|
| Status |
Public on Jan 29, 2009 |
| Title |
Patient_532_Current_Smoker |
| Sample type |
RNA |
| |
|
| Source name |
epithelial cells from right mainstem bronchus
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: Male
Race: African American
Age: 44
PKYRS: 14
Current smoker
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Epithelial cells were obtained from brushing the right mainstem bronchus of current and never smoker volunteers at bronchoscopy. Epithelial cell content yields were generally approximately 90%. RNA was size fractionated, and high molecular weight RNA ( > 200 nucleotides) was obtained from each sample for mRNA microarray analysis.
|
| Label |
biotin labeled
|
| Label protocol |
Ribosomal RNA was first removed from the High molecular weight RNA fraction using the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen, Carlsbad, CA). This treated RNA was then converted to cDNA and subsequently processed and biotin-labeled.
|
| |
|
| Hybridization protocol |
cDNA was end-labeled with a biotinylated dideoxynucleotide using terminal transferase. Five and a half micrograms of biotinylated cDNA was added to a hybridization cocktail, loaded on a Human Exon 1.0 ST GeneChip and hybridized for 16 hours at 45 ºC and 60 rpm. Following hybridization, the array was washed and stained according to the standard Affymetrix protocol.
|
| Scan protocol |
Arrays were scanned using an Affymetrix GeneChip Scanner 3000. These scans were used to generate CEL files for each array.
|
| Description |
High molecular weight RNA (> 200 nucleotides) was treated for removal of ribosomal RNA, from which cDNA was synthesized, biotin-labeled, and hybridized to Human Exon 1.0 ST GeneChips. Transcript level data was obtained using the iterPLIER software package.
B532C.CEL [Embargoed due to pending publication]
|
| Data processing |
The approximately 230,000 “core” exon probesets on the Exon array were used for transcript level analysis, which map to approximately 17,500 empirically supported transcripts (RefSeq and full-length GenBank mRNAs) with a high degree of confidence. Transcript-level expression values were derived using the model-based iterPLIER algorithm as implemented in the ExACT software package (Affymetrix, Santa Clara, CA). The gene annotations used for each probe set were from the annotation file obtained from Affymetrix (http://www.affymetrix.com).
|
| |
|
| Submission date |
Jan 29, 2009 |
| Last update date |
Dec 24, 2010 |
| Contact name |
Sriram Sridhar |
| E-mail(s) |
sridhars@medimmune.com
|
| Phone |
6178771485
|
| Organization name |
MedImmune
|
| Department |
Translational Medicine
|
| Street address |
1 MedImmune Way
|
| City |
Gaithersburg |
| State/province |
MD |
| ZIP/Postal code |
20878 |
| Country |
USA |
| |
|
| Platform ID |
GPL5175 |
| Series (2) |
| GSE14224 |
MicroRNAs as modulators of smoking-induced gene expression changes in human airway epithelium |
| GSE14633 |
Gene expression from bronchial epithelial cell samples of current and never smokers. |
|
