|
| Status |
Public on Oct 19, 2023 |
| Title |
T. ni, fat body, TSA, rep3 [22044R-01-09_S79] |
| Sample type |
SRA |
| |
|
| Source name |
fat body
|
| Organism |
Trichoplusia ni |
| Characteristics |
tissue: fat body
genotype: WT
treatment: TSA
|
| Treatment protocol |
For dietary treatments, the HDAC inhibitors SFN (70 mM) and TSA (330 µM) were solubilized in ethanol and aliquots were added to each well to cover the surface of the AD. The EtOH was fully evaporated for 8h at 20°C.
|
| Growth protocol |
Larvae were raised in 5 ml wells on a standard artificial diet (AD) appropriate for each species with antibiotics at 25°C and 50% humidity. Larvae developed in individual wells and were collected at approximately day 10.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Larvae from each experiment group were dissected to isolate fat body tissue. To obtain sufficient tissue, fat bodies from 3 – 5 individual larvae were pooled per replicate.
Total RNA was extracted from the tissue twice using Buffer A (50 mM sodium acetate pH 5.2, 10 mM EDTA, 1 % SDS) saturated phenol heated to 65 °C, followed by phenol/chloroform (1:1) extraction. Extracts were ethanol precipitated, resuspended in ddH2O and ethanol precipitated again.
Poly(A) selection was performed using the NEBNext Poly(A) mRNA Magnetic Isolation Module (New England Biolabs) following the manufacturer’s protocols. RNA-seq libraries were generated using the NEBNext Ultra II RNA Library Prep Kit for Illumina (New England Biolabs) following manufacturer’s protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
| |
|
| Description |
Tni_raw_counts.txt
Tni_normalized_counts.txt
|
| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence with Trimmomatic (v0.39) using the following parameters: LEADING:5, TRAILING:5, MAXINFO:36:0.2, MINLEN:50.
T. ni reads were aligned to the T. ni Cornell-1 isolate genome (obtained from the T. ni Genome Database on 2022-05-25) and S. exigua reads were aligned to the S. exigua TB_SE_WUR_2020 isolate genome (WGS JACEFF01 obtained from the NCBI Genome Database on 2022-06-06) using HISAT2 (v2.2.1) with the default parameters.
featureCounts implemented in the Rsubread package (v2.12.2) was used to calculate read counts for each gene using the appropriate species-specific annotations.
Low-count genes (mean counts-per-million [CPM] across all samples > 10) were filtered and read counts were normalized using the trimmed mean of M-values (TMM) normalization method.
Assembly: T. ni Cornell-1 isolate (tn1)
Assembly: S. exigua TB_SE_WUR_2020 isolate (GCA_022117675.1)
Supplementary files format and content: tab-delimited text file includes raw counts for each sample
Supplementary files format and content: tab-delimited text file includes TMM-normalized CPM values for each sample
|
| |
|
| Submission date |
Jun 07, 2023 |
| Last update date |
Oct 19, 2023 |
| Contact name |
Dana J. Somers |
| E-mail(s) |
somersd@dickinson.edu
|
| Phone |
717-254-8131
|
| Organization name |
Dickinson College
|
| Department |
Biology
|
| Street address |
P.O. Box 1773
|
| City |
Carlisle |
| State/province |
PA |
| ZIP/Postal code |
17013 |
| Country |
USA |
| |
|
| Platform ID |
GPL29211 |
| Series (1) |
| GSE234351 |
Effect of sulforaphane on gene expression in Spodoptera exigua and Trichoplusia ni |
|
| Relations |
| BioSample |
SAMN35661655 |
| SRA |
SRX20624461 |
