|
| Status |
Public on Feb 10, 2015 |
| Title |
Hopx-/- E16.5 lung, Biological Replicate 1 |
| Sample type |
RNA |
| |
|
| Source name |
Hopx-null_E16.5_lung
|
| Organism |
Mus musculus |
| Characteristics |
strain background: Mixed
genotype/variation: Hopx -/-
developmental stage: E16.5
tissue: lung
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA from embryonic, microdissected lungs was performed according to the manufacturer's instructions.
|
| Label |
Biotin
|
| Label protocol |
Biotinylated cRNA were prepared according the Affymetrix GeneChip Expression Analysis Technical Manual. Briefly, total RNA was converted to first-strand cDNA using Superscript II reverse transcriptase primed by a poly(T) oligomer that incorporated the T7 promoter. Second-strand cDNA synthesis was followed by in vitro transcription for linear amplification of each transcript and incorporation of biotinylated CTP and UTP.
|
| |
|
| Hybridization protocol |
The cRNA products were fragmented to 200 nucleotides or less, heated at 99ºC for 5 min and hybridized for 16 h at 45ºC to Affimatrix MOE 430 2.0 microarrays. 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 at 3um resolution after excitation at 570 nm. The average signal from two sequential scans was calculated for each microarray feature.
|
| Description |
7HOPK1
|
| Data processing |
cel files were RMA normalized using Partek Genomics Suite v6.6
|
| |
|
| Submission date |
Feb 09, 2015 |
| Last update date |
Feb 10, 2015 |
| Contact name |
Rajan Jain |
| Organization name |
University of Pennsylvania
|
| Department |
Cell and Developmental Biology
|
| Lab |
Epstein
|
| Street address |
3400 Civic Center Blvd
|
| City |
Philadelphia |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL1261 |
| Series (1) |
| GSE65755 |
Plasticity of Hopx+ Type I alveolar cells to regenerate Type II cells in the lung |
|
