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Sample GSM5255776 Query DataSets for GSM5255776
Status Public on Jun 06, 2023
Title ovary_R_TP2G_rep3
Sample type SRA
Source name ovary
Organism Bombus terrestris
Characteristics tissue: ovary
treatment: removal (R), eggs removed
time point: time point 2 (TP2G), after 60% of the members of the cohort had died
biological replicate: 3
Treatment protocol Egg removal (R) treatment (to increase the costs of reproduction) and an egg removal and replacement (C) treatment (to control for the effects of disturbance caused by egg removal).
Growth protocol Bumble bee colonies were maintained under standard conditions. See the publication for further details.
Extracted molecule total RNA
Extraction protocol Bumble bee queens were flash-frozen in liquid nitrogen and stored at -80oC. Queens were then defrosted and the brain, fat body and ovaries were dissected out, flash-frozen in liquid nitrogen, and stored at -80oC. Each sample (one tissue from a single queen) was then ground in liquid nitrogen using a micropestle with the resulting powder resuspended in Tri-reagent (Sigma-Aldrich, UK). RNA was extracted using the Direct-zolTM RNA extraction kit (Zymo Research, USA) according to the manufacturer's protocol. An additional DNase treatment was performed using TurboTM DNA-free kit (Thermo Fisher Scientific, UK), according to the manufacturer's protocol.
Illumina TruSeq stranded mRNA-seq libraries constructed by Edinburgh Genomics (Edinburgh, UK)
Library strategy RNA-Seq
Library source transcriptomic
Library selection cDNA
Instrument model Illumina NovaSeq 6000
Description NER0008751_obj1_exp1_ovary_all_expressed_genes.csv
Data processing Sequencing reads were pseudoaligned to the Bombus terrestris transcriptome using Kallisto v0.46.1 with parameter --rf-stranded
Estimated transcript counts were summarised per gene in R v4.0.1 using the tximport package v1.16.1 with parameter type="kallisto"
Differential expression analysis was conducted in R v4.0.1 using the DESeq2 package v1.28.1, with technical replicates (sequencing the same library on different lanes of the sequencing machine) collapsed using the collapseReplicates() function.
Genome_build: Bombus_terrestris.Bter_1.0.cdna.all.fa
Supplementary_files_format_and_content: CSV file with normalized abundance measurements from DESeq2 for all genes expressed in brain
CSV file with normalized abundance measurements from DESeq2 for all genes expressed in fat body (Represents the 22 samples used for the final analysis, as 2 samples did not meet our threshold for the number of reads pseudoaligned to the Bombus terrestris transcriptome with Kallisto. The 2 excluded samples had large numbers of bee virus reads present.)
CSV file with normalized abundance measurements from DESeq2 for all genes expressed in ovary
Submission date Apr 20, 2021
Last update date Jun 06, 2023
Contact name David C. Prince
Organization name University of East Anglia
Street address Norwich Research Park
City Norwich
ZIP/Postal code NR4 7TJ
Country United Kingdom
Platform ID GPL30019
Series (1)
GSE172422 Costs of reproduction and their effect on age-related gene expression in Bombus terrestris queens
BioSample SAMN18810773
SRA SRX10644394

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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