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Sample GSM592120 Query DataSets for GSM592120
Status Public on Oct 01, 2011
Title macrophage_m35_C57BL/6.MOLFc4(51Mb)-Ldlr-/-
Sample type RNA
 
Source name macrophages
Organism Mus musculus
Characteristics tissue: n/a
cell type: macrophage
genetic background: C57BL/6
genotype: C57BL/6.MOLFc4(51Mb)-Ldlr-/-
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 Common genetic variants in a 58-kilobase (kb) region of chromosome 9p21, near the CDKN2A/B cell proliferation inhibitor genes, are strongly associated with coronary artery disease (CAD). We previously reported a congenic mouse model harboring an atherosclerosis susceptibility locus in a region of homology with the human 9p21 locus. We now report markedly decreased Cdkn2a (cyclin-dependent kinase inhibitor 2a) mRNA expression in macrophages and increased circulating levels of Ly6Chigh inflammatory monocytes in congenic mice compared to controls. A bone marrow (BM) transplantation study revealed that BM-derived cells from Cdkn2a+/- mice are capable of conferring accelerated atherosclerosis, increased inflammatory monocyte subsets and monocyte proliferation in the Ldlr-/- mouse model. These findings provide a mechanistic link between decreased expression of Cdkn2a transcripts, increased monocyte proliferation, and accelerated atherosclerosis.
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 Sep 09, 2010
Last update date Oct 01, 2011
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)
GSE24342 Athsq1 is linked to Cdkn2a

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 53.6604 3.7598e-002
100087246_TGI_at 1676.9591 2.4414e-004
100118487_TGI_at 186.8620 2.4414e-004
100098414_TGI_at 18.4378 8.7036e-001
100093140_TGI_at 46.2051 8.8843e-001
100096868_TGI_at 783.4312 2.4414e-004
100110141_TGI_at 5.2527 7.8052e-001
100115501_TGI_at 48.2157 2.9297e-003
100094903_TGI_at 8.1907 9.8926e-001
100113524_TGI_at 4219.2935 2.4414e-004
100093330_TGI_at 15.8742 5.0000e-001
100113914_TGI_at 39.0004 2.1948e-001
100100289_TGI_at 22.6253 1.4966e-001
100114354_TGI_at 11.9727 8.2617e-001
100112279_TGI_at 331.6553 2.4414e-004
100085470_TGI_at 8.2565 8.0542e-001
100109262_TGI_at 8.1360 5.6152e-002
100085458_TGI_at 162.2539 2.4414e-004
100086663_TGI_at 149.6905 7.3242e-004
100097327_TGI_at 32.6170 6.5430e-001

Total number of rows: 38385

Table truncated, full table size 1400 Kbytes.




Supplementary file Size Download File type/resource
GSM592120__52048700786348030610407094603245.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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