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Sample GSM954793 Query DataSets for GSM954793
Status Public on Jan 22, 2013
Title OS_Biopsy_11 (mRNA)
Sample type RNA
 
Source name Osteosarcoma biopsy
Organism Homo sapiens
Characteristics age: 5 years
gender: male
chemotherapy: MAP 2 pre-surgery, 3 post
percent necrosis: >99% necrosis
recurrence: N
death: N
time until first recurrence or latest follow-up (months): 61.1
tissue: osteosarcoma
biopsy/resection pair: NA
Extracted molecule total RNA
Extraction protocol RNA was extracted from FFPE blocks using the Qiagen RNeasy kit according to company protocol.
Label biotin
Label protocol Total RNA underwent a reverse transcription reaction to generate double-stranded cDNA. Standard Illumina protocols followed (Whole-Genome DASL HT Assay Kits #'s DA-905-0024, DA-905-0096, DA-905-1024, DA-905-1096).
 
Hybridization protocol Standard Illumina hybridization protocol. Arrays were washed and stained with strepatavidin-Cy3, and then scanned in the array reader.
Scan protocol Standard Illumina scanning protocol using the Illumina BeadArray Reader.
Data processing Expression data were imported to the R environment and processed using the Illumina-specific package lumi. Variance-stabilizing transformation (VST) and quantile normalization were applied. VST is described in Lin SM, Du P, Huber W, Kibbe WA. Model-based variance-stabilizing transformation for Illumina microarray data. Nucleic Acids Res. 2008 36:e11 (PMID 18178591).
 
Submission date Jul 02, 2012
Last update date Jan 22, 2013
Contact name Katherine Hill
E-mail(s) khill5@bidmc.harvard.edu
Organization name Beth Israel Deaconess Medical Center
Department Medicine
Lab Dimitrios Spentzos
Street address 330 Brookline Avenue, DA-679
City Boston
State/province MA
ZIP/Postal code 02215
Country USA
 
Platform ID GPL14951
Series (2)
GSE39055 mRNA profiling and clinical outcomes in human osteosarcoma (biopsies)
GSE39058 microRNA- and mRNA-based studies in paraffin-archived human osteosarcoma specimens reveal profiles with reproducible and independent prognostic value

Data table header descriptions
ID_REF
VALUE VST+quantile normalization
Detection PVal

Data table
ID_REF VALUE Detection PVal
ILMN_1762337 7.904255881 0.60345
ILMN_2055271 12.55626951 0
ILMN_2383229 8.688757302 0.22759
ILMN_1806310 7.97889167 0.45862
ILMN_1779670 8.109350953 0.40345
ILMN_1717783 12.92229191 0
ILMN_1814316 8.902787926 0.17931
ILMN_2359168 10.14064068 0.03793
ILMN_1731507 7.999358701 0.45172
ILMN_1787689 10.15715569 0.03793
ILMN_3241953 7.841517558 0.92759
ILMN_1745607 11.78794747 0.0069
ILMN_2136495 9.278920592 0.11724
ILMN_1668111 7.84033476 0.92759
ILMN_2295559 8.928402859 0.17931
ILMN_1735045 7.868119196 0.78621
ILMN_1680754 7.841517558 0.92759
ILMN_2375184 8.187371702 0.36897
ILMN_1659452 8.071474247 0.42414
ILMN_1767388 8.13401801 0.39655

Total number of rows: 29377

Table truncated, full table size 928 Kbytes.




Supplementary data files not provided
Processed data included within Sample table

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