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Sample GSM493549 Query DataSets for GSM493549
Status Public on Jan 12, 2010
Title Kidney_BPN_Rep1
Sample type RNA
 
Source name Kidney
Organism Mus musculus
Characteristics tissue: Kidney
condition: BPN
strain: BPN/3J
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
Label protocol Biotin is incorporated during the amplification. This binds a streptavidin-conjugated phycoerythrin during the post-hybridization staining process that provides the measurable signal.
The final in vitro 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-cRNA.
 
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 45oC 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 Kidney from genetically hypertensive blood pressure high (BPH), normotensiveblood pressure normal (BPN), and hypotensive blood pressure low (BPL) inbred mouse strains.
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 Jan 06, 2010
Last update date Jan 11, 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)
GSE19817 Gene expression profiling of hypertensive and hypotensive mice

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

Data table
ID_REF VALUE PVALUE
100113564_TGI_at 6.9280 5.6763e-001
100087246_TGI_at 592.5803 2.9297e-003
100118487_TGI_at 5.5302 1.7139e-001
100098414_TGI_at 19.6974 9.8926e-001
100093140_TGI_at 29.7362 7.8052e-001
100096868_TGI_at 221.5950 2.9297e-003
100110141_TGI_at 4.9314 7.8052e-001
100115501_TGI_at 12.6755 8.7036e-001
100094903_TGI_at 7.6270 2.7417e-001
100113524_TGI_at 1177.2930 2.4414e-004
100093330_TGI_at 18.4578 9.5215e-002
100113914_TGI_at 24.2843 5.6763e-001
100100289_TGI_at 38.7832 2.4609e-001
100114354_TGI_at 24.0432 8.8867e-001
100112279_TGI_at 168.7484 2.4414e-004
100085470_TGI_at 7.2483 6.8872e-001
100109262_TGI_at 5.5001 8.5034e-001
100085458_TGI_at 33.2408 3.0273e-002
100086663_TGI_at 63.1927 1.2964e-001
100097327_TGI_at 1435.9019 1.9531e-003

Total number of rows: 38385

Table truncated, full table size 1391 Kbytes.




Supplementary file Size Download File type/resource
GSM493549.CEL.gz 3.3 Mb (ftp)(http) CEL
Processed data included within Sample table

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