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| Status |
Public on Dec 29, 2018 |
| Title |
Aged_H2O_rep3 |
| Sample type |
SRA |
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| Source name |
Oenocyte
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| Organism |
Drosophila melanogaster |
| Characteristics |
developmental stage: 28 days after eclosion
treatment: Control, water
Sex: Female
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| Treatment protocol |
Flies were maintained on normal food until eclosion. Eclosed flies were collected and allowed to mate for 1 day before separating female and male. 20-25 females were collected in one food vial, allowing them to age under standard condition. For aging condition, flies were transferred to new food every 2 days. Prior to mRNA extraction,10mM Paraquat or water (control) was evenly distributed on standard food surface, let dry for 20 minutes, then flies were transferred on treatment food for 24 hours.
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| Growth protocol |
Flies were maintained at 25°C, 40% relative humidity and 12-hour light/dark. Adults were reared on agar-based diet with 0.8% cornmeal, 10% sugar, and 2.5% yeast
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| Extracted molecule |
total RNA |
| Extraction protocol |
Ribo-tag extraction was performed during 10:00-12:00 PM time period. Flies were frozen and ground in nitrogen liquid. The fly powder was further homogenized in a Dounce tissue grinder containing 5 mL of homogenization buffer (50mM Tris, pH 7.4, 100mM KCl, 12mM MgCl2, 1mM DTT, 1% NP-40, 400 units/ml RNAsin, 100ug/ml of cycloheximide, 1mg/ml heparin and Protease inhibitors) to generate a 3% weight/volume homogenate. The supernatant was first pre-cleaned using SureBeads (By Bio Rad, catalog number: 161-4023) and then incubated with 15ul of anti-FLAG antibody (Sigma-Aldrich, St. Louis, MO, catalog number: F1804) overnight (about 19 hours) at 4 0C. The antibody/lysate mixture lysate was then incubated with SureBeads for 3 hours at 4 0C. Ribosome-bound RNA was purified using Qiagen RNeasy micro plus kit (Qiagen, Germantown MD).
RNA-seq libraries were constructed using 300 ng of total RNA and NEBNext Ultra Directional RNA Library Prep Kit for Illumina (New England Biolabs, Ipswich MA). Poly(A) mRNA (200bp) was obtained and double-stranded cDNA was synthesized according to company manual. Each library was ligated with a NEBNext Adaptor and barcoded with an adaptor-specific index. Libraries were pooled in equal concentrations. The multiplexed libraries were sequenced using Illumina HiSeq 3000 and single-end 50 bp reads format.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 3000 |
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| Data processing |
Base calls performed by Illumina HiSeq 3000 Real-Time Analysis software RTA2
Galaxy-Tophat2: Mapping the reads against a reference genome
Galaxy-Cufflinks: Reconstructing Transcripts
Galaxy-Cuffmerge: Merge together several Cufflinks assemblies
Galaxy-Cuffdiff: Finding significantly differentially expressed genes based on Cuffmerge
Genome_build: Aug. 2014 (BDGP R6 + ISO1 MT/dm6)
Supplementary_files_format_and_content: Average FPKM values for treatment groups, each group contains three replicates, significant changes are indicated as "yes" or "no"
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| Submission date |
Mar 21, 2018 |
| Last update date |
Dec 29, 2018 |
| Contact name |
Kerui Huang |
| E-mail(s) |
[email protected]
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| Phone |
515-294-3842
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| Organization name |
Iowa State University
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| Department |
Genetics and Genomics
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| Lab |
Bai Lab
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| Street address |
2437 Pammel Drive
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| City |
Ames |
| State/province |
IA |
| ZIP/Postal code |
50011 |
| Country |
USA |
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| Platform ID |
GPL23323 |
| Series (1) |
| GSE112146 |
Ribo-tag translatomic profiling of Drosophila oenocyte reveals down-regulation of peroxisome and mitochondria biogenesis under aging and oxidative stress |
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| Relations |
| BioSample |
SAMN08765830 |
| SRA |
SRX3828061 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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