|
| Status |
Public on Jan 24, 2011 |
| Title |
foregut_NF40_RFX6MM_biologicalrep3 |
| Sample type |
RNA |
| |
|
| Source name |
Xenopus laevis tadpoles injected with MM at 8-cell stage, dissected at NF40
|
| Organism |
Xenopus laevis |
| Characteristics |
tissue: foregut
treatment: MM
developmental stage: NF40
|
| Treatment protocol |
Tadpoles were anaesthetized in MS-222
|
| Growth protocol |
Embryos were grown in 0.1XMMR
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Single-stranded, then double-stranded cDNA was synthesized from the poly(A)+ mRNA present in the isolated total RNA (typically 10 μg total RNA starting material each sample reaction) using the SuperScript Double-Stranded cDNA Synthesis Kit (Invitrogen Corp., Carlsbad, CA ) and poly (T)-nucleotide primers that contained a sequence recognized by T7 RNA polymerase. A portion of the resulting ds cDNA was used as a template to generate biotin-tagged cRNA from an in vitro transcription reaction (IVT), using the Affymetrix GeneChip® IVT Labeling Kit. 15 μg of the resulting biotin-tagged cRNA was fragmented to an average strand length of 100 bases (range 35-200 bases) following prescribed protocols (Affymetrix GeneChip® Expression Analysis Technical Manual).
|
| |
|
| Hybridization protocol |
10 μg of fragmented target cRNA was hybridized at 45°C with rotation for 16 hours (Affymetrix GeneChip® Hybridization Oven 640) to probe sets present on an Affymetrix GeneChip Xenopus Genome array.
|
| Scan protocol |
The GeneChip® arrays were washed and then stained (SAPE, streptavidin-phycoerythrin) on an Affymetrix Fluidics Station 450, followed by scanning on a GeneChip® Scanner 3000 7G. The results were quantified and analyzed using GCOS 1.2 software (Affymetrix, Inc.) using default values (Scaling, Target Signal Intensity = 500; Normalization, All Probe Sets; Parameters, all set at default values).
|
| Description |
Gene expression data from MM injected embryo foreguts dissected at NF40
|
| Data processing |
The data were analyzed with Affymetrix expression control using PLIER algorithm and quantile normalization, no scaling was used during the primary analysis.
|
| |
|
| Submission date |
Aug 16, 2010 |
| Last update date |
Jan 24, 2011 |
| Contact name |
Esther J Pearl |
| E-mail(s) |
[email protected]
|
| Phone |
+15149875780
|
| Fax |
+5149875793
|
| Organization name |
Clinical Research Institute of Montreal
|
| Street address |
110 Pine Avenue West
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H2W1R7 |
| Country |
Canada |
| |
|
| Platform ID |
GPL10756 |
| Series (1) |
| GSE23642 |
Expression data from Xenopus anterior gut RFX6 knockdown |
|
