|
| Status |
Public on May 01, 2007 |
| Title |
3wkC |
| Sample type |
RNA |
| |
|
| Source name |
mammary gland, 3wk
|
| Organism |
Mus musculus |
| Characteristics |
Strain: CD1
Gender: female
Age: 3 weeks
Tissue: mammary gland
|
| Biomaterial provider |
The Biomedical Facility, University College Dublin
|
| Treatment protocol |
No treatment
|
| Growth protocol |
All animals were housed in accordance with accepted standards of humane animal care and grown to the appropriate age.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Whole mammary glands (4th inguinal) were dissected and lymph nodes removed. Total RNA was extracted with TriReagent (Molecular Probes) according to the manufacturer's instructions. Total RNA was cleaned with lithium chloride by adding an equal volume of 8M LiCl pH5.2 and storing at -20degreesC for a minimum of 3 hours. After centrifugation, pellet was washed twice with cold 70% ethanol, dried and resuspended in DEPC-treated water.
|
| Label |
biotin
|
| Label protocol |
5 micrograms RNA were used to synthesise double stranded cDNA as per Affymetrix guidelines. cDNA was cleaned with phenol chloroform. A 5 hour in vitro transcription reaction was carried out to produce biotin-labelled cRNA. Labelled cRNA was cleaned with Qiagen RNeasy columns.
|
| |
|
| Hybridization protocol |
Following fragmentation, 15 micrograms cRNA were hybridised for 16 hours at 45degreesC to GeneChip MOE430A arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner 2500.
|
| Description |
Recommended Affymetrix protocols were followed.
|
| Data processing |
Data was imported into Genespring. Per chip normalisation to 50th percentile, per gene normalisation to median and data transformation to set all measurements below 0.001 to 0.001 were performed.
|
| |
|
| Submission date |
Dec 05, 2006 |
| Last update date |
May 01, 2007 |
| Contact name |
Finian Martin |
| E-mail(s) |
finian.martin@ucd.ie
|
| Organization name |
University College Dublin
|
| Department |
UCD School of Biomolecular and Biomedical Science
|
| Street address |
Conway Institute, Belfield
|
| City |
Dublin |
| ZIP/Postal code |
Dublin 4 |
| Country |
Ireland |
| |
|
| Platform ID |
GPL339 |
| Series (1) |
| GSE6453 |
Expression microarray analysis of pubertal mouse mammary gland development |
|
