|
| Status |
Public on Aug 09, 2013 |
| Title |
Whole right lung day 56 post sham surgery |
| Sample type |
RNA |
| |
|
| Source name |
whole right lung
|
| Organism |
Mus musculus |
| Characteristics |
Sex: Male
strain: C57BL/6
treatment: Sham surgery
comment: microarray hybridization data 06/06/2011
tissue: Whole right lung
time: day 56 post sham surgery
|
| Extracted molecule |
total RNA |
| Extraction protocol |
For each experimental sample, RNA quality was assessed by RNA Nano LabChip analysis on an Agilent Bioanalyzer 2100. Concentrations may also be determined using a NanoDrop 1000 spectrophotometer. Under standard conditions processing of RNAs for GeneChip Analysis was in accordance with methods described in the Affymetrix GeneChip Expression Analysis Technical Manual, revision four, as subsequently detailed. Synthesis of cDNA first and second strand is performed using the GeneChip Expression 3’-Amplification Reagents One-Cycle cDNA Synthesis Kit (P/N 900431). Cleanup of the double stranded product is carried according to standard Affymetrix protocols using the Affymetrix GeneChip Cleanup Module (Affymetrix Catalog # 900371).
|
| Label |
Biotin
|
| Label protocol |
In vitro transcription (IVT) is performed using the GeneChip Expression Amplification Reagents kit- 30 reactions (P/N 900449) and is carried out according to the standard Affymetrix protocols and quantification of the IVT samples is carried out on a Bio-Tek UV Plate Reader.
|
| |
|
| Hybridization protocol |
Hybridization is carried out according the Affymetrix GeneChip® Manual. Twenty micrograms of IVT material is the nominal amount used on the GeneChip® arrays. Affymetrix hybridization ovens are used to incubate the arrays at a constant temperature of 45oC overnight. Preparation of microarrays for scanning is carried out with Affymetrix appropriate wash protocols matched to the specific chip type on a Model 450 Fluidics station. Affymetrix GeneChip Operating Software (GCOS) operating system controls the Fluidics station process.
|
| Scan protocol |
Scanning is carried out on a Affymetrix GeneChip® Scanner 3000 7G scanner with autoloader. The Affymetrix GCOS v1.3 operating system controls the Model 3000 7G scanner and data acquisition functions. GCOS maintains the mediated first level data analysis and desktop data management for the entire GeneChip System.
|
| Description |
Whole right lung day 56 post sham surgery
|
| Data processing |
All 21 sample CEL files were inputted into Bioconductor/R to derive Robust Multi-Array Average (RMA) normalized output.
|
| |
|
| Submission date |
Aug 01, 2012 |
| Last update date |
Aug 09, 2013 |
| Contact name |
Alvin T. Kho |
| E-mail(s) |
[email protected]
|
| Phone |
617-919-2182
|
| Organization name |
Boston Children's Hospital
|
| Department |
Informatics Program
|
| Street address |
320 Longwood Avenue
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE39817 |
Identification of de-differentiation and re-development phases during post-pneumonectomy lung growth. |
|
