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| Status |
Public on Oct 18, 2016 |
| Title |
worker_3pm_8 |
| Sample type |
SRA |
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| Source name |
active worker bees collected in the afternoon as they prepared to forage
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| Organism |
Apis mellifera |
| Characteristics |
sex type: worker
collection time: 3pm
tissue: mushroom body (dissected from brain)
colony: 2
pool: 1
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| Treatment protocol |
Behavioral observations and marking were used to identify active drones and workers
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| Growth protocol |
Three colonies used in these experiments was headed by a naturally mated queen (unrelated to each other), contained 8,000-10,000 workers and several hundred drones, and were maintained according to standard methods at the University of Illinois Bee Research Facility, Urbana, Illinois, USA
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| Extracted molecule |
total RNA |
| Extraction protocol |
Bees were flash frozen on liquid nitrogen, heads were incubated in RNAlater ICE, and mushroom bodies were dissected from the brain. Total RNA was extracted using Picopure RNA isolation kits and poly-adenylated RNA was enriched using Oligo(dT)25 dynabeads
Libraries were constructed using the NEXTflex Directional RNA-Seq Kit from Bioo Scientific
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Description |
s.2w34
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| Data processing |
Each pool of 8 samples was quantitated by qPCR and sequenced on one lane for 101 cycles from each end of the fragments on a HiSeq2000 using a TruSeq SBS sequencing kit version 3.
FastQ files were generated and demultiplexed with Casava 1.8.2
Each sample's pair of fastq files were run through trimmomatic 0.30 to first remove any remaining standard Illumina PE v3 adapters, then trim bases from both ends with quality scores below 28, and finally to remove individual reads shorter than 30 bp and their paired read, regardless of length (parameters ILLUMINACLIP:/home/apps/trimmomatic/trimmomatic-0.30/adapters/TruSeq3-PE.fa:2:30:10 TRAILING:28 LEADING:28 MINLEN:30)
Paired reads per samples were aligned to Amel 4.5 genome and OGS 3.2 gene models using Tophat2 2.0.10 with parameters --library-type fr-firststrand --mate-inner-dist 150 --mate-std-dev 40. Alignment bam files were sorted by read name using "samtools sort -n".
Fragment counts for each gene were obtained using htseq-count (htseq 0.5.4) with parameters -s reverse -m union -a 0 -t gene -i ID
Genome_build: Amel 4.5
Supplementary_files_format_and_content: tab-delimited text files of raw fragment counts per gene per sample were used directly in edgeR 3.4.2 for statistical analysis and thus are the "normalized" data.
Supplementary_files_format_and_content: Those identifiers are from Beebase.org's OGSv3.2, which is the official gene set for Apis mellifera genome assembly Amel_4.5. It is available for download from here:
http://hymenopteragenome.org/beebase/?q=download_sequences
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| Submission date |
Aug 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Amy Cash |
| E-mail(s) |
amycash@illinois.edu
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| Organization name |
University of Illinois
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| Department |
Biology
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| Lab |
Gene Robinson
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| Street address |
1206 W. Gregory Dr
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| City |
Urbana |
| State/province |
IL |
| ZIP/Postal code |
61801 |
| Country |
USA |
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| Platform ID |
GPL16097 |
| Series (1) |
| GSE85433 |
Transcriptomic Analysis of Instinctive and Learned Reward-Related Behaviors in Honey Bees |
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| Relations |
| BioSample |
SAMN05558761 |
| SRA |
SRX2011569 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2266865_2w34_GCCAAT_L001.Amel4.5_OGS3.2_counts.txt.gz |
58.1 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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