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Sample GSM569168 Query DataSets for GSM569168
Status Public on Nov 22, 2010
Title ApoB, 17068 C57BL6#33
Sample type RNA
 
Source name Liver
Organism Mus musculus
Characteristics sample type: ApoB, 17068 C57BL6#33
tissue: liver
treatment: ApoB, 17068
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

Data table header descriptions
ID_REF Rosetta generated unique probe identifier
VALUE RMA signal
PVALUE P-value of expression level

Data table
ID_REF VALUE PVALUE
100113564_TGI_at 43.1681 3.0273e-002
100087246_TGI_at 1515.1808 2.4414e-004
100118487_TGI_at 301.7267 2.4414e-004
100098414_TGI_at 21.7541 9.3237e-001
100093140_TGI_at 29.9158 9.3237e-001
100096868_TGI_at 471.7691 2.4414e-004
100110141_TGI_at 4.0793 9.7607e-001
100115501_TGI_at 34.8869 8.0566e-002
100094903_TGI_at 6.5776 9.9707e-001
100113524_TGI_at 3173.9314 2.4414e-004
100093330_TGI_at 5.0057 6.9629e-001
100113914_TGI_at 27.0840 1.7139e-001
100100289_TGI_at 22.7480 8.0566e-002
100114354_TGI_at 14.8981 1.7383e-001
100112279_TGI_at 66.6099 2.4414e-004
100085470_TGI_at 7.1083 3.0371e-001
100109262_TGI_at 87.0247 2.4414e-004
100085458_TGI_at 92.3619 2.4414e-004
100086663_TGI_at 158.9224 1.9531e-003
100097327_TGI_at 10.7339 8.8867e-001

Total number of rows: 38385

Table truncated, full table size 1393 Kbytes.




Supplementary file Size Download File type/resource
GSM569168__52048700762518091510408275837852.CEL.gz 3.4 Mb (ftp)(http) CEL
Processed data included within Sample table

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