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| Status |
Public on Jan 28, 2009 |
| Title |
miRNA profiles of diffuse large B cell lymphoma (DLBCL) derived cell lines |
| Organism |
Homo sapiens |
| Experiment type |
Non-coding RNA profiling by array
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| Summary |
miRNA profiling of human Diffuse Large B Cell Lymphoma (DLBCL) cell lines derived from the two main subtypes of this disease: Activated B Cell like (ABC-DLBCL) and Germinal Center B cell like (GCB-DLBCL), analyzing the 711 human miRNAs present in miRBase V10.0. Five ABC-like DLBCL cell lines (RIVA, Oci-Ly3, Oci-Ly10, HBL1 and U2932) and three GCB-like DLBCL cell lines (Oci-Ly7, Oci-Ly19 and SUDHL-6) were cultured in IMDM (Cellgro) with 20% human plasma, 1% penicillin/streptomycin/L-glutamine (Cellgro,) and 0,2% beta mercaptoethanol (Invitrogen). Total RNA was extracted from cell pellets using the mirVana™ miRNA Isolation Kit (Ambion), and sent to LC Sciences facility for microarray hybridization using microfluidics technology. FirstChoice® Human Skeletal Muscle Total RNA (Ambion) was used as common reference for all hybridizations. Background substracted and normalized data from each channel was used to calculate log ratios sample/reference.
Keywords: miRNA profiling
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| Overall design |
Dual channel experiments using FirstChoice® Human Skeletal Muscle Total RNA (Ambion) as common reference for all hybridizations. Reference was labeled with Cy5 and the cell line extracted RNA with Cy3. Biological replicates: 5 ABC-DLBCL cell lines and 3 GCB-DLBCL cell lines. Microarray hybridization was performed at LC Sciences, using slides containing in situ synthesized oligonucleotides to detect the 711 miRNAs present in miRBase V10.0. Probes hsa-miR-337 and hsa-miR-542-5p were excluded due to systematic dye bias, according to the manufacturer intructions. Background substracted and normalized detectable data was used to calculate log ratios sample/reference. Background is determined using a regression-based background mapping method. The regression is performed on 5% to 25% of the lowest intensity data points excluding blank spots. Raw data matrix is then subtracted by the background matrix. Normalization was carried out using a LOWESS (Locally-weighted Regression) method on the background-subtracted data. A transcript to be listed as detectable must meets at least two conditions: signal intensity higher than 3×(background standard deviation) and spot CV < 0.5. CV is calculated by (standard deviation)/(signal intensity). When repeating probes are present on an array, a transcript is listed as detectable only if the signals from at least 50% of the repeating probes are above detection level.
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| Contributor(s) |
Malumbres R, Lossos IS |
| Citation(s) |
19047678 |
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| Submission date |
Sep 25, 2008 |
| Last update date |
Mar 20, 2012 |
| Contact name |
Raquel Malumbres |
| E-mail(s) |
rmalumbres@yahoo.com
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| Phone |
+34 948194700
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| Organization name |
University of Navarra/ Clínica Universidad de Navarra
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| Department |
Hemato-Oncology
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| Lab |
Multiple Myeloma
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| Street address |
Avenida Pio XII 55
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| City |
Pamplona |
| State/province |
Navarra |
| ZIP/Postal code |
31008 |
| Country |
Spain |
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| Platforms (1) |
| GPL7373 |
LC Sciences_miRNA_Human_v10(1).0 |
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| Samples (8)
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| Relations |
| BioProject |
PRJNA110857 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE12933_RAW.tar |
6.4 Mb |
(http)(custom) |
TAR (of TXT, XLS) |
| Processed data included within Sample table |
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