|
| Status |
Public on May 31, 2008 |
| Title |
Human_Control15 |
| Sample type |
RNA |
| |
|
| Source name |
Whole Lung
|
| Organism |
Homo sapiens |
| Characteristics |
Age: 71; Race: Caucasuian; Gender: Female; Ht: 66in.
|
| 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 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. Chip library files specific to each array and necessary for scan interpretation are stored on the computer workstation controlling the scanner and are updated regularly as necessary when updates are made available from Affymetrix. Collected research data is stored on the hard drive of the instrument computer, transferred to a mirrored storage disk and to a raid 5 server operating on the Partners Healthcare network and backed up nightly via the Partners Healthcare Systems IT backup utility. All systems are CFR21-11 and HIPPA compliant
|
| Description |
FEV1: 2.42; Ratio: 80; Diagnosis: Lymphoma; ArrayID: 840C
|
| Data processing |
MAS5
|
| |
|
| Submission date |
Jul 24, 2007 |
| Last update date |
Aug 28, 2018 |
| Contact name |
Soumyaroop Bhattacharya |
| E-mail(s) |
Soumyaroop_Bhattacharya@URMC.rochester.edu
|
| Phone |
585-276-4683
|
| Fax |
585-276-2642
|
| URL |
http://lungtranscriptome.bwh.harvard.edu/
|
| Organization name |
University of Rochester Medical Center
|
| Department |
Pediatrics
|
| Lab |
Mariani
|
| Street address |
601 Elmwood Avenue Box 850
|
| City |
Rochester |
| State/province |
NY |
| ZIP/Postal code |
14642 |
| Country |
USA |
| |
|
| Platform ID |
GPL570 |
| Series (1) |
| GSE8581 |
Human Chronic Obstructive Pulmonary Disorder (COPD) Biomarker |
|
| Relations |
| Reanalyzed by |
GSE60486 |
| Reanalyzed by |
GSE119087 |
