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Sample GSM442724 Query DataSets for GSM442724
Status Public on Nov 06, 2009
Title MM-239_GEP
Sample type RNA
Source name Human multiple myeloma patient MM-239
Organism Homo sapiens
Characteristics sex: F
age at diagnosis (years): 72
stage (durie-salmon): nd
monoclonal component: Gk
tc classification: TC3
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). RNA was purified using the Rneasy Mini Kit according to the manufacturer's instruction (Qiagen).
Label biotin
Label protocol Biotinylated cRNA were prepared according to the standard Affymetrix protocol from 5 micrograms of total RNA (Expression Analysis Technical Manual, Affymetrix).
Hybridization protocol Following fragmentation, 15 micrograms of cRNA were hybridized for 16 hr and 30 minutes at 45°C on GeneChip HG-U133A Arrays. GeneChips were washed and stained in the Affymetrix Fluidics Station 450.
Scan protocol HG-U133A arrays were scanned using the Agilent GeneArray Scanner G2500A (Affymetrix).
Description Gene expression profiling data from human multiple myeloma patient MM-239
Same raw data (CEL file) as GSM342042
Data processing The probe-level signals were converted to expression values using custom GeneAnnot-based Chip Annotation Files version 2.0.1 (CDF), available at the URL, and the Bioconductor function for Robust Multi-array Analysis (RMA), in which perfect match intensities are background adjusted, normalized by means of quantile-quantile normalization, and log2 transformed.
Submission date Aug 20, 2009
Last update date Nov 05, 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 GPL9021
Series (1)
GSE17498 Identification of MicroRNA Expression Patterns and a MicroRNAs/mRNA Regulatory Network in Multiple Myeloma

Data table header descriptions
VALUE RMA normalized signal intensity (40 samples)

Data table
GC00U921857_at 5.796972484
GC00U922298_at 4.807042975
GC00U990668_at 4.224431758
GC00U990680_at 5.705905904
GC00U990706_at 5.705354502
GC00U990756_at 6.086016753
GC00U990780_at 7.054278816
GC00U990809_at 5.722860861
GC00U990811_at 4.545237136
GC00U990813_at 6.128528072
GC00U991001_at 4.525466239
GC01M000752_at 4.281760868
GC01M000869_at 7.754151304
GC01M001136_at 7.701798302
GC01M001143_at 8.962354211
GC01M001236_at 9.01565202
GC01M001261_at 7.137602329
GC01M001329_at 4.378767342
GC01M001646_at 5.140112155
GC01M001715_at 7.662217964

Total number of rows: 12279

Table truncated, full table size 322 Kbytes.

Supplementary file Size Download File type/resource
GSM442724.CEL.gz 2.2 Mb (ftp)(http) CEL
Processed data included within Sample table

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