|
| Status |
Public on Feb 21, 2013 |
| Title |
A549 cell line, round 0, before in vivo injection |
| Sample type |
genomic |
| |
|
| Source name |
A549 cell line, round 0, before in vivo injection
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: A549 lung adenocarcinoma
|
| Treatment protocol |
For all mouse experiments, we used eight- to ten-weeks-old NOD.CB17-Prkdc<scid>/J [nonobese diabetic/severe combined immunodeficient (NOD/SCID)] mice, obtained either by breeding in our in-house facility or from Charles River (Wilmington, MA, USA). To analyze metastasis development after i.v. tumor cell injection, NOD/SCID mice were irradiated with a single dose of 3.5 Gy from a cobalt-60 unit 1 day before injection. A total of 2 x 105 (A549) highly or low metastatic, exposed and released or untreated cells were injected i.v. into the tail vein. Mice were followed up for 4 weeks. At this time, mice were sacrificed and lung nodules were counted. In all experiments, treatment groups were randomized to prevent cage effects. Removal of tumor nodules from the lungs and subsequent re-injection led to a rapid increase in metastatic capacity. A highly aggressive phenotype which was stable over time was evident after three rounds (R3) of in vivo selection for the A549 cell line.
|
| Growth protocol |
A549 lung adenocarcinoma cells were cultured and maintained in Dulbecco's MEM modified with 10% FBS. Cell line identity was confirmed by STR marker analysis.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
For SNP analysis, high-quality genomic DNA was extracted from the A549 cells after three rounds (R3) of in vivo selection
|
| Label |
biotin
|
| Label protocol |
according to Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 protocol
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| |
|
| Hybridization protocol |
according to Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 protocol
|
| Scan protocol |
according to Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 protocol using GeneChip Scanner 3000 7G controlled by AGCC software.
|
| Data processing |
according to Affymetrix® Genome-Wide Human SNP Nsp/Sty 6.0 protocol
High-quality genomic DNA from the lung cancer cell line (A549) samples was processed according to the Genome-Wide Human SNP Nsp/Sty 6.0 protocol and hybridized to 6.0 SNP arrays according to the manufacturer's instructions (Affymetrix). After appropriate normalization of mean array intensities, signal ratios were calculated between tumors and anonymous normal references [own-lab-generated] in an allele-specific manner using AsCNAR ("allele-specific copy-number analysis using anonymous references") algorithm (Yamamoto G. et al, 2007). Genome-wide determination of allele-specific copy numbers (AsCNs) and detection of CNN-LOH at each SNP were inferred from the observed signal ratios based on the hidden Markov model using CNAG/AsCNAR algorithms.
We analyzed the SNP6.0 data using CNAG/AsCNAR ver 3.3.0.0 which can be downloaded from http://www.genome.umin.jp/. Results file in .CFA format. CFA file readable only in CNAG "version3.3.0.0".
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| |
|
| Submission date |
Feb 21, 2013 |
| Last update date |
Feb 22, 2013 |
| Contact name |
Nils H Thoennissen |
| E-mail(s) |
[email protected]
|
| Organization name |
University Hospital of Münster
|
| Department |
Hematology Oncology
|
| Street address |
Albert-Schweitzer-Str. 33
|
| City |
Münster |
| ZIP/Postal code |
48149 |
| Country |
Germany |
| |
|
| Platform ID |
GPL6801 |
| Series (1) |
| GSE44549 |
Genomic changes in low vs high metastatic A549 NSCLC cell line |
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