may require an additional financial contribution from the awardee but can evolve the award from a pilot to a robust experiment.