|
| Status |
Public on Nov 22, 2010 |
| Title |
ApoB, 17063 C57BL6#40 |
| Sample type |
RNA |
| |
|
| Source name |
Liver
|
| Organism |
Mus musculus |
| Characteristics |
sample type: ApoB, 17063 C57BL6#40
tissue: liver
treatment: ApoB, 17063
genotype: C57BL6
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Samples are processed in parallel in 96-well plates to minimize potential variation. Reaction purification is achieved using magnetic binding beads for cDNA and Qiagen RNeasy kits for cRNA purification.
|
| Label |
Biotin is incorporated during the amplification. This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.
|
| Label protocol |
The reverse transcription incorporates biotin moieties that are later labeled with phycoerythrin. After amplification, samples are put through a controlled fragmentation to improve hybridization sensitivity and consistency. The labeled molecules are biotinylated-cDNA.
|
| |
|
| Hybridization protocol |
GeneChip microarrays are loaded with the fragmented target sample/hybridization buffer mix using standard manual techniques. Arrays are hybridized for 18 hours at 45?C with vigorous mixing. Unbound sample is removed and staining is accomplished through the binding of streptavidin conjugated phycoerythrin to the hybridized target. Excess label is removed. Washing and staining steps are performed by the Affymetrix FS450 fluidics station using standard protocols.
|
| Scan protocol |
Arrays are scanned using a GeneChip Scanner 3000 7G with a 48 array autoloader. The scanner maintains the optimal temperature for the arrays prior to and during scanning.
|
| Description |
C57Bl6 or B6-Ldlr(tm1)Tg(APOA1-CETP) treated with control PBS or two oligoes against apoB, 17063 or 17068
|
| Data processing |
Data were loaded into the Rosetta Resolver? system (Rosetta Biosoftware, Seattle, WA) and processed using the RMA algorithm (http://0-www-ncbi-nlm-nih-gov.brum.beds.ac.uk/sites/entrez?cmd=Retrieve&db=PubMed&list_uids=12582260). Intensities were calculated based on RMA, a Rosetta-developed error, and a MAS-5 p-value. The Rosetta-developed error is used in the calculation of xdev for the ratio p-values as described in section 2.2 (http://0-bioinformatics-oxfordjournals-org.brum.beds.ac.uk/cgi/content/full/22/9/1111).
|
| |
|
| Submission date |
Jul 22, 2010 |
| Last update date |
Nov 22, 2010 |
| Contact name |
Oscar Puig |
| E-mail(s) |
oscar_puig@merck.com
|
| Organization name |
Merck Research Laboratories
|
| Department |
Molecular Profiling Research Informatics
|
| Street address |
126 East Lincoln Ave
|
| City |
Rahway |
| State/province |
NJ |
| ZIP/Postal code |
07065 |
| Country |
USA |
| |
|
| Platform ID |
GPL9734 |
| Series (1) |
| GSE23088 |
siRNAs induced long-term liver ApoB mRNA knockdown significantly lowers serum cholesterol in a mouse model with human-like serum lipids |
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