|
| Status |
Public on Dec 19, 2016 |
| Title |
merged_N2-2 |
| Sample type |
SRA |
| |
|
| Source name |
Whole animal
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
strain: N2 wild type
Stage: young non gravid adult hermaphrodite
diet: OP50 food
|
| Treatment protocol |
Animals (N2 and hyl-2) were fed a glucose-supplemented diet. Glucose (Sigma) solution is spread evenly, fully covering the entire plate, and allowed to dry before being seeded with bacteria (OP50, HT115 or appropriate RNAi strain).
|
| Growth protocol |
The wild-type Bristol (N2) and hyl-2(tm2031) strains were cultured using NGM plates seeded with E. coli (OP50 or HT115) and raised at 20ºC. To obtain animals of the specified stage of development for each experiment as noted below, one-day old adult hermaphrodites were allowed to lay eggs on a plate (1-2 hours), and anatomical markers such as gonad morphology and time post molting stage were used to identify the developmental stage of the subsequent offspring.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
4 volumes of Trizol per volume of animals were added. The tubes were immediately frozen in liquid nitrogen, thawed and briefly vortexed; this step was repeated and then followed by a 5-minute incubation at room temperature. To each tube 0.2 ml of chloroform per 1 ml of Trizol was added, mixed gently, for 15 seconds, incubated at room temperature for 2-3 minutes, and then centrifuged at 12,000g for 15 minutes at 4ºC. The colorless upper phase was transferred to an RNase free tube. RNA was then purified using an Ambion PureLink RNA Mini Kit (Cat#12183018A). Following RNA purification, the RNA was treated with DNase I (Life Technologies Cat# 12185010), quantified using a NanoDrop Spectrophotometer and stored at -80ºC.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
Used Tophat and Bowtie for read alignment onto Caenorhabditis elegans reference genome and Cufflinks for obtaining the FPKMs and assessment of significance of fold change
Genome_build: C. elegans genome build WS195
Supplementary_files_format_and_content: Tab-delimited file (opens in Excel); FPKMs for wild-type Bristol (N2), hyl-2(tm2031), glucose-fed N2, and glucose-fed hyl-2(tm2031)
|
| |
|
| Submission date |
Jun 29, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Rajeev K. Azad |
| Organization name |
University of North Texas
|
| Street address |
1155 Union Circle #305220
|
| City |
Denton |
| State/province |
Texas |
| ZIP/Postal code |
76210 |
| Country |
USA |
| |
|
| Platform ID |
GPL13657 |
| Series (1) |
| GSE83887 |
Glucose or Altered Ceramide Biosynthesis Mediate Oxygen Deprivation Sensitivity Through Novel Pathways Revealed by Transcriptome Analysis in Caenorhabditis elegans |
|
| Relations |
| BioSample |
SAMN05332096 |
| SRA |
SRX1889667 |
