|
| Status |
Public on Nov 27, 2012 |
| Title |
Trachea_GSM463940 |
| Sample type |
RNA |
| |
|
| Source name |
pooled Human trachea total RNA
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: trachea
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.
|
| Data processing |
The data were digitalized using GeneChip Operating Software (GCOS) v.1.3 (Affymetrix).
Gene expression array data were normalized using MAS5 algorithm (Affymetrix). Then, to correct for bias between chips, quantile normalization (Bolstad, B. M. et al. Bioinformatics 19, 185-193 (2003)) was applied to all array data using R software.
The intensities were converted to a logarithmic scale (base 2). Signal reliability of each probe was determined based on the MAS5 Call algorithm (Affymetrix), and each probe was assigned to one of three flags (P: present, M: marginal, and A: absent).
|
| |
|
| Submission date |
Nov 21, 2011 |
| Last update date |
Nov 27, 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 (1) |
| GSE33846 |
Expression data of hepatocytes isolated from chimeric mouse livers repopulated with human hepatocytes and from normal human livers |
|
| Relations |
| Reanalysis of |
GSM463940 |
