|
| Status |
Public on Jan 20, 2023 |
| Title |
dcap-1 (reduction of function), biological rep. 1 |
| Sample type |
RNA |
| |
|
| Source name |
dcap-1 reduction of function Caenorhabditis elegans
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: whole worm
strain: dcap-1(tm3163)
age: 9 days
developmental stage: adult
treatment: 10μg/ml FUDR
|
| Treatment protocol |
Three populations of each strain were harvested from plates with M9 buffer, washed at least three times with M9 and their pellets were frozen at -80°C, until they were independently processed and analyzed.
|
| Growth protocol |
Age-synchronized wild-type (N2) and dcap-1(tm3163) worms, grown at 20°C on OP50 bacteria in the presence of 10μg/ml 5-fluoro-2’-deoxyuridine (FUDR) were collected at the 9th day of adulthood.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from frozen worm pellets (200-300 worms per sample) of each sample using NucleoSpin RNA XS kit (Macherey-Nagel). Quality and quantity of RNA samples were determined using Nanodrop 2000 Spectrophotometer (Thermo Scientific).
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNAs were prepared according to the standard Affymetrix protocol from 150ng total RNA (GeneChip 3' IVT PLUS Reagent Manual, 2000, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 μg of cRNA were hybridized for 16 hours at 45°C on GeneChip C.elegans Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the AffyGeneChip Scanner 7G
|
| Description |
Gene expression data from dcap-1 reduction of function samples
|
| Data processing |
Raw CEL files were background corrected, normalized and summarized using the RMA algorithm (PMID: 12582260) with Celegans_Ce_ENSG_21.0.0 (November 2016) as a custom Chip Description File (CDF) from the BrainArray project (PMID: 16284200). The Ensembl IDs were mapped to gene symbols using Ensembl BioMart and the Caenorhabditis elegans reference assembly WBcel235. Software versions: R v3.3.0, Bioconductor v3.3
RMA (Robust Multi-Array Average) signal intensity (PMID: 12582260)
|
| |
|
| Submission date |
Mar 30, 2022 |
| Last update date |
Jan 20, 2023 |
| Contact name |
Popi Syntichaki |
| E-mail(s) |
synticha@bioacademy.gr
|
| Organization name |
Biomedical Research Foundation of the Academy of Athens
|
| Department |
Center of Basic Research
|
| Street address |
Soranou tou Efessiou 4
|
| City |
Athens |
| State/province |
Papagou |
| ZIP/Postal code |
11527 |
| Country |
Greece |
| |
|
| Platform ID |
GPL32098 |
| Series (1) |
| GSE199807 |
Expression data from mid-aged decapping mutant C. elegans nematodes |
|
