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Sample GSM436244 Query DataSets for GSM436244
Status Public on Oct 30, 2009
Title MM-115_miRNA
Sample type RNA
 
Source name Multiple myeloma patient MM-115
Organism Homo sapiens
Characteristics disease status: multiple myeloma patient
sex: F
age at diagnosis (years): 53
stage (durie-salmon): IIIA
monoclonal component: Gk
tc classification: TC1
related gene expression profiling (gep) data available (geo id): GSM341956
related genome-wide dna analysis data available (geo id): no
Treatment protocol Plasma cells were purified from bone marrow samples using CD138 immunomagnetic microbeads according to the manufacturer's instructions (MidiMACS system, Miltenyi Biotec); the purity of the positively selected PCs was assessed by morphology and flow cytometry and was >90% in all cases.
Extracted molecule total RNA
Extraction protocol Trizol extraction of total RNA was performed according to the manufacturer's instructions (Gibco BRL).
Label Cy3
Label protocol Labeled miRNAs were obtained from 500 ng of total RNA by ligating 5'-cytidine bisphosphate-Cy3 (pCp-Cy3, Agilent Technologies) to the 3'-ends. To enhance the ligation efficiency of the pCp-Cy3 T4 RNA ligase (Promega, Madison, WI), the total RNA was previously treated with alkaline phosphatase (Amersham, GE Healthcare, Buckinghamshire, UK) at 37°C for 30 min. The labeled RNA was purifed on chromatography columns (Micro Biospin 6, Bio-Rad, Hercules, CA).
 
Hybridization protocol Sample was hybridized on an Agilent microarray (G4470B) at 55°C for 17 hr in a rotating oven.
Scan protocol Image at 5 um resolution was generated using an Agilent scanner G2505B and the Feature Extraction 9.5 software (Agilent Technologies) was used to obtain the microarray raw data. The human miRNAs included in the platform were annotated according to Sanger miRBase Release 12.0.
Description MicroRNA profiling data from multiple myeloma patient MM-115
Data processing After discarding non-human miRNAs, the data were normalized using the Aroma Light package for Bioconductor. To overcome scaling biases due to background subtraction, the data were converted to obtain positive values throughout the dataset, at a minimum value of 1.
 
Submission date Aug 04, 2009
Last update date Oct 30, 2009
Contact name Luca Agnelli
E-mail(s) luca.agnelli@istitutotumori.mi.it, luca.agnelli@gmail.com
Phone +390223903581
Organization name IRCCS Istituto Nazionale dei Tumori
Department Department of Advanced Diagnostics
Street address Venezian 1
City MILAN
ZIP/Postal code 20133
Country Italy
 
Platform ID GPL8227
Series (1)
GSE17498 Identification of MicroRNA Expression Patterns and a MicroRNAs/mRNA Regulatory Network in Multiple Myeloma

Data table header descriptions
ID_REF
VALUE Aroma light (bioconductor) normalized signal intensity

Data table
ID_REF VALUE
hsa-let-7a 441.33047
hsa-let-7a* 3.395419
hsa-let-7b 141.86947
hsa-let-7b* 13.41647
hsa-let-7c 51.87097
hsa-let-7c* 2.411232
hsa-let-7d 112.33447
hsa-let-7d* 3.0280627
hsa-let-7e 9.43601
hsa-let-7e* 3.563802
hsa-let-7f 1273.12247
hsa-let-7f-1* 4.05663
hsa-let-7f-2* 2.710227
hsa-let-7g 667.69747
hsa-let-7g* 3.234093
hsa-let-7i 334.33547
hsa-let-7i* 3.358236
hsa-miR-1 3.636646
hsa-miR-100 34.87217
hsa-miR-100* 2.512763

Total number of rows: 722

Table truncated, full table size 15 Kbytes.




Supplementary file Size Download File type/resource
GSM436244.txt.gz 1.7 Mb (ftp)(http) TXT
Processed data included within Sample table

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