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Sample GSM356595 Query DataSets for GSM356595
Status Public on Aug 31, 2009
Title MM_1
Sample type RNA
 
Source name Human bone marrow endothelial cells from Multiple Myeloma patient MM
Organism Homo sapiens
Characteristics Legend: Durie-Salmon Staging System in Multiple Myeloma (Durie BG, Salmon SE Cancer, 1975); immunoglobulin (Ig) protein monoclonal component
Sex: M; stage IIIA; 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 Multiple Myeloma patient MM_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 10.042153
1053_at 6.436573
117_at 7.481084
121_at 9.916602
1255_g_at 4.963584
1294_at 7.815209
1316_at 6.743475
1320_at 6.965162
1405_i_at 5.492522
1431_at 4.992001
1438_at 8.659988
1487_at 8.366762
1494_f_at 8.071032
1598_g_at 13.670973
160020_at 10.587826
1729_at 8.741311
1773_at 7.987967
177_at 6.484589
179_at 10.674553
1861_at 7.771257

Total number of rows: 22283

Table truncated, full table size 433 Kbytes.




Supplementary file Size Download File type/resource
GSM356595.CEL.gz 3.5 Mb (ftp)(http) CEL
Processed data included within Sample table

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