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Sample GSM1198333 Query DataSets for GSM1198333
Status Public on Feb 20, 2014
Title DGAT1_Study2_Cmpd6_2
Sample type RNA
 
Source name Skin
Organism Mus musculus
Characteristics treatment: DGAT1 inhibitor compound 6
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 19.98
100087246_TGI_at 629.8
100118487_TGI_at 136.7
100098414_TGI_at 14.4
100093140_TGI_at 18.86
100096868_TGI_at 260.7
100110141_TGI_at 2.681
100115501_TGI_at 19.27
100094903_TGI_at 4.8
100113524_TGI_at 1911
100093330_TGI_at 4.232
100113914_TGI_at 17.47
100100289_TGI_at 7.088
100114354_TGI_at 7.938
100112279_TGI_at 59.52
100085470_TGI_at 3.657
100109262_TGI_at 6.013
100085458_TGI_at 87.76
100086663_TGI_at 88.5
100097327_TGI_at 5296

Total number of rows: 38385

Table truncated, full table size 855 Kbytes.




Supplementary file Size Download File type/resource
GSM1198333__52048700762757121712412415461972.CEL.gz 3.1 Mb (ftp)(http) CEL
Processed data included within Sample table

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