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| Status |
Public on Jul 10, 2022 |
| Title |
Medulloblastoma cell line C05_70062 |
| Sample type |
genomic |
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| Source name |
Medulloblastoma cell line C05_70062
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| Organism |
Homo sapiens |
| Characteristics |
cell type: medulloblastoma
cell line: C05_70062
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| Treatment protocol |
Snap-frozen tumors were obtained from Children's Oncology Group (ACNS02B3; n = 89) and from Children's Hospital Boston (n = 55), University of Washington Medical Center (n = 27), Texas Children's Hospital (n = 24), and Johns Hopkins Medical Center (n = 10). Normal cerebellum (n = 11) was obtained from University of Washington Medical Center and NICHD Brain and Tissue Bank for Developmental Disorders, University of Maryland, Baltimore, MD. All samples were collected with approval from respective institutional review boards, and proper informed consent and/or assent was obtained from all patients or their parents. Tumors were processed at Children's Hospital Boston except for samples from Texas Children's, where similar protocols were used
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| Growth protocol |
Cell lines were grown according to standard conditions.
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| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA was prepared by using the Puregene DNA Extraction Kit (Gentra Systems, Minneapolis, MN), and total RNA was extracted by using Trizol (Invitrogen, Carlsbad, CA), both per manufacturers' instructions.
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| Label |
Biotin
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| Label protocol |
As per manufacturer (Affymetrix)
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| Hybridization protocol |
Genomic DNA was digested, adaptor ligated, and amplified by polymerase chain reaction to achieve fragments ranging from 200 base pairs to 1,100 base pairs. These fragments were pooled, concentrated, and additionally fragmented with DNaseI, which was followed by labeling, denaturing, and hybridization to arrays in batches of 96 samples
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| Scan protocol |
Arrays were then scanned by using the GeneChip Scanner 3000 7G (Affymetrix).
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| Description |
Affymetrix_250K_Sty
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| Data processing |
Signal intensities were normalized against a reference set of normal genomic DNA data, as previously described.
The processed data was generated using archived module (SNPFileCreator_SNP6) on the GenePattern Server. That module is currently archived in GitHub: https://github.com/genepattern/SNPFileCreator_SNP6.
column header informaton:
1. Sample (sample name)
2. Chromosome (chromosome number)
3. Start Position (segment start position, in bases)
4. End Position (segment end position, in bases)
5. Num markers (number of markers in segment)
6. Seg.CN (log2() -1 of copy number)]
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| Submission date |
Jul 08, 2022 |
| Last update date |
Jul 10, 2022 |
| Contact name |
Jill P Mesirov |
| Organization name |
University of California, San Diego
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| Department |
Medicine
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| Street address |
9500 Gilman Drive
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| City |
San Diego |
| State/province |
CA |
| ZIP/Postal code |
92093 |
| Country |
USA |
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| Platform ID |
GPL3720 |
| Series (1) |
| GSE207762 |
Integrative Genomic Analysis of Medulloblastoma Identiļ¬es a Molecular Subgroup That Drives Poor Clinical Outcome [DNA copy number] |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM6315030_COMET_p_Sty15_Mapping250K_Sty_C05_70062.CEL.gz |
24.4 Mb |
(ftp)(http) |
CEL |
| Processed data are available on Series record |
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