|
| Status |
Public on Jun 29, 2010 |
| Title |
e9.5_embryo_rep3 [exon version] |
| Sample type |
RNA |
| |
|
| Source name |
embryo, e9.5
|
| Organism |
Mus musculus |
| Characteristics |
age: e9.5
tissue: embryo
strain: C57BL/6J
|
| Treatment protocol |
Embryos for RNA isolation were stored in RNAlater (Ambion) prior to extraction.
|
| Growth protocol |
To generate embryos, C57BL/6J females were placed with C57BL/6J males overnight and checked for the presence of a vaginal plug in the morning. The day that a plug was detected was considered embryonic day (E) 0.5. All mouse breeding and manipulations were performed in accordance with the Canadian Council on Animal Research. Embryos were collected between E6.5 – E11.5 for RNA isolation.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using TriZOL (Invitrogen) according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
cDNA was synthesized using the GeneChip Whole Transcript Sense Target Labeling and Control Reagents kit (Affymetrix) on 1 µg of total RNA treated with the RiboMinus Human/Mouse Transcriptome Isolation Kit (Invitrogen). This sense cDNA was then labeled using the GeneChip WT Terminal labeling kit (Affymetrix). All the protocols used were provided by the manufacturers.
|
| |
|
| Hybridization protocol |
5 micrograms of biotinylated target was incubated with the GeneChip Human Exon 1.0 ST array (Affymetrix) at 45°C for 16–20 h. After hybridization, nonspecifically bound material was removed by washing and specifically bound target was detected using the GeneChip Hybridization, Wash and Stain kit, and the GeneChip Fluidics Station 450 (Affymetrix).
|
| Scan protocol |
The arrays were scanned using the GeneChip Scanner 3000 7G (Affymetrix) and raw data was extracted from the scanned images and analyzed with the Affymetrix Power Tools software package (Affymetrix).
|
| Data processing |
Affymetrix Power Tools and PLIER, on core PS and MPS only. For more info, refer to Revil, T. et al. 2010. BMC Genomics.
probe group file MoEx-1_0-st-v1.r2.pgf
meta-probeset file MoEx-1_0-st-v1.r2.dt1.mm8.core.mps
|
| |
|
| Submission date |
May 24, 2010 |
| Last update date |
Jun 29, 2010 |
| Contact name |
Timothee Revil |
| Organization name |
McGill University
|
| Department |
Human Genetics
|
| Lab |
Loydie Majewska
|
| Street address |
4060 Ste-Catherine W PT420
|
| City |
Montreal |
| State/province |
Quebec |
| ZIP/Postal code |
H3Z2Z3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL6193 |
| Series (1) |
| GSE21971 |
Alternative splicing is frequent during early embryonic development in mouse |
|
| Relations |
| Alternative to |
GSM546302 (gene-level) |
