|
| Status |
Public on Oct 01, 2009 |
| Title |
Mouse_Klf4Loxp/Loxp_3mo_rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Mouse, Control
|
| Organism |
Mus musculus |
| Characteristics |
genotype/variation: control (lacking the Cre transgene)
gender: female
strain: mixed genetic background
tissue: esophagus
cell type: epithelial
age: 3 months
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA extraction was performed using Qiagen RNeasy mini kit according to the manufacturer's instructions.
|
| 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, and the resulting cRNA was fragmented and assessed by Bioanalyzer.
|
| |
|
| Hybridization protocol |
15ug biotinylated cRNA were added to Affymetrix hybridization cocktails, heated at 99ºC for 2 min and hybridized for 16 h at 45ºC to MOE430 2.0 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 |
An Affymetrix GCS3000 7G scanner was used to collect fluorescence signal after excitation at 570 nm.
|
| Description |
no additional information
|
| Data processing |
rma was calculated with Partek Genomics Suite v6.4 from cel files, using default settings to exclude Afftymetrix-annotated control probesets, yielding values for 28853 non-control probesets.
|
| |
|
| Submission date |
Jul 31, 2009 |
| Last update date |
Aug 13, 2009 |
| Contact name |
Jonathan P. Katz |
| E-mail(s) |
[email protected]
|
| Organization name |
University of Pennsylvania
|
| Department |
Medicine/Gastroenterology
|
| Street address |
913 BRBII/III, 421 Curie Blvd.
|
| City |
Philadelphia |
| State/province |
PA |
| ZIP/Postal code |
19104 |
| Country |
USA |
| |
|
| Platform ID |
GPL6246 |
| Series (1) |
| GSE17447 |
Expression data using esophageal epithelia from 3 month old-mice lacking the transcription factor Klf4 |
|
