|
| Status |
Public on Oct 21, 2009 |
| Title |
cultured cells TSC2-/- rep3 |
| Sample type |
RNA |
| |
|
| Source name |
cultured cells TSC2-/-
|
| Organism |
Homo sapiens |
| Characteristics |
tissue type: angiomyolipoma (AML) derived from LAM patient
genotype: TSC2-/-
|
| Biomaterial provider |
cultured cells TSC2-/- rep3
|
| Treatment protocol |
N/A
|
| Growth protocol |
Cells are in phenol red-free serum-free alpha-MEM media.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from cells using the Qiagen RNeasy kit (Qiagen Inc., Valencia, CA). The quality of the total RNA was assessed by analysis on the Agilent 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA). The ratio of the 28S/18S bands was required to be ≥ 2.0.
|
| Label |
Cy5
|
| Label protocol |
RNA was first reverse transcribed using a T7-Oligo (dT) promoter primer, followed by second strand cDNA synthesis using RNase H. Double-stranded cDNA was purified and used as a template in the IVT using T7 RNA Polymerase and a biotinylated nucleotide analog/ribonucleotide mix for to generate biotin-labeled cRNA.
|
| |
|
| Hybridization protocol |
For hybridization to the CodeLink arrays 10 μg of labeled cRNA was fragmented, denatured at 90°C for 5 min, and then hybridized at 37°C for 20 hours. After washing, the arrays were incubated with streptavidin-phycoerythrin and biotinylated anti-streptavidin antibodies. , and the arrays scanned on a GenePix 4000B scanner (Axon Instrument, Sunnyvale, CA).
|
| Scan protocol |
The arrays scanned on a GenePix 4000B scanner (Axon Instrument, Sunnyvale, CA).
|
| Description |
cultured cells TSC2-/- rep3
|
| Data processing |
The gene expression levels on each array were normalized to a median expression level of 1.0 using the CodeLink software.
|
| |
|
| Submission date |
Jul 10, 2009 |
| Last update date |
Oct 21, 2009 |
| Contact name |
Po-Shun Lee |
| E-mail(s) |
plee@rics.bwh.harvard.edu
|
| Phone |
617-355-9012
|
| Fax |
617-355-9016
|
| Organization name |
Brigham & Women's Hospital
|
| Department |
Medicine
|
| Street address |
1 Blackfan Circle, Karp 6
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02115 |
| Country |
USA |
| |
|
| Platform ID |
GPL2895 |
| Series (1) |
| GSE16944 |
Rapamycin-insensitive up-regulation of MMP2 and other genes in TSC2- deficient LAM-like cells |
|
