|
| Status |
Public on Feb 10, 2010 |
| Title |
adult colon wt vs. Spdef ko 1 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
adult colon Spdef ko
|
| Organism |
Mus musculus |
| Characteristics |
tissue: colon
developmental stage: adult
genotype: Spdef ko mouse
|
| Treatment protocol |
Tissue from wildtype and Spdef knockout mice were used for the study
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from dissected whole small intestines or colons using TRIzol Reagent (Invitrogen, Carlsbad, CA). Pooled total RNA from 2-3 littermates were utilized for each experiment.
|
| Label |
Cy5
|
| Label protocol |
500 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).
|
| |
|
| Channel 2 |
| Source name |
adult colon wt
|
| Organism |
Mus musculus |
| Characteristics |
tissue: colon
developmental stage: adult
genotype: wildtype mouse
|
| Treatment protocol |
Tissue from wildtype and Spdef knockout mice were used for the study
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated from dissected whole small intestines or colons using TRIzol Reagent (Invitrogen, Carlsbad, CA). Pooled total RNA from 2-3 littermates were utilized for each experiment.
|
| Label |
Cy3
|
| Label protocol |
500 ng of total RNA was labeled using low RNA Input Linear Amp kit (Agilent Technologies, Pato Alto, CA, USA).
|
| |
|
| |
| Hybridization protocol |
according to Agilent guidelines
|
| Scan protocol |
according to Agilent guidelines
|
| Description |
7703_1
|
| Data processing |
Microarray signal and background information were retrieved using Feature Extraction (V.9.5.3, Agilent Technologies). All data analyses were performed using ArrayAssist (5.5.1, Stratagene) and Microsoft Excel (Microsoft Corporation). Raw signal intensities were corrected by subtracting local background. Negative values were changed into a positive value close to zero (standard deviation of the local background) in order to allow calculation of ratios between intensities for features only present in one sample (wt or Spdef-/-). Data were filtered if both (wt or Spdef-/-) intensities were changed or if both intensities were less than two times the background signal and normalized with a LOESS algorithm.
|
| |
|
| Submission date |
Feb 18, 2009 |
| Last update date |
Feb 18, 2009 |
| Contact name |
Daniel E. Stange |
| E-mail(s) |
daniel.stange@uniklinikum-dresden.de
|
| Organization name |
University Clinic Dresden
|
| Street address |
Fetscherstr. 74
|
| City |
Dresden |
| ZIP/Postal code |
01307 |
| Country |
Germany |
| |
|
| Platform ID |
GPL4134 |
| Series (1) |
| GSE14892 |
The Ets domain transcription factor Spdef drives maturation of Goblet and Paneth cells in the intestinal epithelium |
|
