|
| Status |
Public on May 14, 2019 |
| Title |
high density, replicate 2 |
| Sample type |
RNA |
| |
|
| Source name |
Ovary, high density
|
| Organism |
Danio rerio |
| Characteristics |
strain/background: AB
gender: Female
age: 90 dpf
tissue: Ovary
condition: High density
|
| Treatment protocol |
The high density effects were studied during gonadal development (6–90 dpf).
|
| Growth protocol |
At 6 days post fertilization (dpf), fish were placed in 2.8-liter.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
At 90 dpf, fish were sacrificed and gonads were dissected and flash frozen. RNA was extracted by Trizol (Sigma).
|
| Label |
Cy3
|
| Label protocol |
Cyanine-3 (Cy3) labeled cRNA was prepared from 100ng of total RNA using the LowInputQuick Amp Labeling kit – Agilent 5190-2305 according to the manufacturer's instructions, followed by RNeasy column purification (QIAGEN, Valencia, CA). Dye incorporation and cRNA yield were checked with the NanoDrop ND-1000 Spectrophotometer.
|
| |
|
| Hybridization protocol |
After fragmentation, 600 ng of labeled cRNA from each sample was hybridized to the array in in situ hybridization oven (Agilent) for 17 h at 65ºC and washed during 1 min at rt in Gene Expression Wash Buffer 1 (Agilent) and 1 min at 37 ºC with Gene Expression Wash buffer 2 (Agilent).
|
| Scan protocol |
Scanned on an Agilent G2539A scanner at 5um resolution and 100% PMT. The intensity data of each individual hybridization were extracted and the quality was assessed with the Feature Extraction software 10.7 (Agilent).
|
| Description |
2G4x_1_2
Gene expression in zebrafish ovary exposed at high density at 90 dpf.
|
| Data processing |
Raw data was corrected for background noise using the normexp method. Quantile normalization was applied to assure comparability across samples.
|
| |
|
| Submission date |
Jul 05, 2018 |
| Last update date |
May 14, 2019 |
| Contact name |
Alejandro Valdivieso |
| E-mail(s) |
valdivieso@icm.csic.es
|
| Organization name |
Insituto de Ciencias del Mar
|
| Street address |
PASSEIG MARÍTIM DE LA BARCELONETA, 37-49
|
| City |
BARCELONA |
| State/province |
BARCELONA |
| ZIP/Postal code |
08003 |
| Country |
Spain |
| |
|
| Platform ID |
GPL14688 |
| Series (1) |
| GSE116700 |
Valdivieso A, Ribas L, Piferrer F. Ovarian transcriptomic signatures of zebrafish females resistant to different environmental perturbations. |
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