|
| Status |
Public on Jun 06, 2023 |
| Title |
brain_R_TP2G_rep4 |
| Sample type |
SRA |
| |
|
| Source name |
brain
|
| Organism |
Bombus terrestris |
| Characteristics |
tissue: brain
treatment: removal (R), eggs removed
time point: time point 2 (TP2G), after 60% of the members of the cohort had died
biological replicate: 4
|
| 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_brain_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 |
|
| Relations |
| BioSample |
SAMN18810789 |
| SRA |
SRX10644348 |
