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GEO help: Mouse over screen elements for information. |
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| Status |
Public on Aug 08, 2013 |
| Title |
Chronic lymphocytic leukemia cells are activated and proliferate in response to specific Th cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
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| Summary |
Changes in gene expression profile of CLL cells in response to an antigen-specific Th cell clone that is specific for a Ckappa peptide of mouse Abs. Mouse anti human BCR mAbs were used to ligate BCR and deliver antigen to CLL cells.
32-45 x10e6 PBMC were incubated overnight with or without 2 μg/ml of Ms κ+IgG anti-kappa and anti-lambda mAbs. The PBMC were then cultured in presence or absence of 12.5 x10e6 T18 cells. On day 3, CLL cells were purified by negative selection using CD3 and CD14 Dynabeads (Invitrogen). RNA from CLL cells was controlled and quantified on a NanoDrop1000 (Thermo Scientific, Wilmington, DE, USA). 290ng per sample was amplified and labeled with the TotalPrep™-96 RNA Amplification Kit (Illumina, San Diego, CA, USA). Sample quality was further tested by Agilent 2100 bioanalyzer (Agilent, Santa Clara, CA, USA). 1500ng of biotin labeled cRNA was used to hybridize onto Illumina HumanWG-6 v3 Expression BeadChips. After scanning, the results were imported into Illumina GenomeStudio v. 2010.1, Gene Expression module v. 1.6.0 for quality control and data export. Analysis was performed utilizing GeneSpring GX v11 software (Agilent, Santa Clara, CA, USA). In GeneSpring GX, Logbase 2-transformed data were normalized to the 75 percentile with baseline transformation to median of all samples. Flag Information: Lower cutoff for 'Present' call: 0.8, Upper cutoff for 'Absent' call: 0.6
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| Overall design |
Testing antigen dependent Th cell - CLL cell collaboration, effects on gene expression of CLL cells
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| Contributor(s) |
Os A, Bürgler S, Parente Ribes A, Funderud A, Wang D, Thompson KM, Tjønnfjord GE, Bogen B, Munthe LA |
| Citation(s) |
23933259 |
| Submission date |
Jun 25, 2013 |
| Last update date |
Feb 18, 2019 |
| Contact name |
Ludvig A Munthe |
| Organization name |
University of Oslo
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| Department |
Institute of Clinical Medicine
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| Street address |
Sognsvannsveien 20
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| City |
Oslo |
| State/province |
Oslo |
| ZIP/Postal code |
NO-0424 Oslo |
| Country |
Norway |
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| Platforms (1) |
| GPL6884 |
Illumina HumanWG-6 v3.0 expression beadchip |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA209462 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE48268_RAW.tar |
6.3 Mb |
(http)(custom) |
TAR |
| GSE48268_non-normalized_matrix.txt.gz |
3.9 Mb |
(ftp)(http) |
TXT |
| Processed data included within Sample table |
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