|
| Status |
Public on Jul 20, 2017 |
| Title |
Dmoj_S1_LPHS |
| Sample type |
SRA |
| |
|
| Source name |
Whole larvae
|
| Organism |
Drosophila mojavensis |
| Characteristics |
developmental stage: Third instar
diet: low protein-high sugar
|
| Treatment protocol |
Third instar larvae were exposed for 24 hours to diets either high in protein relative to sugar (HPLS), diets with equal amounts of protein and sugar (EPS) , and diets low in protein but high in sugar (LPHS).
|
| Growth protocol |
All stocks, prior to use in experiments, were grown at room temperature (~25°C) in standard banana-opuntia media. To obtain larvae for development or transcriptomic studies, sexually mature adults were placed in yeasted egg collecting chambers (Genesee Scientific) and the embryos were allowed to develop to early third instar at which time they were transferred to the experimental diets for 24 hours.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Frozen samples were homogenized with Tri-Reagent using Teflon homogenizers and extracted using Direct-zolTM RNA MiniPrep extraction kit (Zymo Research) according to the manufacturer’s protocol. Three aliquots of each sample were taken, one to measure RNA concentration in NanoDrop (Thermo Scientific), another for analyses in a 1% agarose gel, and one for the sequencing core facility at LANGEBIO.
Libraries were prepared with TruSeq® RNA Sample Preparation Kit v2 (Illumina), selecting only polyA mRNAs and synthetizing double stranded cDNAs to attach to the Illumina adapters.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
100bp of insert
Dmoj_Diet_counts.txt
Dmoj2r_gene_exp.diff
|
| Data processing |
Transcriptome analysis was performed using the TopHat-Cufflinks pipeline (Trapnell et al., 2013).
Two replicates of each treatment (species/diets) were done, and paired-end reads were mapped with “bowtie2/tophat2”.
For D. arizonae, “cufflinks” and “cuffmerge” were applied to generate a GTF file, containing the locations of predicted transcripts.
Differential expression was calculated with “cuffdiff2”, using the BAM files that TopHat generated, with default settings and FDR ≤ 0.05 (Trapnell et al., 2013).
Genome_build: Reference genomes were indexed with “bowtie2-build”, using genome versions: r6.04 for D. melanogaster (FlyBase), first release for D. arizonae (Sanchez-Flores et al., 2016) and r1.3 for D. mojavensis (FlyBase).
Supplementary_files_format_and_content: There are two different processed files: "Diet_counts.txt" and "gene_exp.diff". "Diet_counts.txt" are tab-delimited text files that include count values of each samples (by species). "gene_exp.diff" are output files from cuffdiff2: this are tab delimited files that list the results of differential expression testing between samples for genes (comparisons between diets by species)(http://cole-trapnell-lab.github.io/cufflinks/cuffdiff/#cuffdiff-output-files).
|
| |
|
| Submission date |
Jul 20, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
NESTOR OCTAVIO NAZARIO-YEPIZ |
| E-mail(s) |
[email protected]
|
| Organization name |
LANGEBIO-CINVESTAV Irapuato
|
| Lab |
Lab-03
|
| Street address |
Km 9.6 Libramiento Norte Carretera León
|
| City |
Irapuato |
| State/province |
Guanajuato |
| ZIP/Postal code |
36821 |
| Country |
Mexico |
| |
|
| Platform ID |
GPL13311 |
| Series (1) |
| GSE101664 |
TRANSCRIPTIONAL RESPONSES OF ECOLOGICALLY DIVERSE DROSOPHILA SPECIES TO LARVAL DIETS DIFFERING IN RELATIVE SUGAR AND PROTEIN RATIOS |
|
| Relations |
| BioSample |
SAMN07372032 |
| SRA |
SRX3021607 |
