|
| Status |
Public on Mar 30, 2015 |
| Title |
Forskolin,biological replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
AGM VE-cadherin+ cells_Forskolin
|
| Organism |
Mus musculus |
| Characteristics |
strain: C57Bl/6
developmental stage: E11.5 embryo
tissue: aorta-gonad-mesonephros (AGM) region
cell type: VE-cadherin+ cells
treated with: forskolin (25uM) for 8 hrs
|
| Treatment protocol |
Cells were treated with BMP4 (4ng/ml) or forskolin (25uM) or both for 8 hours.
|
| Growth protocol |
E11.5 aorta-gonad-mesonephros region was microdissected, dissociated using DNase I, Collagenase IV and Hyaluronidase, then sorted for VE-cadherin+ cells. Cells were cultured in serum-free media containing 2% BSA / IMDM (vol/vol) supplemented with Insulin-Transferrin-Selenium (ITS-G; Life Technologies), 25 μg/ml ascorbic acid, 450 μM monothioglycerol, 2 mM penicillin/streptomycin/glutamate and of 20 ng/ml VEGF (R&D), 50 ng/ml IL3 (R&D), 50 ng/ml IL6 (R&D), 50 ng/ml SCF (R&D), 50 ng/ml FLT3L (R&D), 50 ng/ml TPO (R&D), 50 ng/ml IL6R (SBH Sciences)
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted with RNeasy Micro Kit (Qiagen)
|
| Label |
biotin
|
| Label protocol |
NuGen amplified, biotinylated cRNA were prepared according to the standard Affymetrix protocol from total RNA.
|
| |
|
| Hybridization protocol |
Following fragmentation, cRNA were hybridized for 16 hr at 45C on GeneChip Mouse Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Forskolin_rep_1
2_021014.CEL
|
| Data processing |
The data were filtered using nsFilter from the genefilter package and Multi-array Average-summarized, quantile normalized using R (v.2.15)/Bioconductor v.2.11 (BiocInstaller 1.8.3).
After nsFilter (backup, var.filter=FALSE, require.entrez=FALSE, require.symbol=FALSE, remove.dupEntrez=TRUE) removing duplicate Entrez entries, the reduced data set of 20,757 rows was obtained.
|
| |
|
| Submission date |
Oct 20, 2014 |
| Last update date |
Mar 30, 2015 |
| Contact name |
Peter Geon Kim |
| Organization name |
Dana Farber Cancer Institute
|
| Department |
Hematology/Oncology
|
| Lab |
Ben Ebert
|
| Street address |
360 Longwood Ave, Lc8202
|
| City |
Boston |
| State/province |
MA |
| ZIP/Postal code |
02215 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE62517 |
Flow-induced Protein Kinase A / CREB pathway acts via BMP signaling to promote AGM hematopoiesis |
|
