|
| Status |
Public on Sep 29, 2015 |
| Title |
Rh4-PAX3-FOXO1 siRNA transfected for 24h-1 |
| Sample type |
RNA |
| |
|
| Source name |
Rh4 cells treated with siRNA directed against PAX3-FOXO1 for 24h, sample 1
|
| Organism |
Homo sapiens |
| Characteristics |
tissue: alveolar rhadomyosarcoma
|
| Treatment protocol |
Transfection was carried using 7 microl of GeneEraser (Stratagene, La Jolla, CA, USA) and 20 nm siRNA (final concentration) per 6-well
|
| Growth protocol |
Rh4 cells were grown in DMEM/10% FBS
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the RNAeasy kit including the DNAse digestion step
|
| Label |
Biotin
|
| Label protocol |
RNA amplification and labeling were done according to the GeneChip eukaryotic small sample target labeling technical note (Affymetrix, Santa Clara, CA).
|
| |
|
| Hybridization protocol |
Fifteen microg of labeled cRNA was fragmented at 94°C for 35 min in a buffer containing 40 mM Tris-acetate (pH 8.1), 100 mM potassium acetate, and 30 mM magnesium acetate. Fragmented cRNA was mixed with a mixture containing 0.1 M 4-morpholinepropanesulfonic acid (pH 6.5–6.7), 1 M NaCl, 20 mM EDTA, 0.01% Tween-20, 0.5 mg/ml acetylated bovine serum albumin, 0.1 mg/ml herring sperm DNA, 1x eukaryotic hybridization control mix, and 50 pM B2 control oligo (Affymetrix). This mixture was heated to 95°C for 5 min, followed by incubation at 45°C for 5 min and centrifugation for 5 min at maximum speed. The probe array was incubated at 45°C for 16 h at constant rotation (60 rpm).
|
| Scan protocol |
Stained arrays were scanned in a Gene Array Scanner (Agilent)
|
| Description |
Gene expression data from Rh4 cells treated for 24h with siRNA directed against PAX3-FOXO1
|
| Data processing |
Data was imported in dCHIP and normalized
|
| |
|
| Submission date |
Sep 28, 2015 |
| Last update date |
Sep 29, 2015 |
| Contact name |
Beat Schäfer |
| E-mail(s) |
[email protected]
|
| Phone |
+41446348853
|
| Organization name |
University Childrens Hospital
|
| Department |
Oncology
|
| Street address |
Balgrist Campus Lengghalde 5
|
| City |
Zurich |
| State/province |
ZH |
| ZIP/Postal code |
8008 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL96 |
| Series (1) |
| GSE73483 |
Expression data for analysis of genes affected by PAX3-FOXO1 in alveolar rhabdomyosarcoma cell line Rh4 |
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