|
| Status |
Public on Jun 27, 2013 |
| Title |
NormalT_#7 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
Normal T lymphocyte cells, MspI representation of genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Normal T lymphocyte cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)
|
| Label |
Cy3
|
| Label protocol |
Random priming with 9-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)
|
| |
|
| Channel 2 |
| Source name |
Normal T lymphocyte cells, HpaII representation of genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
cell type: Normal T lymphocyte cells
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Representation of the genome generated by digestion with either MspI or HpaII and amplification by ligation-mediated PCR according to the HELP protocol (See B. Khulan, et al. Genome Res. 2006 Aug;16(8):1046-55)
|
| Label |
Cy5
|
| Label protocol |
Random priming with 9-mers pre-labeled with either Cy3 or Cy5 according to manufacturer's instructions using the NimbleGen Dual-Color DNA Labeling Kit (cat # 05223547001)
|
| |
|
| |
| Hybridization protocol |
See Roche NimbleGen website and Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319. for details
|
| Scan protocol |
Scanning was performed using a GenePix 4000B scanner (Axon Instruments) as previously described in Selzer RR, Richmond TA, Pofahl NJ, Green RD, Eis PS, et al. (2005) Analysis of chromosome breakpoints in neuroblastoma at sub-kilobase resolution using fine-tiling oligonucleotide array CGH. Genes Chromosomes Cancer 44: 305-319.
|
| Data processing |
Signal intensities at each HpaII amplifiable fragment were calculated as a robust (25% trimmed) mean of their component probe-level signal intensities. Any fragments found within the level of background MspI signal intensity, measured as 2.5 mean-absolute-differences (MAD) above the median of random probe signals, were categorized as failed. These failed loci therefore represent the population of fragments that did not amplify by PCR, whatever the biological (e.g. genomic deletions and other sequence errors) or experimental cause. On the other hand, Methylated loci were so designated when the level of HpaII signal intensity was similarly indistinguishable from background. PCR-amplifying fragments (those not flagged as either methylated or failed) were normalized using an intra-array quantile approach wherein HpaII/MspI ratios are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167. Interarray normalization was performed independently for each channel using a quantile normalization, and after that the log(ratio) for each array was calculated as Log2 (HpaII signal) - Log2(MspI signal)
|
| |
|
| Submission date |
Mar 05, 2013 |
| Last update date |
Jun 27, 2013 |
| Contact name |
Charles G Mullighan |
| E-mail(s) |
charles.mullighan@stjude.org
|
| Phone |
1-901-595-3387
|
| Organization name |
St Jude Children's Research Hospital
|
| Department |
Pathology
|
| Street address |
262 Danny Thomas Place
|
| City |
Memphis |
| State/province |
TN |
| ZIP/Postal code |
38105 |
| Country |
USA |
| |
|
| Platform ID |
GPL6604 |
| Series (2) |
| GSE44860 |
Integrated Genetic and Epigenetic Analysis of Childhood ALL Reveals a Synergistic Role for Structural and Epigenetic Lesions In Determining Disease Phenotype [194 samples] |
| GSE44862 |
Integrated Genetic and Epigenetic Analysis of Childhood ALL Reveals a Synergistic Role for Structural and Epigenetic Lesions In Determining Disease Phenotype |
|
