Viewing options:

Abstract
Full text
PDF (271KB)
Additional files

Associated material:

PubMed record

Related literature:

Articles citing this article
on BioMed Central
on Google Scholar
on ISI Web of Science
on PubMed Central
Other articles by authors
on Google Scholar

Weaver DB
Anzola JM
Evans JD
Reid JG
Reese JT
Childs KL
Zdobnov EM
Samanta MP
Miller J
Elsik CG

on PubMed

Weaver DB
Anzola JM
Evans JD
Reid JG
Reese JT
Childs KL
Zdobnov EM
Samanta MP
Miller J
Elsik CG
Related articles/pages
on Google

on Google Scholar

on PubMed

Tools:

Post to:

Research

Computational and transcriptional evidence for microRNAs in the honey bee genome

Daniel B Weaver^*¹ , Juan M Anzola^*² , Jay D Evans^*³ , Jeffrey G Reid^*⁴ , Justin T Reese² , Kevin L Childs²^,8 , Evgeny M Zdobnov⁵^,9 , Manoj P Samanta⁶ , Jonathan Miller⁷ and Christine G Elsik²

¹Bee Power, LP, Lynn Grove Road, 16481 CR 319, Navasota, TX 77868 USA

²Department of Animal Science, Texas A&M University, College Station, Texas 77843, USA

³Bee Research Laboratory, USDA-ARS, BARC-E, Beltsville, MD, USA

⁴WM Keck Center for Interdisciplinary BioScience Training, Houston, TX 77005, USA

⁵European Molecular Biology Laboratory, Meyerhofstr., Heidelberg, Germany

⁶Systemix Institute, Los Altos, CA 94024, USA

⁷Department of Biochemistry, Baylor College of Medicine, Houston, TX 77030, USA

⁸The Institute for Genome Research, Rockville, MD 20850, USA

⁹Department of Genetic Medicine and Development, University of Geneva Medical School (CMU), rue Michel-Servet 1, 1211 Geneva 4, Switzerland

author email corresponding author email* Contributed equally

Genome Biology 2007, 8:R97doi:10.1186/gb-2007-8-6-r97


Published:	1 June 2007

Subject areas: Molecular biology, Bioinformatics, Development, Genetics

Additional files

Additional data file 1:

Includes miR designation, the sequence of the putative mature honey bee miRNA, the sequences 110 bp up- and downstream of each mature miRNA candidate (putative precursor region), the genomic coordinates of each occurrence of mature and putative precursor miRNA sequences within the bee genome assembly release 4, whether the candidate miRNA is intergenic, intronic, or overlapping a CDS, the GC content of the GC content domain in which the miRNA is embedded (described in [15]), and folding energy.

Format: XLS Size: 45KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional data file 2:

Double strands of precursors are shown, with mature miRNA indicated as lower case embedded in the sense strand, which is otherwise uppercase. Note that reverse primers are shown in the 3' to 5' direction, to show alignment to the sense strand.

Format: XLS Size: 48KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional data file 3:

The ID column corresponds to gel lanes in part b of Additional data file 9. C_Tis a predetermined threshold at which fluorescence from PCR products exceeds background fluorescence.

Format: XLS Size: 37KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional data file 4:

Mean expression values for queen and worker honey bee tissue-specific samples.

Format: XLS Size: 29KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional data file 5:

Primers employed in expression analyses, and expression estimates for pooled samples.

Format: XLS Size: 28KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional data file 6:

The RNA sample from array B had a higher concentration of bee brain and thorax than the first.

Format: XLS Size: 17KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional data file 7:

There is a different worksheet containing the results of 10 replicates each, for honey bee and Drosophila. Each worksheet provides E-score, Bonferroni corrected E-score, and GO term.

Format: XLS Size: 88KB Download file

This file can be viewed with: Microsoft Excel Viewer

Additional data file 8:

Folded hairpins for precursors of novel honey bee miRNAs.

Format: PDF Size: 48KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 9:

Figure A shows a 15% PAGE separation of small-enriched RNAs from honey bee queen head, thorax, and abdomen, and worker head, thorax, and abdomen. RNA sized at 18-30 nt was excised from the gel and purified for qPCR as described in the text. The left lane shows a 10 nt RNA size marker, with the 10 nt band at bottom left. Figure B shows the size variation of PCR products generated from small-enriched RNA pools and candidate primers. Most products were approximately 75-90 bp in length. Alphanumeric label refers to sample ID as described in Additional data file 3.

Format: PDF Size: 66KB Download file

This file can be viewed with: Adobe Acrobat Reader

Additional data file 10:

Values indicate relative expressions levels as log₁₀scale, with SD for three sample replicates, as described in the text.

Format: PDF Size: 27KB Download file

This file can be viewed with: Adobe Acrobat Reader