Data Archive for "Identifying a developmental transition in honey bees using gene expression data"

This data archive contains gene expression data used in the following publication: Identifying a developmental transition in honey bees using gene expression data. Bryan C. Daniels, Ying Wang, Robert E. Page, Jr, and Gro V. Amdam. A preprint of the manuscript is available on biorxiv here: https://doi.org/10.1101/2022.11.03.514986 Code used in the publication is available here: https://github.com/Collective-Logic-Lab/landau A summary of data collection methods follows: The bee collection was conducted during March 18th to April 7th, 2016. Five strong wild type colonies were chosen as sources of newly emerging bees. Two small nuclear colonies with 9 frames in each were used as recipient colonies that had similar supplies of pollen and honey, and similar numbers of brood and adult bees. The emerging frames from source colonies were put into incubator (37 degrees C) and about 200 newly emerged bees were collected, marked in a color on the bee thoraxes and distributed evenly to the recipient colonies. This procedure was repeated for three consecutive days. About 600 newly emerged bees were introduced in the recipient colonies from March 19th to March 21st, 2016. Ten each of 1 day old, 3 day old, 5 day old, 10 day old and 15 day old bees from each recipient colony were collected in the following days. Therefore, there were total 20 sample bees for further experiment from two recipient colonies for each age. RNA was extracted from 16 randomly selected bees of each age using TRIZOL method. The quality of RNA was measured by Nanodrop and 260/280 was between 1.85-2.00, indicating good quality of RNA. RNA samples were sent to the University of Arizona Core lab for Nanostring analysis, a method to quantify the copy of RNA for the target genes. 94 genes were selected based on prior knowledge and the potential association between these genes, VG production, and social behavior. Genes were selected from the honey bee Apis mellifera assembly and gene annotation information at NCBI (https://www.ncbi.nlm.nih.gov). Genes were prioritized using a pragmatic approach. In brief, our strategy integrated information on a specific biological process (the nurse-forager transition) with information on genes that were suggestively, correlatively, or potentially causally involved. Thus, gene selection relied on a process of extensive literature review as well as interdisciplinary biological expertise. The gene prioritization was reviewed by three members of the interdisciplinary team (YW, GVA, and REP) to minimize operator biases. Four housekeeping genes, actin (GB17681), rp49 (GB10903), GAPDH (LOC410122) and RPS18 (LOC552726) were used for sample normalization. Finally, the vitellogenin (VG) protein was measured in the honey bee hemolymph.