|
| Status |
Public on Aug 02, 2012 |
| Title |
Lung Shh-cre:Foxp1flox/flox:Foxp4flox/flox(Mut2) |
| Sample type |
RNA |
| |
|
| Source name |
Shh-cre:Foxp1flox/flox:Foxp4flox/flox-Lung
|
| Organism |
Mus musculus |
| Characteristics |
developmental stage: E14.5
tissue: lung
mouse background: C57BL/6 and 129X1,129S1
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using Rneasy mini kit (Qiagene)
|
| Label |
Biotin
|
| Label protocol |
100ng of total RNA was converted to first-strand cDNA using reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 RNA polymerase promoter. Second-strand cDNA synthesis was followed by in vitro transcription (Affymetrix One-Cycle Target Labeling Kit) for linear amplification and biotinylation of each transcript.
|
| |
|
| Hybridization protocol |
cDNAs were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to GeneChips (Affymetrix Inc., Santa Clara CA). The microarrays were then washed at low (6X SSPE) and high (100mM MES, 0.1M NaCl) stringency and stained with streptavidin-phycoerythrin. Fluorescence was amplified by adding biotinylated anti-streptavidin and an additional aliquot of streptavidin-phycoerythrin stain.
|
| Scan protocol |
A confocal scanner was used to collect fluorescence signal after excitation at 570 nm.
|
| Data processing |
Affymetrix Command Console was used to quantitate expression levels for targeted genes; default values provided by Affymetrix were applied to all analysis parameters. Probes for each targeted gene were averaged and inter-array normalization performed using the RMA algorithm .
3 independent biological replicates for each condition were assayed on microarrays. Significance Analysis of Microarrays (SAM v3.0, www-stat.stanford.edu/~tibs/SAM/) was used to generate lists of statistically significant differentially expressed genes in pairwise comparisons of replicate averages between conditions.
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| |
|
| Submission date |
Dec 20, 2011 |
| Last update date |
Aug 02, 2012 |
| Contact name |
Shanru Li |
| E-mail(s) |
[email protected]
|
| Phone |
001-215-573-7052
|
| Fax |
001-215-573-2094
|
| Organization name |
University of Pennsylvania
|
| Department |
Medicine
|
| Lab |
Edward Morrisey
|
| Street address |
3400 Civic Center Blvd, Bldg 421
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE34584 |
The role of Foxp1/4 in lung development |
|
