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Sample GSM315704 Query DataSets for GSM315704
Status Public on Jan 26, 2009
Title MIFS_case_2
Sample type RNA
 
Source name Case 2
Organism Homo sapiens
Characteristics RNA from fresh frozen tumor biopsy
Biomaterial provider Dept of Clinical Genetics, Lund University Hospital, Sweden
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from frozen tumor biopsies using Trizol reagent (Invitrogen, Carlsbad, CA, USA) and RNeasy (Qiagen, Valencia, CA, USA) according to the manufacturers' instructions.
RNA quality and concentration were measured using an Agilent 2100 bioanalyzer and Nanodrop ND-1000, respectively. cDNA was generated with the GeneChip® Whole Transcript (WT) cDNA Synthesis and Amplification Kit (Affymetrix) using 300 ng total RNA. Amplified cDNA was fragmented and end labeled using the GeneChip® WT Terminal Labelling Kit (Affymetrix). Subsequently, the fragmented and biotinylated cDNA was hybridized to the GeneChip® Human Gene 1.0 ST Arrays (Affymetrix). The arrays were washed and stained on a GeneChip® Fluidics Station 450 (Affymetrix) according to the manufacturer’s recommendations.
Label biotin
Label protocol GeneChip® WT Terminal Labelling Kit (Affymetrix Inc, Santa Clara, CA, USA)
 
Hybridization protocol Arrays were hybridized and washed according to the manufacturer's specifications (Affymetrix Inc., Santa Clara, CA, USA)
Scan protocol Arrays were scanned in a GeneChip® Scanner 3000 (Affymetrix Inc., Santa Clara, CA, USA)
Description Genome-wide gene expression profiling of MIFS using the Affymetrix GeneChip® Human Gene 1.0 ST Arrays (Affymetrix Inc., Santa Clara, CA, USA)
Data processing Image analysis was performed using GeneChip® Operating Software (GCOS, Affymetrix). Expression data was normalized, background corrected and summarized using the RMA algorithm implemented in the Affymetrix Expression Console™ version 1.0 software.
 
Submission date Aug 27, 2008
Last update date Jan 26, 2009
Contact name Karolin H Nord
Organization name Lund University
Department Dept of Clinical Genetics
Street address BMC C13
City Lund
ZIP/Postal code SE-22184
Country Sweden
 
Platform ID GPL6244
Series (2)
GSE12592 Gene expression analysis of myxoinflammatory fibroblastic sarcoma, and morphologically similar lesions
GSE12595 Two genetic pathways in myxoinflammatory fibroblastic sarcoma and morphologically similar lesions

Data table header descriptions
ID_REF
VALUE RMA-normalized intensities

Data table
ID_REF VALUE
7892501 2.109669
7892502 4.892608
7892503 3.18094
7892504 9.367878
7892505 2.527702
7892506 3.261998
7892507 4.789819
7892508 5.976036
7892509 9.37336
7892510 5.449892
7892511 3.904593
7892512 7.68842
7892513 3.185129
7892514 9.506344
7892515 9.005604
7892516 3.626882
7892517 5.962981
7892518 1.8302
7892519 5.28682
7892520 9.312763

Total number of rows: 33297

Table truncated, full table size 549 Kbytes.




Supplementary file Size Download File type/resource
GSM315704.CEL.gz 3.9 Mb (ftp)(http) CEL
Processed data included within Sample table

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