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Sample GSM1198318 Query DataSets for GSM1198318
Status Public on Feb 20, 2014
Title DGAT1_Study1_Cmpd2_7
Sample type RNA
 
Source name Skin
Organism Mus musculus
Characteristics treatment: DGAT1 inhibitor compound 2
tissue: dorsal skin
genotype: C57BL/6
age: 8 weeks
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 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 45C 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 Gene expression data from dorsal skin taken after 14 days of treatment with DGAT1 inhibitor.
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 30, 2013
Last update date Feb 21, 2014
Contact name eric muise
E-mail(s) eric_muise@merck.com
Organization name Merck
Department Genetics and Pharmacogenomics
Street address 33 Ave Louis Pasteur
City Boston
State/province MA
ZIP/Postal code 02115
Country USA
 
Platform ID GPL9734
Series (1)
GSE49375 DGAT1 Inhibitor-Induced Gene Expression in Mouse Skin

Data table header descriptions
ID_REF
VALUE Normalized intensity.

Data table
ID_REF VALUE
100113564_TGI_at 16.54
100087246_TGI_at 593.7
100118487_TGI_at 228.7
100098414_TGI_at 18.27
100093140_TGI_at 15.35
100096868_TGI_at 280.5
100110141_TGI_at 2.483
100115501_TGI_at 20.42
100094903_TGI_at 5.406
100113524_TGI_at 1836
100093330_TGI_at 4.102
100113914_TGI_at 15.99
100100289_TGI_at 8.111
100114354_TGI_at 8.127
100112279_TGI_at 75.54
100085470_TGI_at 4.248
100109262_TGI_at 3.216
100085458_TGI_at 43.77
100086663_TGI_at 64.93
100097327_TGI_at 4889

Total number of rows: 38385

Table truncated, full table size 854 Kbytes.




Supplementary file Size Download File type/resource
GSM1198318__52048700762976113012412215921400.CEL.gz 3.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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