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Sample GSM556554 Query DataSets for GSM556554
Status Public on Dec 15, 2010
Title 63969_MCCw156
Sample type RNA
 
Source name Merkel cell carcinoma
Organism Homo sapiens
Characteristics age: 65 year old
tissue: Merkel cell carcinoma primary tumor
sample type: Merkel cell carcinoma primary tumor RNA (macrodissected, from wide local excision, includes stroma) from a 65 year old
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 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 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 Merkel cell carcinoma primary tumor RNA (macrodissected, from wide local excision, includes stroma) from a 65 year old
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 Jun 15, 2010
Last update date Dec 15, 2010
Contact name Michele Cleary
E-mail(s) michele_cleary@merck.com
Phone 215 652-6104
Organization name Merck and Co., Inc.
Department Genetics and Pharmacogenomics
Lab Target & Pathway Biology
Street address 770 Sumneytown Pike
City West Point
State/province PA
ZIP/Postal code 19486
Country USA
 
Platform ID GPL10379
Series (1)
GSE22396 Gene expression analysis of Merkel Cell Carcinoma

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
merck-N79601_RC_at 139.7340 2.4414e-004
merck-AK128290_at 14.8863 1.8555e-002
merck-NC_001526_ORF_1178_at 5.6136 9.6973e-001
merck-NC_001526_ORF_1179_at 8.5305 2.4609e-001
merck-NC_001526_ORF_1180_at 7.4557 5.0000e-001
merck-NC_001526_ORF_1181_s_at 16.3536 6.0107e-001
merck-NC_001526_ORF_1182_at 5.5917 8.2275e-001
merck-NC_001357_ORF_1183_at 6.8777 3.9893e-001
merck-NC_001357_ORF_1184_at 23.0259 1.0742e-002
merck-NC_001357_ORF_1185_at 6.8719 3.0371e-001
merck-NC_001357_ORF_1186_at 6.5713 4.6606e-001
merck-NC_001357_ORF_1187_a_at 20.4104 1.9458e-001
merck-NC_001357_ORF_1188_a_at 7.1017 6.5845e-001
merck-NC_001357_ORF_1189_s_at 20.2138 6.0107e-001
merck-NC_001357_ORF_1190_at 21.4833 5.6763e-001
merck-X04370_ORF_1249_s_at 17.7514 2.1948e-001
merck-X04370_ORF_1258_s_at 6.1050 6.9629e-001
merck-X04370_ORF_1261_s_at 6.0164 9.9585e-001
merck-NC_001526_ORF_1177_at 4.9517 9.4385e-001
merck-NC_001545_ORF_1341_at 11.0725 1.9458e-001

Total number of rows: 52378

Table truncated, full table size 1925 Kbytes.




Supplementary file Size Download File type/resource
GSM556554__52070900797039031010407111021362.CEL.gz 4.8 Mb (ftp)(http) CEL
Processed data included within Sample table

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