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Sample GSM1405684 Query DataSets for GSM1405684
Status Public on Jul 29, 2016
Title Hamster_Control_Sample
Sample type RNA
Source name ATCC CCL-49 (RPMI 1826)
Organism Mesocricetus auratus
Characteristics hybrid: : Mesocricetus auratus
original tumor type: Melanoma
sample type: Cultured monolayer
Treatment protocol Tissue samples were preserved as formalin-fixed paraffin-embedded (FFPE) tissue blocks for up to 40 years and sectioned to 5-10 um thick for nucleic acid isolation.
Growth protocol Various human tumors were inidividually grafted to the cheek pouches of adult, unconditioned golden hamsters (Mesocricetus auratus), and the resulting tumor for each was serially passaged in hamsters for multiple years.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted using the RNeasy FFPE Kit (Qiagen, Germantown, MD) according to manufacturer’s instructions (3h incubation at 55 degrees C followed by glass fiber filtration). RNA purity was checked by OD260/280 readings and RNA integrity was checked using Agilent Bioanalyzer capillary electrophoresis profiles.
Label biotin
Label protocol Biotinylated cDNA from each sample weas prepared by conversion of 50 ng total RNA to cDNA by reverse transcription, amplification by the SPIA method, and fragmentation and labeling with biotin using the Ovation Pico WTA System v2 and Encore Biotin Module kits according to the manufacturer’s instructions (NuGEN, San Carlos CA).
Hybridization protocol 5.5 ug of fragmented, biotin-labeled cDNA were hybridized for 16 hr at 45 degrees C on GeneChip Human U133_X3P arrays (Affymetrix; catalog no. 900516). GeneChips were washed and stained with streptavidin-phycoerythrin using the Affymetrix Fluidics Station 450, according to the manufacturer's recommended protocol.
Scan protocol GeneChips were scanned using the Affymetrix GCS 3000 7G.
Description ATCC CCL-49 (RPMI 1826)
Data processing Fluorescent signals were collected and processed by AGCC and MAS 5.0 using Affymetrix default analysis settings and global scaling as the normalization method in Expression Colsole. The trimmed mean target intensity (TGT) of each array was set to 250. Following MAS 5.0 normalization and global scaling, unannotated probe sets and probe sets for which no signal value was greater than the median signal for AFFX spike-in controls with all Absent Detection Calls were omitted from further analysis. Subsequently, because an intact hamster cell line (sample IMM006, cell line CCL-49) control RNA sample was used for comparison with the four human-hamster hybrid FFPE samples, all remaining signal values for the hamster cell line sample were multiplied by the ratio of the median signal in all FFPE hybrid samples for AFFX spike-in control probe sets called present in all samples divided by the median signal for the same probe sets in the hamster control sample.
Submission date Jun 06, 2014
Last update date Jul 29, 2016
Contact name David M Goldenberg
Organization name Garden State Cancer Center
Department Center for Molecular Medicine and Immunology
Street address 300 The American Road
City Morris Plains
State/province NJ
ZIP/Postal code 07950
Country USA
Platform ID GPL1352
Series (1)
GSE58277 In-Vivo Fusion of Human Cancer and Hamster Stromal Cells Permanently Transduces and Transcribes Human DNA

Data table header descriptions
VALUE MAS5.0 signal intensity

Data table
1053_3p_at 2852.115878 A 0.5819307
117_3p_at 6368.87809 M 0.05447043
1494_3p_f_at 499.5570891 A 0.8612349
1552275_3p_s_at 1343.438998 A 0.0952148
1552281_3p_at 3073.982226 A 0.27417
1552296_3p_at 4640.75955 A 0.334473
1552302_3p_at 544.5478222 A 0.696289
1552311_3p_a_at 3948.663948 A 0.567627
1552321_3p_a_at 2830.867617 A 0.601074
1552340_3p_at 3358.912508 A 0.171387
1552343_3p_s_at 1477.170325 A 0.366211
1552354_3p_at 640.8842043 A 0.780518
1552476_3p_s_at 685.6697236 A 0.7993164
1552480_3p_s_at 758.1600678 A 0.27417
1552504_3p_a_at 994.1128106 A 0.5
1552518_3p_s_at 171.9867794 A 0.9604492
1552528_3p_at 3373.919008 A 0.601074
1552535_3p_at 844.0828074 A 0.633789
1552566_3p_at 3851.720555 A 0.696289
1552575_3p_a_at 285.4927499 A 0.780518

Total number of rows: 46123

Table truncated, full table size 1904 Kbytes.

Supplementary file Size Download File type/resource
GSM1405684_IMM006-U133_X3P.CEL.gz 4.3 Mb (ftp)(http) CEL
GSM1405684_IMM006-U133_X3P.mas5.CHP.gz 345.8 Kb (ftp)(http) CHP
Processed data included within Sample table
Processed data provided as supplementary file

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