|
| Status |
Public on Nov 10, 2010 |
| Title |
220 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
S220.1b_Mouse_Wnt1Cre-R26R_YFP+ cells from 10 embryos pooled
|
| Organism |
Mus musculus |
| Characteristics |
gender: Mixed genders
strain: Mixed background
developmental state: E10.5
tissue extraction: The entire region from just above the eye to below pharyngeal arch 6 was dissected out and subjected to FACS and YFP+ cells were pooled from 10 embryos
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Equal number of Wnt1Cre,R26R YFP+ and Wnt1Cre,R26R YFP- were harvested at E10.5. After removal from the embryonic sac, the region from just above the eyes to just below pharyngeal arch 6 was dissected out and placed in ice-cold PBS (Ca2+ and Mg2+ free). The tissue was then sonicated to break up the tissue. The tissue was then treated with 0.05% Trypsin/EDTA to generate single cells. The cells were spun, resuspended in DMEM, and passed through a 40um nylon filter. Cells from ten E10.5 embryos were sorted into YFP+ and YFP- populations and pooled.
Total RNA was isolated from sorted cells using Trizol following the manufacturer's recommended protocols.
|
| Label |
Cy5
|
| Label protocol |
Cy5 and Cy3 labeling protocol according to manufacturer's (Exiqon) recommendations
|
| |
|
| Channel 2 |
| Source name |
S220.1a_Mouse_Wnt1Cre-R26R_YFP- cells from 10 embryos pooled
|
| Organism |
Mus musculus |
| Characteristics |
gender: Mixed genders
strain: Mixed background
developmental state: E10.5
tissue extraction: The entire region from just above the eye to below pharyngeal arch 6 was dissected out and subjected to FACS and YFP- cells were pooled from 10 embryos
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Equal number of Wnt1Cre,R26R YFP+ and Wnt1Cre,R26R YFP- were harvested at E10.5. After removal from the embryonic sac, the region from just above the eyes to just below pharyngeal arch 6 was dissected out and placed in ice-cold PBS (Ca2+ and Mg2+ free). The tissue was then sonicated to break up the tissue. The tissue was then treated with 0.05% Trypsin/EDTA to generate single cells. The cells were spun, resuspended in DMEM, and passed through a 40um nylon filter. Cells from ten E10.5 embryos were sorted into YFP+ and YFP- populations and pooled.
Total RNA was isolated from sorted cells using Trizol following the manufacturer's recommended protocols.
|
| Label |
Cy3
|
| Label protocol |
Cy5 and Cy3 labeling protocol according to manufacturer's (Exiqon) recommendations
|
| |
|
| |
| Hybridization protocol |
According to manufacturer's (Exiqon) recommendations
|
| Scan protocol |
According to manufacturer's (Exiqon) recommendations
|
| Description |
Mouse_Wnt1Cre-R26R_YFP+ vs. YFP-_E10.5 embryos_cells from 10 embryos pooled
|
| Data processing |
GPR files were read into R/Bioconductor using the m-array package. GenePix flagged spots were removed from subsequent analysis. Only good (unflagged) miR probes were used for normalization and subsequent analysis. M (log2 ratios) of Cy5 to Cy3 signals were calculated for each array (with NO background subtraction), and normalized by loess normalization. For each miRNA with more than 1 good probes, the median of normalized M of the replicate probes was taken as its summary value for each array.
|
| |
|
| Submission date |
Nov 10, 2010 |
| Last update date |
Nov 10, 2010 |
| Contact name |
Deepak Srivastava |
| E-mail(s) |
[email protected]
|
| Organization name |
J. David Gladstone Institutes
|
| Department |
Gladstone Institute of Cardiovascular Disease
|
| Lab |
Deepak Srivastava
|
| Street address |
1650 Owens St.
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94158 |
| Country |
USA |
| |
|
| Platform ID |
GPL7722 |
| Series (1) |
| GSE25256 |
The neural crest-enriched microRNA miR-452 regulates epithelial-mesenchymal signaling in the first pharyngeal arch |
|
