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Sample GSM356590 Query DataSets for GSM356590
Status Public on Aug 31, 2009
Title MGUS_1
Sample type RNA
 
Source name Human bone marrow endothelial cells from Monoclonal Gammopathy of Undetermined Significance patient MGUS
Organism Homo sapiens
Characteristics Legend: Immunoglobulin (Ig) protein monoclonal component
Sex: M; IgG
Treatment protocol Centrifugation on Ficoll gradient of heparinized BM-aspirates was followed by polystyrene flask adherence to isolate stromal cells from plasma cells in suspension. Adherent stromal elements were first immunodepleted of macrophages and residual plasma cells with CD14 and CD38 monoclonal antibody (mAb)-coated flasks (mAbs were from Immunotech, Coulter, Marseilles, France), and then incubated with magnetic microbeads coated with Ulex europaeus-1 lectin. The purity and viability of EC cultures grown at least one passage (more than 97% viable cells) were assessed by fluorescence-activated cell sorting (FACS, FACS Canto II, Becton Dickinson, San Jose, CA) with double positivity for factor VIII-related antigen (FVIII-RA, a highly specific EC marker) and CD105 (or endoglyn) as well as for CD14 and CD38 negativity. Analysis of mRNA transcripts for FVIII-RA, CD38, CD105 and IgH VDJ region was also performed by RT-PCR, and EC viability was assessed by trypan blue viable staining.
Growth protocol Freshly-isolated ECs were cultured in complete medium RPMI-1640 medium supplemented with 10% heat-inactivated FCS and 1% glutamine to allow cell spreading and growth.
Extracted molecule total RNA
Extraction protocol Total RNA was extracted from frozen ECs with TRIzol reagent (Invitrogen, Carlsbad, CA), purified with the RNeasy total RNA Isolation Kit (Qiagen, Valencia, CA).
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 of endothelial cells from Monoclonal Gammopathy of Undetermined Significance patient MGUS_1
Data processing The probe-level signals were converted to expression values using 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 Dec 30, 2008
Last update date Sep 01, 2016
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 GPL96
Series (1)
GSE14230 Gene expression profiling of bone marrow endothelial cells in patients with multiple myeloma
Relations
Reanalyzed by GSE86363

Data table header descriptions
ID_REF
VALUE RMA-calculated Signal intensity

Data table
ID_REF VALUE
1007_s_at 9.344707
1053_at 6.86523
117_at 7.83342
121_at 9.930328
1255_g_at 4.858638
1294_at 8.471923
1316_at 6.590234
1320_at 6.957784
1405_i_at 5.43999
1431_at 4.957101
1438_at 8.457273
1487_at 8.670483
1494_f_at 8.037942
1598_g_at 13.265562
160020_at 10.981765
1729_at 8.810036
1773_at 8.205231
177_at 6.484627
179_at 10.919186
1861_at 8.259741

Total number of rows: 22283

Table truncated, full table size 433 Kbytes.




Supplementary file Size Download File type/resource
GSM356590.CEL.gz 3.6 Mb (ftp)(http) CEL
Processed data included within Sample table

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