|
| Status |
Public on May 05, 2023 |
| Title |
Water treated N2 animals, Independent Trial 1 |
| Sample type |
RNA |
| |
|
| Source name |
C. elegans water
|
| Organism |
Caenorhabditis elegans |
| Characteristics |
tissue: Whole animal
genotype: Wild-type N2
age: 3 days after hacht, young adults
|
| Treatment protocol |
16-18 hours after haching L1 larvae were treated with 100 uM of each food colorant either Ponceau Red or Tartrazine in S. medium for 48 hours at 20 ºC
|
| Growth protocol |
N2 worm were syncronized using the bleaching protocol, from adultworms maintained in standart NGM agar plates at 20 ºC
|
| Extracted molecule |
total RNA |
| Extraction protocol |
TRIzol extraction of total RNA was performed according to the manufacturer's instructions, followed by a purification using PureLink TM RNA Mini Kit from Invitrogen
|
| Label |
BIOTIN
|
| Label protocol |
Ss-cDNA was synthetized from 3.5 ng of each sample using the GeneChip WT Pico Reagent kit (Affymetrix, P/N 703262). The amount and quality of ss-cDNA were checked by Nanodrop and Bioanalyzer. ss-cDNA targets were cleaned up, and after fragmentation and terminal labelling with biotin
|
| |
|
| Hybridization protocol |
3.75 µg of fragmented and biotinylated ss-cDNA were included in the hybridization mix, using the GenAtlas Hybridization, Wash and Stain kit for WT Array Strips (Affymetrix, P/N 901667) according to the recommendations of the manufacturer. The resulting preparations were hybridized to GeneChip® C. elegans Gene 1.1 ST Array Strip (Affymetrix, 902157) with 26 unique sequences of each transcript. After applying hybridization (spike controls) and labeling tests it was observed that the 20 chips had fulfilled the quality criteria.
|
| Scan protocol |
GeneAtlas Microarray System from Affymetrix
|
| Description |
Gene expression data from control (non treated) animals
|
| Data processing |
After scanning, microarrays data were processed using Affymetrix Expression Command Console (Affymetrix) and all samples were within bounds for hybridization and labeling tests. Three independent RNA samples were employed. Samples from worms treated with food colorants were grouped as “treatment” and worms with no exposition were grouped as “control”. Data analysis was then performed with RMA (Robust Multiarray Average) allowing raw intensity values to be background corrected, log2 transformed and then quantile normalized in order to obtain an individual intensity value for each probe set.
log2 transformed and then quantile normalized in order to obtain an individual intensity value for each probe set.
|
| |
|
| Submission date |
Jan 14, 2020 |
| Last update date |
May 05, 2023 |
| Contact name |
Fernando Gandía-Herrero |
| E-mail(s) |
fgandia@um.es
|
| Phone |
868889592
|
| Organization name |
University of Murcia
|
| Department |
Biochemistry and Moleular Biology
|
| Lab |
Garcia-Carmona's Lab
|
| Street address |
Universidad de Murcia, Campus Espinardo - Edificio Veterinaria
|
| City |
Murcia |
| State/province |
Murcia |
| ZIP/Postal code |
E-30100 |
| Country |
Spain |
| |
|
| Platform ID |
GPL28002 |
| Series (1) |
| GSE143611 |
Expression data from food colorants treated C. elegans |
|
