|
| Status |
Public on Mar 19, 2019 |
| Title |
Marfan, Véh 20 |
| Sample type |
RNA |
| |
|
| Source name |
Lung
|
| Organism |
Mus musculus |
| Characteristics |
age: 6m
|
| Treatment protocol |
Treated with sildenafil in the drinking water from 6 weeks of age to 6 months
|
| Growth protocol |
Sacrifice at 6 months of age
|
| Extracted molecule |
total RNA |
| Extraction protocol |
QIAzol Rneasy
|
| Label |
biotin
|
| Label protocol |
Microarray was performed at the GenomeQuebec in Montreal. RNA integrity was examined on a bioanalyzer (Agilent). High-quality RNA (RNA integrity number >8.5) was used for expression microarray analysis. 700 pg of total RNA was used to generate double strand cDNA, which was fragmented and biotin labeled according to Affymetrix GeneChip Pico Reagent Kit manual (Thermo Fisher).
|
| |
|
| Hybridization protocol |
5.5 μg of the fragmented and labeled cDNA was hybridized to Mouse Clariom S array for 16 h at 45°C and 60 rpm in an Affymetrix Hybridization Oven 640. Arrays were washed and stained with Streptavidin Phycoerythrin in an Affymetrix Fluidics Station 450 according to Affymetrix GeneChip Pico Reagent Kit guide (Thermo Fisher).
|
| Scan protocol |
The arrays were scanned using the Affymetrix Gene Chip Scanner 3000 7G and CEL. intensity files were generated by Affymetrix GeneChip Command Console Software (AGCC, Thermo Fisher).
|
| Description |
Marfan, Véh
20
|
| Data processing |
The Affymetric Clariom S microarrays were further analyzed using Affymetrix Expression Console with the SST-RMA procedure. The gene-level differential expression was performed using the Affymetrix Transcriptome Anaylsis Console (TAC) Software using default parameters. The significant genes were ranked by fold-change with a cutoff of 2 and the ANOVA p-value less than 0.05 according to Affymetrix. affymetrix-algorithm-name = sst-rma-gene-full affymetrix-algorithm-version = 1.0 affymetrix-array-type = Clariom_S_Mouse program-name = Expression Console program-version = 1.4.1.46
Samples 2, 3, 7 and 19 were removed due to poor cDNA quality, did not pass quality control criteria.
|
| |
|
| Submission date |
Mar 18, 2019 |
| Last update date |
Mar 19, 2019 |
| Contact name |
Nadia Milad |
| E-mail(s) |
nadia.milad.1@ulaval.ca
|
| Organization name |
Université Laval
|
| Street address |
2725 Chemin Ste-Foy
|
| City |
Québec |
| State/province |
Québec |
| ZIP/Postal code |
G1V 4G5 |
| Country |
Canada |
| |
|
| Platform ID |
GPL24242 |
| Series (1) |
| GSE128481 |
Murine Marfan Syndrome Sildenafil Treatment |
|
