|
| Status |
Public on Sep 13, 2023 |
| Title |
Midgut, 10 minutes after feeding, replicate 4 |
| Sample type |
SRA |
| |
|
| Source name |
midgut
|
| Organism |
Schistocerca gregaria |
| Characteristics |
tissue: midgut
genotype: WT
treatment: 10 minutes after feeding
|
| Treatment protocol |
Animals were fed for 10 minutes ('10 minutes after feeding') or 2 hours ('2 hours after feeding'). Animals were dissected 10 minutes after removing the food. For the '24 hours after feeding' treatment food was removed and animals were dissected 24 hous later.
|
| Growth protocol |
Animals were kept at 30°C and RH 40-60% and were fed twice a day for one hour periods on cabbage (Brassica oleracea). Animals were kept in incubators, eggs were disinfected in ethanol and transferred to autoclaved soil to ensure that animals were gregarine-free (gut parasite).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNeasy lipid tissue extraction kit (Qiagen) according to the manufacturer’s protocol. An additional DNaseI treatment (Qiagen) was performed to remove potential genomic DNA contamination.
For Illumina® deep sequencing, mRNA was first purified from the total RNA mixture in every sample. From each sample, 1 μg of RNA was used to perform an Illumina® sequencing library preparation using the TruSeq® Stranded mRNA Library prep kit (Illumina®) according to the manufacturer's protocol.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Description |
Midgut, equal male/female ratio, day 5 of the 5th (final) nymphal stage, animals grown in a clean (gregarine-free) environment, each replicate contains tissues from 6 individuals
|
| Data processing |
Illumina® adapter sequences were trimmed from sequence reads at the 3’ end using Cutadapt (version 1.11)
Next, short sequencing reads were mapped to S. gregaria whole body transcriptome (2.3.3) (GenBank accession number GJPN000000000.1 ) using Bowtie2 (version 2.2.5).
Transcript abundance was quantified using the RSEM software package (RNA-seq by Expectation Maximization, version 1.2.31).
Mapped transcripts were annotated using Trinotate (http://trinotate.github.io). Transdecoder (http://transdecoder.github.io) was first used to translate the nucleotide sequences to their predicted best CDS. Next, all transcript sequences and their predicted CDS were used as query for BLAST in the annotated UniProtKB/Swiss-Prot databases. Standard parameters for BLAST were used, with BLAST e-value cut-off set at 1e-5.
Assembly: Sequence reads were mapped to an in-house S. gregaria whole body transcriptome (GenBank accession number GJPN000000000.1 ).
Supplementary files format and content: tab-delimited text files include gene_id, transcirpt_id(s), gene length, effective_length, expected_counts, TPM an FPKM for each sample
|
| |
|
| Submission date |
Mar 07, 2023 |
| Last update date |
Sep 13, 2023 |
| Contact name |
Laurentijn Tilleman |
| Organization name |
Ghent University
|
| Street address |
Ottergemsesteenweg 460
|
| City |
Gent |
| ZIP/Postal code |
9000 |
| Country |
Belgium |
| |
|
| Platform ID |
GPL33225 |
| Series (1) |
| GSE226871 |
Differential midgut transcriptomics comparing nutritional status reveals a crucial role for V-ATPase subunit a and Niemann-pick 1b protein in the digestive physiology of the desert locust. |
|
| Relations |
| BioSample |
SAMN33619996 |
| SRA |
SRX19582360 |
