|
| Status |
Public on Nov 12, 2012 |
| Title |
Stomach |
| Sample type |
RNA |
| |
|
| Source name |
pooled Human stomach total RNA
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: stomach
ethnicity: caucasian
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples of total RNA from Human tissues were purchased from several companies (Clontech, Ambion, Stratagene, Cell Applications). HeLa and SH-SY5Y cells were cultured in standard DMEM / 10% FBS medium. Total RNA was extracted from cells with TRIzol regent (Invitrogen). Additionally, total RNA was purified with Rneasy Mini Kit (Qiagen) and treated with RNase-free DNase Set (Qiagen) to remove any contaminating genomic DNA.
|
| Label |
biotin
|
| Label protocol |
Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 2 ug total RNA (Expression Analysis Technical Manual, Rev. 3, 2009, Affymetrix).
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Human Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
|
| Scan protocol |
GeneChips were scanned using the Affymetrix Scanner 3000 7G.
|
| Description |
Gene expression data of Human stomach
|
| Data processing |
The data were normalized with MAS5 and quantile normalization using R software.
MAS5 and quantile normalization signal intensity. Note that the intensities were converted to a logarithmic scale (base 2). The call in an absolute analysis by MAS5call that indicates if the transcript was present (P), marginal (M) or absent (A).
|
| |
|
| Submission date |
Oct 21, 2009 |
| Last update date |
Nov 13, 2012 |
| Contact name |
Fuyuki Miya |
| E-mail(s) |
fmiya@keio.jp
|
| Phone |
+81-3-5363-3890
|
| Organization name |
Keio University
|
| Department |
School of Medicine
|
| Lab |
Center for Medical Genetics
|
| Street address |
35 Shinanomachi, Shinjuku-ku
|
| City |
Tokyo |
| State/province |
Tokyo |
| ZIP/Postal code |
160-8582 |
| Country |
Japan |
| |
|
| Platform ID |
GPL570 |
| Series (3) |
| GSE18490 |
Whole genome transcriptional profile of human tissues and cells |
| GSE18674 |
Gene expression profile of Human tissues and cells |
| GSE18676 |
Whole genome expression in human tissues |
|
| Relations |
| Reanalyzed by |
GSM837766 |
| Reanalyzed by |
GSM956911 |
