LoBase is a database of putative mature microRNAs (miRs) from the spiny lobster, Panulirus interruptus. It was generated by deep sequencing 13 small RNA libraries comprising over 90 million mappable reads. The majority of entries were mapped to miRBase; however, a small fraction was mapped to predicted hairpins in arthropod genomes but not found in miRBase.

Spiny Lobster miRnome
In total, 1,618 unique putative lobster miR sequences can be grouped into 669 mir families, e.g. the let-7 family. The number of unique members within a family ranged from 1 to 61. Some of the family members may represent edited versions of others. In the majority of cases only one or a few family members were predominantly expressed; the remaining members were expressed at trace levels, e.g. a summed total of 5 reads observed for 7 animals. Additionally, some families contained a single entity that was expressed at trace levels. Nevertheless, all sequences were included here regardless of their expression levels.

Nomenclature
Putative spiny lobster miRs were designated pint-mirs, for Panulirus interruptus. The usual 3 letter species designation could not be used because pin-mir was already assigned to the species Phytophthora infestans. Each pint-miR was named according to its mapped miRBase sequence. For example, if the pint-mir mapped to dme-let-7 in miRBase, then it was named pint-let-7; if another unique pint-miR sequence mapped to dre-let-7c-1 in miRBase, then it was also named pint-let-7. Multiple unique sequences with the same name were classified as a family. Unique sequences in a family were simply designated by a lower case letter(s) after the family name. For example, there were 22 members in the let-7 family and they were named pint-let-7-a through pint-let-7-v. The lower case letters are not meant to imply orthological relationships, and any similarity in lower case letters across species is coincidental. The lower case letters do not provide information on genomic organization; nothing is known about the genomic organization of these putative pint-miRs. Unfortunately, the putative pint-miRs cannot be mapped to the P. interruptus genome because it has not been sequenced. The 94 putative pint-miRs that did not map to miRBase were named according to their read ID.

Database Organization
A complete list of putative pint-miRs mapped to miRBase can be viewed by clicking the “pint-miRs in miRbase” link on the home page. A complete list of putative pint-miRs not mapped to miRBase, but mapped to arthropod genomic sequences with the propensity to form hairpins, can be viewed by clicking the “pint-miRs not in miRBase” link on the home page. The data were obtained from experiments listed under the project menu. The projects show the number of reads for each putative pint-miR in a given experiment. Users can download the project data as Excel spreadsheets. Users can also search the database by miR name. If you make use of these data, please cite the database and the manuscripts associated with the projects.

Support
This work was supported by NSF Grant 1456971, as well as the Brains & Behavior and the Molecular Basis of Disease programs at Georgia State University.

Disclaimer
The data contained in LoBase are for academic research only. In no event will any member of the research team be liable to any party for direct, indirect, special, incidental, or consequential damages arising out of the use of LoBase.