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| Status |
Public on Apr 28, 2022 |
| Title |
MD_A05_rep172 |
| Sample type |
RNA |
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| Source name |
Brain
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| Organism |
Homo sapiens |
| Characteristics |
tissue: primary medulloblastoma
subtype: classic
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| Treatment protocol |
none
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| Growth 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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| Extracted molecule |
total RNA |
| 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 |
standard Affymetrix protocol
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| Hybridization protocol |
Gene expression data was generated by hybridizing labeled RNAs to Affymetrix HT HG-U133A arrays (Affymetrix, Santa Clara, CA). Samples meeting a minimum of 37% p-calls were used in this analysis. A number of samples with borderline 3′/5′ GAPDH and ACTIN ratios were identified but did not contribute to any batch effects in our non-negative matrix factorization (NMF) analysis; these remained in our subsequent analyses. Gene expression data from Kool et al3 and Fattet et al7 were obtained from the Gene Expression Omnibus (GSE10327 and GSE12992, respectively). Gene expression data from Thomson et al4 was downloaded from http://www.stjuderesearch.org/data/medulloblastoma/. All data sets were preprocessed with the Robust Multichip Average (RMA) algorithm to generate the .gct files used in subsequent analyses (Irizarry RA, et al: Biostatistics 4:249-264, 2003).
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| Scan protocol |
standard Affymetrix protocol
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| Description |
MD_train_set_expression_dataset.gct
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| Data processing |
Briefly, genomic DNA was digested, adaptor-ligated, and amplified by polymerase chain reaction to achieve fragments ranging from 200 to 1,100 base pairs. These fragments were pooled, concentrated, and further fragmented with DNaseI (Affymetrix) followed by labeling, denaturing, and hybridization to arrays in batches of 96 samples. Gene expression data were generated by hybridizing labeled RNAs to Affymetrix U133A2 high-throughput arrays (Affymetrix, Santa Clara, CA). Samples meeting a minimum of 37% p-calls were used in this analysis. Data were preprocessed by using the robust multichip average (Irizarry RA et al: Biostatistics 4:249-264, 2003) to generate the.gct files used in subsequent analyses.
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| Submission date |
Apr 26, 2022 |
| Last update date |
Apr 28, 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 |
GPL3921 |
| Series (2) |
| GSE201583 |
Predicting Relapse in Patients With Medulloblastoma by Integrating Evidence From Clinical and Genomic Feature |
| GSE202043 |
Integrative Genomic Analysis of Medulloblastoma Identifies a Molecular Subgroup That Drives Poor Clinical Outcome |
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| Supplementary file |
Size |
Download |
File type/resource |
| GSM6067891_5500024024214122006610.A05.CEL.gz |
2.5 Mb |
(ftp)(http) |
CEL |
| Processed data are available on Series record |
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