|
| Status |
Public on Oct 17, 2008 |
| Title |
3398 |
| Sample type |
RNA |
| |
|
| Source name |
Snap frozen lung tissue specimen
|
| Organism |
Homo sapiens |
| Characteristics |
PatientID: 519
Histology: adeno
N Stage: N0
Stage: III
Sex: female
Race: White
Chemo: none
Radiation: none
Age: 73.5
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Forty, 5-micron sections from each tissue block were cut and placed immediately in Qiagen RNA lysis buffer. RNA was isolated using Qiagen kits with on-column DNAse treatment to remove genomic DNA followed by precipitation.
|
| Label |
biotin
|
| Label protocol |
2 µg of total RNA from each of 20 tumor/normal paired specimens (n=40) was labeled with reagents from Affymetrix according to the manufacturers instructions.
|
| |
|
| Hybridization protocol |
Hybridization cocktails containing 5 to 5.5 µg of fragmented, end-labeled single-stranded cDNA were prepared and hybridized to GeneChip Human Exon 1.0 ST arrays.
|
| Scan protocol |
GeneChip Scanner 3000 7G
|
| Description |
3398_Exon.CEL
|
| Data processing |
All exon array data was analyzed using tools in Partek Genomic Suite 6.4 software (Partek Inc., St. Louis, MO). The Robust Multi-array Analysis (RMA) (Irizarry, Hobbs, Collin, Beazer-Barclay, Antonellis, Scherf, and Speed 2003) algorithm was used for probeset (exon-level) intensity analysis .
|
| |
|
| Submission date |
Jul 24, 2008 |
| Last update date |
Apr 27, 2009 |
| Contact name |
Liqiang Xi |
| E-mail(s) |
xil2@mail.nih.gov
|
| Phone |
301-594-1525
|
| Fax |
301-402-0043
|
| Organization name |
NIH/NCI
|
| Department |
Lab of Pathology
|
| Street address |
10 Center Dr. Bldg 10 Rm 2N110
|
| City |
Bethesda |
| State/province |
MD |
| ZIP/Postal code |
20892 |
| Country |
USA |
| |
|
| Platform ID |
GPL5188 |
| Series (1) |
| GSE12236 |
Whole Genome Exon Arrays Identify Differential Expression of Alternatively Spliced, Cancer-related Genes in Lung Cancer |
|
