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| Status |
Public on Dec 31, 2010 |
| Title |
Integrated genome, transcriptome and translatome profiling of neuroblastoma cells |
| Organism |
Homo sapiens |
| Experiment type |
Expression profiling by array
Genome variation profiling by genome tiling array
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| Summary |
Microarray-based genome-wide measurements of copy number alterations and of transcriptome variations are proposed for neuroblastoma prognosis and possible treatment choice. Nonetheless, they lack to provide clues on a neglected layer of systems-level changes, the translatome, whose variations are defined by the activity of the translational regulatory machinery. Our study extends the conventional genome-wide approaches to translatome profiling in neuroblastoma, by means of polysomal sucrose gradient separation followed by microarray analysis. The panel of fourteen parental (not subcloned) neuroblastoma cell lines used in the study includes: CHP-134, SIMA, NB-69, LAN-1, KELLY, CHP-126, CHP-212, SK-N-BE(2), IMR-32, SK-N-AS, SK-N-SH, STA-NB-7, STA-NB-1, STA-NB-10 cells. Each cell line has been profiled with high resolution array CGH analysis for copy number changes, and for transcriptome and translatome variations. The integration of these three types of data sets obtained from the same cells can provide information on the impact in neuroblastoma of a defined pattern of genomic lesions on both transcriptional and translational alterations of gene expression.
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| Overall design |
We analyzed the following human neuroblastoma cell lines: STA-NB-1, SK-N-AS, NB-69, KELLY, LAN-1, CHP-134, SK-N-SH, SK-N-BE(2), STA-NB-7, CHP-126, CHP-212, IMR-32, SIMA, STA-NB-10.
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| Contributor(s) |
Scaruffi P, Stigliani S, Tonini G, Quattrone A, Re A, Arseni N, Dassi E |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Jul 07, 2010 |
| Last update date |
Jan 23, 2019 |
| Contact name |
PAOLA SCARUFFI |
| E-mail(s) |
paola.scaruffi@hsanmartino.it
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| Organization name |
"San Martino" Hospital
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| Lab |
Center of Physiopathology of Human Reproduction
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| Street address |
LARGO R. BENZI, 10
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| City |
Genova |
| State/province |
GE |
| ZIP/Postal code |
16132 |
| Country |
Italy |
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| Platforms (2) |
| GPL6480 |
Agilent-014850 Whole Human Genome Microarray 4x44K G4112F (Probe Name version) |
| GPL9128 |
Agilent-014693 Human Genome CGH Microarray 244A (Probe name version) |
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| Samples (42)
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| Relations |
| BioProject |
PRJNA127827 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE22785_RAW.tar |
1.3 Gb |
(http)(custom) |
TAR (of TXT) |
| Processed data included within Sample table |
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