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Sample GSM436258 Query DataSets for GSM436258
Status Public on Oct 30, 2009
Title PCL-006_miRNA
Sample type RNA
Source name Multiple myeloma patient PCL-006
Organism Homo sapiens
Characteristics disease status: multiple myeloma patient
sex: M
age at diagnosis (years): 55
stage (durie-salmon): PCL
monoclonal component: Gk
tc classification: TC5
related gene expression profiling (gep) data available (geo id): GSM342080
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 PCL-006
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
Phone +390223903581
Organization name IRCCS Istituto Nazionale dei Tumori
Department Department of Advanced Diagnostics
Street address Venezian 1
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
VALUE Aroma light (bioconductor) normalized signal intensity

Data table
hsa-let-7a 1063.03247
hsa-let-7a* 2.891224
hsa-let-7b 141.86947
hsa-let-7b* 6.21128
hsa-let-7c 112.33447
hsa-let-7c* 3.1219472
hsa-let-7d 316.79347
hsa-let-7d* 2.431261
hsa-let-7e 6.14677
hsa-let-7e* 2.08044
hsa-let-7f 469.59147
hsa-let-7f-1* 4.72708
hsa-let-7f-2* 3.572233
hsa-let-7g 554.63047
hsa-let-7g* 2.442868
hsa-let-7i 308.79147
hsa-let-7i* 2.802177
hsa-miR-1 3.940904
hsa-miR-100 5.23451
hsa-miR-100* 2.951634

Total number of rows: 722

Table truncated, full table size 15 Kbytes.

Supplementary file Size Download File type/resource
GSM436258.txt.gz 1.8 Mb (ftp)(http) TXT
Processed data included within Sample table

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