|
| Status |
Public on Jul 31, 2023 |
| Title |
ZF_Hypoxia_LowFlow_rep1 |
| Sample type |
RNA |
| |
|
| Source name |
post-anal muscle block, 4kPa, 7cm/sec rep1
|
| Organism |
Danio rerio |
| Characteristics |
tissue: skeletal muscle
age: 4 months
Sex: unspecified (mixed)
|
| Treatment protocol |
On 5th day of each experiment, fish were euthanized by stunning and rapid decapitation. After rapid removal of tail and fins and scales, the post-anal block was dissected, minced and placed in 4ml Trizol solution on ice and then stored at -80C. After thawing samples were homogenized, spun at 10,000g for 10 minutes. Chloroform extraction was performed on supernatant and RNA precipitated in isopropyl alcohol.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was further cleaned and purified using Qiagen MinElute RNA cleanup column and quantified using a NanoDrop Spectrophotometer ND-1000 (NanoDrop Technologies, Inc.) and integrity checked using a 2100 Bioanalyzer (Agilent Technologies).
|
| Label |
Cy3
|
| Label protocol |
Cyanine 3-labeled CTP cRNA was produced with 50 ng of total RNA using the Low Input Quick Amp Labeling Kit, according to manufacturer’s instructions (Agilent Technologies, Inc). The labeled cRNA was then normalized at 1650 ng, fragmented and hybridized on Zebrafish GE Microarray 4x44K.
|
| |
|
| Hybridization protocol |
The arrays were incubated in an Agilent Hybridization oven at 65°C for 17 hours at 10 rpm.
|
| Scan protocol |
They were washed and scanned on an Agilent DNA Microarray Scanner C. All these steps were done according to Agilent One-Color Microarray-Based Gene Expression Analysis protocol (Agilent Technologies, Inc).
|
| Description |
Gene expression after 5 days at hypoxic conditions with low flow to prompt similar activity level to controls
|
| Data processing |
The scanned images were analysed using Feature Extraction software (Agilent) with deafult parameters (Protocol GE1_107_Sep09, Grid US09473739). Features were excluded from analysis if failed to achieve the default 'glsWellAboveBkg' threshold for the Agilent Feature Extraction Software.
|
| |
|
| Submission date |
Jul 02, 2021 |
| Last update date |
Jul 31, 2023 |
| Contact name |
R. Thomas Jagoe |
| E-mail(s) |
thomas.jagoe@mcgill.ca
|
| Phone |
15143408222
|
| Organization name |
McGill University
|
| Department |
Medicine
|
| Street address |
Jewish General Hospital, 3755 Cote Ste Catherine
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3T 1E2 |
| Country |
Canada |
| |
|
| Platform ID |
GPL14688 |
| Series (1) |
| GSE179311 |
Skeletal muscle transcriptional adaptions to hypoxia and maximal exercise |
|
