|
Status |
Public on Oct 17, 2008 |
Title |
MS857 |
Sample type |
RNA |
|
|
Source name |
Snap frozen lung tissue specimen
|
Organism |
Homo sapiens |
Characteristics |
PatientID: 541 Histology: normal N Stage: N0 Stage: I Sex: male Race: White Chemo: none Radiation: none Age: 56.7
|
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 |
MS857_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 |
|