Comment[GEAAccession]	E-GEAD-356
MAGE-TAB Version	1.1
Investigation Title	Caste differences of gene expression in the brain in a bumble bee, Bombus ignitus
Experiment Description	The bumble bee, Bombus ignitus is a species of social insects in Hymenoptera with the reproductive division of labor. Females in this species differentiate to two castes: queens and workers. The former is specialized for reproduction, the latter is an infertile and engaged in brood care, defense of the nest and foraging. To explore the brain molecular mechanisms underlying the behavioral differentiation, gene expression in the brain were compared comprehensively between newly emerged queens and workers in B. ignitus. Each RNA sample was extracted from two brains, reverse-transcripted and then sequenced de novo at 100 bp read length with a paired end library by Illumine NOVAseq 6000. Five each sample of queens or workers from three different colonies were examined.
Experimental Design	development or differentiation design
Experimental Factor Name	caste	colony
Experimental Factor Type	caste	colony
Person Last Name	Yokoi
Person First Name	Kakeru
Person Affiliation	Division of Applied Genetics/Insect Genome Research and Engineering Unit, Institute of Agrobiological Sciences, The National Agriculture and Food Research Organization
Person Roles	submitter
Public Release Date	2021-04-30
Protocol Name	P-GEAD-432	P-GEAD-433	P-GEAD-434	P-GEAD-435	P-GEAD-436
Protocol Type	sample collection protocol	nucleic acid extraction protocol	nucleic acid library construction protocol	nucleic acid sequencing protocol	normalization data transformation protocol
Protocol Description	Commercially reared bumble bee (B. ignitus) colonies were kept in wooden boxes with transparent windows at the top and steel nets at the bottom at 28????????????????C in constant darkness. Bees were given ad libitum pollen kneaded with sugar solution (fructose and sucrose). Newly emerged workers in the colonies before male emergence and new queens emerged in the same colonies after male emergence were collected. Bees were collected from three experimental colonies. The heads of these 0-day-old workers and queens were dissected, and the whole brains were used as samples.	RNA was extracted from the tissue of two brains by a RNA isolation kit: ISOGEN (Nippongene, Tokyo, Japan). Homogenizations were conducted for each tissue using an electric automatic homogenizer. The extracted RNA was treated by DNase (RT Grade for Heat Stop, Nippongene) at 37 ????????????????C for 15 min and then mixed with stop solution at 70????????????????C during 10 min. The extracted RNA were qualified and quantified by using a spectrophotometer set at 230, 260, and 280 nm. Ten pairs (workers and queens) of RNA samples were prepared, and five sets of them were selected in good condition for RNAs.	The sequencing library is prepared by random fragmentation of the cDNA sample, followed by 5' and 3' adapter ligation. Adapter-ligated fragments are then PCR amplified and gel purified. A paired end library was constructed by TruSeq Stranded mRNA LT Sample Prep Kit as following TruSeq Stranded mRNA Sample Preparation Guide, Part #15031047 Rev. E.	Illumina NovaSeq 6000	Illumina adapter sequences were trimed and 100 > bp sequemces in law fastq data were removed by the Trimmomatic version 0.36. The sequencial quality control were performed by FastQC Version 0.11.6. Using the sequences and TSA contig (Accession no. ICPS01000001-ICPS01132255), abunce related data of each contig was calculated by RSEM bundeled with Trinity r20140717.
SDRF File	E-GEAD-356.sdrf.txt
Comment[AEExperimentType]	RNA-seq of coding RNA
Comment[BioProject]	PRJDB9797
Comment[Last Update Date]	2021-06-01