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Sample GSM1152300 Query DataSets for GSM1152300
Status Public on May 22, 2014
Title Bone-Marrow_MGUS_G800
Sample type RNA
 
Source name Bone Marrow MGUS patient
Organism Homo sapiens
Characteristics tissue type: Bone Marrow
cell type: Monoclonal Gammopathy of Undetermined Significance (MGUS) plasma cells
Extracted molecule total RNA
Extraction protocol In all the samples a CD138-positive PC isolation using the AutoMACs separation system (Miltenyi-Biotec) was carried out. Final purity was >95% in all MM and SMM cases, and >90% in MGUS patients and healthy donors. Total RNA was extracted from normal and tumor plasma cells using miRNEasy Mini Kit (Qiagen, Valencia, USA) following manufacturer's protocol. The RNA integrity was assessed using Agilent 2100 Bioanalyzer (Agilent, Palo Alto, CA).
Label biotin
Label protocol Labelling and hybridizations were performed according to protocols from Affymetrix. Briefly, 100-300 ng of total RNA were amplified and labeled using the WT Sense Target labelling and control reagents kit (Affymetrix Inc., Santa Clara, CA, USA)
 
Hybridization protocol Labeled RNA was hybridized to Human Gene 1.0 ST Array
Scan protocol Washing and scanning were performed using GeneChip System of Affymetrix (GeneChip Hybridization Oven 640, GeneChip Fluidics Station 450 and GeneChip Scanner 7G).
Data processing Normalization was carried out by using the expression console (Affymetrix) with RMA algorithm which includes background correction, normalization and calculation of expression values (log2). Since myeloid contamination signature can be detected even in samples with high purity, those probes identifying genes exclusive of myeloid lineage were subtracted from the analysis from the out set.
Unsupervised analysis: In order to classify the samples, multidimensional scaling method (MDS) implemented with SIMFIT statistical package (version 6.4.1, available at http://www.simfit.manchester.ac.uk) was performed using Euclidean distance. In addition, an unsupervised hierarchical clustering with Euclidean distance as the distance measure, and group average as clustering method was carried out.
Supervised analysis: Significant Analysis of Microarrays (SAM) algorithm (http://www-stat.standford.edu/-tibs/SAM) was used to identify genes with statistically significant changes in expression between different classes(25). All data were permutated over 1,000 cycles by using the two-class and multiclass response format, without considering equal variances. Significant genes were selected based on the lowest q-value (q-value < 10-5).
Gene function analysis: The probe sets were functionally annotated and grouped according to their biological function using Gene Ontology biological process descriptions. The functional analysis to identify the most relevant biological mechanisms, pathways and functional categories in the data sets of genes selected by statistical analysis, was generated through the use of IPA (Ingenuity Systems, www.ingenuity.com).
probe group file: HuGene-1_0-st-v1.r4.pgf
meta-probeset file: HuGene-1_0-st-v1.r4.mps
 
Submission date May 31, 2013
Last update date May 22, 2014
Contact name Norma C. Gutiérrez
E-mail(s) normagu@usal.es
Phone +34923291384
Organization name Centro de Investigación del Cáncer de Salamanca
Department Hematologia
Lab 12
Street address Campus Miguel de Unamuno
City Salamanca
State/province Salamanca
ZIP/Postal code 37007
Country Spain
 
Platform ID GPL6244
Series (1)
GSE47552 Transcriptome analysis reveals molecular profiles associated with evolving steps of monoclonal gammopathies

Data table header descriptions
ID_REF
VALUE Quantile normalized log2 gene level expression values from Affymetrix Expression Console

Data table
ID_REF VALUE
7892501 5.05767
7892502 5.157679
7892503 2.88162
7892504 8.752307
7892505 2.697657
7892506 3.639632
7892507 3.753513
7892508 3.307723
7892509 9.477245
7892510 3.184569
7892511 2.205253
7892512 7.186049
7892513 3.593026
7892514 10.5661
7892515 8.094343
7892516 2.318421
7892517 4.79696
7892518 2.996744
7892519 4.646751
7892520 8.537889

Total number of rows: 33297

Table truncated, full table size 549 Kbytes.




Supplementary file Size Download File type/resource
GSM1152300_G800.CEL.gz 3.9 Mb (ftp)(http) CEL
Raw data provided as supplementary file
Processed data included within Sample table

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