|
| Status |
Public on Dec 28, 2012 |
| Title |
batch1a-MPNST_AS13 |
| Sample type |
RNA |
| |
|
| Source name |
human_MPNST
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: malignant peripheral nerve sheath tumors (MPNST)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from frozen human tissue and cells using the RNeasy kit (Qiagen) and verified RNA integrity with an Agilent Bioanalyser 2100 (with typical 28S/18S ratios = 2 +/- 0.1). For mouse, total RNA was isolated from nerves and tumors using the Qiagen fibrous tissue protocol (Qiagen, Inc. Valencia, CA).
|
| Label |
biotin
|
| Label protocol |
We generated biotinylated cDNA probes from a single round of DNA displacement synthesis amplification of 20ng total RNA (Ovation Biotin RNA Amplification and Labelling System; NuGen) for hybridization to the whole-genome Affymetrix GeneChips using the Affymetrix protocol.
|
| |
|
| Hybridization protocol |
The hybridization cocktail was hybridized for 16 hr at 45 degrees C on GeneChips. GeneChips were washed and stained in the Affymetrix Fluidics Station 450:FS450_0004.
|
| Scan protocol |
GeneChips were scanned and quantified using an Affymetrix Gene Array scanner and GeneChip Operating Software V1.4 (default settings.)
|
| Description |
AS13
SAMPLE 79
|
| Data processing |
Microarrays were analyzed with Affymetrix Microarray Suite 5.0 to generate “CEL” files that were processed using Robust Multichip Analysis (RMA) in Bioconductor/R. A custom CDF was used for each species (mouse: Brainarray, Mouse4302_Mm_REFSEQ_11.0.1; Human, Brainarray, HGU133Plus2_Hs_REFSEQ_11.0.1).
|
| |
|
| Submission date |
Oct 22, 2012 |
| Last update date |
Dec 28, 2012 |
| Contact name |
Nancy Ratner |
| E-mail(s) |
nancy.ratner@cchmc.org
|
| Phone |
513-636-9469
|
| Organization name |
Cincinnati Children's Hospital Medical Center
|
| Street address |
3333 Burnet Ave.
|
| City |
Cincinnati |
| State/province |
OH |
| ZIP/Postal code |
45229 |
| Country |
USA |
| |
|
| Platform ID |
GPL10371 |
| Series (1) |
| GSE41747 |
MEK inhibition exhibits efficacy in human and mouse neurofibromatosis tumors, despite transcriptional feedback onto ERK. |
|
| Relations |
| Reanalysis of |
GSM352453 |
