|
| Status |
Public on Nov 16, 2020 |
| Title |
03_EQ3 |
| Sample type |
SRA |
| |
|
| Source name |
Whole larvae_Early instar larvae_Queen destined
|
| Organism |
Bombus terrestris audax |
| Characteristics |
developmental stage: Early instar larvae
caste fate: Queen destined
Sex: female
tissue: whole larvae
|
| Growth protocol |
Queen-destined and Worker-destined female larvae were harvested from eight Bombus terrestris colonies. These were separated into early-instar queen-destined larvae from the first and second larval instars (EQ), early-instar worker destined larvae from the first and second larval instars (EW) , mid-instar queen-destined larvae from the third larval instar (MQ), mid-instar worker-destined larvae from the third larval instar (MW), late-instar queen-destined larvae from the fourth larval instar (LQ), late-instar queen-destined larvae from the fourth larval instar (LQ) .
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TotalRNA was extracted from each larva using Tri-reagent (Thermofisher Scientific) according to the manusfacturers protocol. The RNA was then dnase treated with the TURBO DNAfree kit (Thermofisher Scientific) to remove any DNA contamination.
standard mRNA-seq conducted by The Genome Analysis Centre (Norwich, UK) on an Illumina HiSeq 2500 sequences using Illumina TruSeq adapters
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Reads were filtered and only those which did not contain Ns, adapter sequences and did not have low sequence complexity (dinucleotide motifs constituting more than 70% of read length, single nucleotide motifs constituting more than 50% of read length) were included in further analysis (on average 93% of total number of reads across samples)
For comparison purposes, the reads in every sample were resampled to a fixed total (the method is called subsampling normalization)
Reads mapped to the Bombus terrestris genome (Bter_1.0, RefSeq assembly accession: GCF_000214255.1) using PatMan (Prüfer et al. 2008), full length, one mismatch allowed.
The expression levels were obtained as indicated in Mortazavi et al. 2008
The differential expression was determined using confidence intervals on replicates. The DE amplitude was calculated using offset fold change, with offset=20
Genome_build: Bter_1.0 (https://www.ncbi.nlm.nih.gov/assembly/294348)
Supplementary_files_format_and_content: csv file containing normalized expression levels for features (genes and novel transcripts) designated by feature-ids of format Accession.version_start-position-on-sequence_stop-position-on-sequence. Example: NC_015762.1_10000432_10107258
|
| |
|
| Submission date |
Dec 01, 2016 |
| Last update date |
Nov 16, 2020 |
| Contact name |
Anders M. Wirén |
| E-mail(s) |
anders.wiren@regionorebrolan.se
|
| Organization name |
Region Orebro lan
|
| Department |
Clinical research centre
|
| Lab |
Clinical Epidemiology and Biostatistics
|
| Street address |
Sodra Grev Rosengatan 42b
|
| City |
Orebro |
| ZIP/Postal code |
SE-701 85 |
| Country |
Sweden |
| |
|
| Platform ID |
GPL22726 |
| Series (1) |
| GSE90751 |
Evolution and molecular basis of caste differentiation in bees |
|
| Relations |
| BioSample |
SAMN06093835 |
| SRA |
SRX2388505 |
