|
| Status |
Public on Jun 02, 2010 |
| Title |
Caseum 3 |
| Sample type |
RNA |
| |
|
| Source name |
Caseous human pulmonary TB granuloma
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: caseous granuloma
|
| Treatment protocol |
Cryosections were made from human lung tissues. After fixation in graded alcohol containing 0.5% sodium azide, caseous granuloma or normal lung parenchyma was dissected out by using laser capture microdissection. The dissected materials were stored at -80°C until further processing.
|
| Growth protocol |
Human pulmonary TB tissues and normal lung tissues were excised from TB patients who underwent surgery.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA were isolated using PicoPure RNA Isolation Kit (Molecular devices), and sufficient quantities of messenger RNA were produced by two-rounds of linear amplification using RiboAmp HS Amplification Kit (Molecular Devices).
|
| Label |
biotin
|
| Label protocol |
Biotinylated aRNA were generated by using BioArray High Yield RNA Transcript Lableing Kit (Enzo Life Sciences).
|
| |
|
| Hybridization protocol |
Fifteen microgram of fragmented aRNA were hybridized onto GeneChip Human X3P array (Affymetrix) for 16 hours at 45°C. Genechips were washed and stained in Affymetrix Fluidics Station FS450.
|
| Scan protocol |
Genechips were scanned using Affymetrix GeneChip Scanner 3000 7G.
|
| Description |
Gene expression data from caseous human pulmonary TB granuloma
|
| Data processing |
The data for caseous granulomas only were analyzed using R and Bioconductor, and the raw PM probes only were subjected to background correction using MAS5 method, log-transformed and median-centered. And informative PM probes from each probe set were selected as having the highest mean across all arrays. The data for caseous granulomas and normal lung parenchyma were analyzed using GeneSpring GX 10.0.2 program. MAS5 method was used to summarize raw CEL files, the normalization was done by scaling to median of all samples and the baseline was transformed to the median of all samples.
|
| |
|
| Submission date |
Jan 26, 2010 |
| Last update date |
Jun 02, 2010 |
| Contact name |
Mi-Jeong Kim |
| E-mail(s) |
mk376@cornell.edu
|
| Phone |
6072534060
|
| Fax |
6072399124
|
| Organization name |
Cornell University
|
| Department |
Microbiology and Immunology
|
| Street address |
C5 104 VMC Cornell University
|
| City |
Ithaca |
| State/province |
NY |
| ZIP/Postal code |
14853 |
| Country |
USA |
| |
|
| Platform ID |
GPL1352 |
| Series (1) |
| GSE20050 |
Gene expression profiles of caseous human pulmonary TB granulomas derived from TB patients |
|
