|
| Status |
Public on Oct 05, 2011 |
| Title |
Bone marrow transduced with CALM(400-648)+AF10 (677-758), biological replicate-1 |
| Sample type |
RNA |
| |
|
| Source name |
Adult mouse bone marrow
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57/BL6/C3H
cell type: bone marrow cells
transducer: CALM(400-648)+AF10 (677-758)
|
| Treatment protocol |
After 48 hours of pre-stimulation, the BM cells were transduced with different viruses, containing the relevent constructs, by overlaying them on virus-producing irradiated (40 Gy) GFP+E86 producers in the presence of cytokines and protamine sulfate (5ug/ml). The transduction was stopped by removing the BM cells from the GFP+E86 cells and plating them in BM medium with cytokines for another 48 hours to allow for GFP expression. Retrovirally transduced cells were FACS sorted based on expression of GFP.
|
| Growth protocol |
Adult C57/BL6/C3H mice were injected with 30µg/µl working solution of 5-Fluorouracil (100µl per 20gr of weight) to enrich for stem and progenitor cells. Four days post injection, total bone marrow
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from FACS sorted GFP+ cells using the Qiagen miRNeasy Mini Kit For purification of microRNA and total RNA from tissues and cells per manufacturer's instructions
|
| Label |
biotin
|
| Label protocol |
Samples were labeled using the FlashTag™ Biotin HSR Kit from Genisphere starting with 1µg of totel RNA according to the protocol of the manufaturer
|
| |
|
| Hybridization protocol |
accoring to the recommended protocol followed by washing at a Fluidics Station 450 using fluidics script FS450_0003
|
| Scan protocol |
according to Affymetrix protocols using a GeneChip 3000 Scanner
|
| Description |
Gene expression data from bone marrow cells 96 hours post-transdution with CALM(400-648)+AF10 (677-758)
|
| Data processing |
Data were processed using the miRNAQC tool from Affymetrix following the recommended workflow from Genisphere (Background Detection -> RMA Global Background Correction -> Quantile Normalization -> Median polish Summarization); Statistical analysis was done using BRB Array-Tools Software by Richard Simon
|
| |
|
| Submission date |
Feb 24, 2011 |
| Last update date |
Oct 05, 2011 |
| Contact name |
Karlheinz Holzmann |
| E-mail(s) |
[email protected]
|
| Organization name |
Ulm University
|
| Department |
Medical Faculty
|
| Lab |
Genomics Core Facility
|
| Street address |
Helmholtzstreet 8/1
|
| City |
Ulm |
| ZIP/Postal code |
D-89081 |
| Country |
Germany |
| |
|
| Platform ID |
GPL8786 |
| Series (2) |
| GSE27512 |
Identification of a Potently Oncogenic CALM-AF10 Minimal-Fusion Mutant (miRNA) |
| GSE27514 |
Identification of a Potently Oncogenic CALM-AF10 Minimal-Fusion Mutant |
|
