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Sample GSM6315105 Query DataSets for GSM6315105
Status Public on Jul 10, 2022
Title Medulloblastoma cell line D01_88932
Sample type genomic
Source name Medulloblastoma cell line D01_88932
Organism Homo sapiens
Characteristics cell type: medulloblastoma
cell line: D01_88932
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
Growth protocol Cell lines were grown according to standard conditions.
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.
Label Biotin
Label protocol As per manufacturer (Affymetrix)
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
Scan protocol Arrays were then scanned by using the GeneChip Scanner 3000 7G (Affymetrix).
Description Affymetrix_250K_Sty
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:
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)]
Submission date Jul 08, 2022
Last update date Jul 10, 2022
Contact name Jill P Mesirov
Organization name University of California, San Diego
Department Medicine
Street address 9500 Gilman Drive
City San Diego
State/province CA
ZIP/Postal code 92093
Country USA
Platform ID GPL3720
Series (1)
GSE207762 Integrative Genomic Analysis of Medulloblastoma Identiļ¬es a Molecular Subgroup That Drives Poor Clinical Outcome [DNA copy number]

Supplementary file Size Download File type/resource
GSM6315105_SOARS_p_Sty23_Mapping250K_Sty_D01_88932.CEL.gz 22.7 Mb (ftp)(http) CEL
Processed data are available on Series record

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