|
| Status |
Public on Dec 11, 2015 |
| Title |
Cry11Aa LC50 0Hr replicate 2 |
| Sample type |
SRA |
| |
|
| Source name |
intestine
|
| Organism |
Aedes aegypti |
| Characteristics |
developmental stage: 4th instar
breed: IBT-UNAM
tissue: intestine
timepoint: 0 hr
|
| Treatment protocol |
Larvae were fed with a LC50 of purified Cry11Aa toxin crystals starting at same hour for each replicate. At 0,3,6,9 or 12 hours, dead and dying larvae were discarded and all others dissected to extract intestinal tissue
|
| Growth protocol |
Mosquito larvae were reared in controlled temperature and humidity, fed with yeast diet, until 4th instar
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Total RNA was isolated by TRIzol reagent, treated with DNAseI, and purified by RNeasy columns
PolyA RNA cDNA library was prepared with Illumina TruSeq RNA Sample Preparation Kit
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina Genome Analyzer IIx |
| |
|
| Data processing |
Reads were checked for quality with FastQC utility and trimmed to 72 bp if necessary to remove adapter and low quality ends using Fastx trimmer
Reads were aligned to Aedes aegypti transcripts v 3.2 with TopHat2 v2.0.12 in Transcriptome mode with the following parameters: -N 2 -r 150 --mate-std-dev 50
Reads counts were summarized using HTSeq-Count v0.5.4p5 with the following parameters: -m intersection-nonempty -s no -t gene -i gene_id using Aaegl3.2 basefeatures.gtf
A count table for all samples was derived from HTSeq-Count outputs
Differential expression predictions were determined with EdgeR v3.6.8 and DESeq2 v1.4.5, both in GLM mode using treatment tim and biological replicate in model design.
Genome_build: AaegL3.2
Supplementary_files_format_and_content: For each sample, data files contain tab separated gene ID, as identified in Vectorbase Database, counts summarized by HTSeq-Count, and normalized abundance from DEseq2 and EdgeR.
|
| |
|
| Submission date |
Nov 06, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Pablo Emiliano Canton |
| E-mail(s) |
pemiliano.canton@gmail.com
|
| Phone |
001525554070301
|
| Organization name |
University of Florida
|
| Department |
Entomology and Nematology
|
| Lab |
Bonning
|
| Street address |
Natural Area Dr.
|
| City |
Gainesville |
| State/province |
Florida |
| ZIP/Postal code |
32611 |
| Country |
USA |
| |
|
| Platform ID |
GPL14869 |
| Series (1) |
| GSE74785 |
Aedes aegypti Cry11Aa intoxication curve transcriptome |
|
| Relations |
| BioSample |
SAMN04232060 |
| SRA |
SRX1411067 |
