Gene expression profiling suggests PCNSL to be derived from a late germinal center B cell.
From ArrayWiki
| PubMed ID: | none |
|---|---|
| Contact: | Manuel Montesinos-Rongen
|
| Species: | Homo sapiens |
| Platform: | Affymetrix GeneChip Human Genome U95 Version [1 or 2] Set HG-U95A |
| Number of Samples: | 21 |
| Date Range: | 02/25/2003 - 10/07/2005 |
| Experiment Quality: | 87.46 2.47 % 92.5 |
| Link to Repository: | GSE6047 |
| Original Intensity Data: | Download |
| Clean Intensity Data: | Download |
| Original PLIER Data: | Download |
| Clean PLIER Data: | Download |
| Clean CEL Files: | Download |
| Data Rank: | 
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To characterize the molecular origin of primary lymphomas of the central nervous system (PCNSL), 21 PCNSL of immunocompetent patients were investigated by microarray-based gene expression profiling. Comparison of the transcriptional profile of PCNSL with various normal and neoplastic B cell subsets demonstrated PCNSL (i) to display gene expression patterns most closely related to late germinal center B cells, (ii) to display a gene expression profile similar to systemic diffuse large B cell lymphomas (DLBCL), and (iii) to be in part assigned to the activated B cell-like (ABC) or the germinal center B cell-like (GCB) subtype of DLBCL.
Design: Total RNA was extracted from tissue blocks containing > 80% tumor cells using the TRIzol reagent (Invitrogen, Carlsbad, CA) and purified using RNeasy Kit (Qiagen, Valencia, CA). Double-stranded cDNA (ds-cDNA) was generated from 5 μg of total RNA using the SuperScript Double Stranded cDNA Synthesis Kit (Invitrogen) and a poly-dT oligonucleotide that contains T7 RNA polymerase initiation site (Sigma-Proligo, St. Louis, MO). The ds-cDNA was used as template to generate biotinylated cRNA by in vitro transcription using MEGA-script T7 High Yield Transcription Kit (Ambion, Austin, TX), biotin-11-CTP, and biotin-11-UTP (Perkin Elmer, Altham, MA). The biotinylated cRNA was purified by RNAeasy Kit (Qiagen) and fragmented according to the Affymetrix protocol. 15 μg of fragmented cRNA was hybridized to HG-U95Av2 microarrays (Affymetrix, Santa Clara, CA). Gene expression values were determined by GCOS1.2 software (Affymetrix) using the global scaling option.
Type: PCNSL – DLBCL – gene expression profiling
Contents |
[edit] Contributors
- Manuel Montesinos-Rongen
- Anna Brunn
- Stefan Bentink
- Katia Basso
- Wei K Lim
- Wolfram Klapper
- Carlo Schaller
- Guido Reifenberger
- James Rubenstein
- Otmar D Wiestler
- Rainer Spang
- Riccardo Dalla-Favera
- Reiner Siebert
- Martina Deckert
[edit] Protocols
[edit] References
[edit] Links
GEO Accession for this experiment: GSE6047. (Public on Dec 16 2007)
RAW data: tar file.
[edit] Analysis
 Before Normalization |
 After Normalization & Cleaning |
[edit] Samples/Quality Control
| Sample | Date Scanned | Source Link | Probe Variance Data | Artifact Mask | Quality Score |
|---|---|---|---|---|---|
| PCNSL biopsy (PCNSL03) | 02/25/03 10:57:07 | GSM140260 | 
| 
| 87.6063 5.92 % 90.84 |
| PCNSL biopsy (PCNSL04) | 02/25/03 11:08:06 | GSM140261 | 
| 
| 93.067 1.32 % 95.87 |
| PCNSL biopsy (PCNSL05) | 02/25/03 11:19:11 | GSM140262 | 
| 
| 92.9266 0.54 % 96.19 |
| PCNSL biopsy (PCNSL06) | 02/25/03 11:32:23 | GSM140263 | 
| 
| 92.3736 0.63 % 95.87 |
| PCNSL biopsy (PCNSL07) | 02/27/03 11:25:05 | GSM140264 | 
| 
| 92.5354 0.48 % 96.03 |
| PCNSL biopsy (PCNSL09) | 03/04/03 11:27:52 | GSM140265 | 
| 
| 93.9954 0 % 97 |
| PCNSL biopsy (PCNSL10) | 02/27/03 11:14:14 | GSM140266 | 
| 
| 93.7506 0.05 % 96.85 |
| PCNSL biopsy (PCNSL11) | 03/04/03 11:39:32 | GSM140267 | 
| 
| 93.8948 0.06 % 96.92 |
| PCNSL biopsy (PCNSL14) | 03/04/03 11:51:36 | GSM140268 | 
| 
| 93.645 0.05 % 96.8 |
| PCNSL biopsy (PCNSL16) | 03/04/03 12:21:13 | GSM140269 | 
| 
| 91.3143 0.26 % 95.53 |
| PCNSL biopsy (PCNSL17) | 03/04/03 13:04:29 | GSM140270 | 
| 
| 90.1245 0.63 % 94.75 |
| PCNSL biopsy (PCNSL18) | 03/04/03 13:19:41 | GSM140281 | 
| 
| 91.4483 0.11 % 95.67 |
| PCNSL biopsy (PCNSL20) | 03/04/03 14:38:47 | GSM140282 | 
| 
| 93.9402 0.21 % 96.86 |
| PCNSL biopsy (PCNSL21) | 03/06/03 11:08:24 | GSM140283 | 
| 
| 92.0862 0.62 % 95.73 |
| PCNSL biopsy (PCNSL22) | 03/04/03 15:00:06 | GSM140284 | 
| 
| 92.8135 0.14 % 96.34 |
| PCNSL biopsy (PCNSL23) | 10/04/05 10:33:30 | GSM140285 | 
| 
| 91.9954 2.31 % 94.84 |
| PCNSL biopsy (PCNSL24) | 10/04/05 11:44:27 | GSM140286 | 
| 
| 83.8032 26.71 % 78.55 |
| PCNSL biopsy (PCNSL25) | 10/06/05 13:30:41 | GSM140287 | 
| 
| 91.0308 2.6 % 94.22 |
| PCNSL biopsy (PCNSL26) | 10/04/05 12:24:12 | GSM140288 | 
| 
| 91.4249 0.71 % 95.36 |
| PCNSL biopsy (PCNSL27) | 10/04/05 13:01:26 | GSM140289 | 
| 
| 92.2646 1.08 % 95.59 |
| PCNSL biopsy (PCNSL28) | 10/07/05 10:26:47 | GSM140290 | 
| 
| 87.9912 9.82 % 89.09 |
