|
| Status |
Public on Jan 12, 2010 |
| Title |
322 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
AML blast cells
|
| Organism |
Homo sapiens |
| Characteristics |
digestion: MspI
age: 43
gender: female
fab: M3
cytogenetic_class: Other
cytogenetic_risk: Intermediate
11q23: Neg
3q: Neg
7q: Neg
5q: Neg
t(15;17): Pos
t(8;21): Neg
inv(16): Neg
tri 8: Neg
t(6;9): Neg
t(9;22): Neg
complex: Neg
other: Pos
normal karyotype: Neg
flt3itd: Pos
flt3tkd: Neg
flt3itdortkd: Pos
npm1: Neg
npm1plusflt3itdplus: Neg
npm1plusflt3itdneg: Neg
flt3itdplusnpm1neg: Pos
nras: Neg
kras: Neg
cebpa: Neg
ckit_exon8_id: Neg
ckit_exon17_d816: Neg
|
| 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 9-mers pre-labeled with either Cy3 or Cy5
|
| |
|
| Channel 2 |
| Source name |
AML blast cells
|
| Organism |
Homo sapiens |
| Characteristics |
digestion: HpaII
age: 43
gender: female
fab: M3
cytogenetic_class: Other
cytogenetic_risk: Intermediate
11q23: Neg
3q: Neg
7q: Neg
5q: Neg
t(15;17): Pos
t(8;21): Neg
inv(16): Neg
tri 8: Neg
t(6;9): Neg
t(9;22): Neg
complex: Neg
other: Pos
normal karyotype: Neg
flt3itd: Pos
flt3tkd: Neg
flt3itdortkd: Pos
npm1: Neg
npm1plusflt3itdplus: Neg
npm1plusflt3itdneg: Neg
flt3itdplusnpm1neg: Pos
nras: Neg
kras: Neg
cebpa: Neg
ckit_exon8_id: Neg
ckit_exon17_d816: Neg
|
| 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 9-mers pre-labeled with either Cy3 or Cy5
|
| |
|
| |
| 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.
|
| Description |
none
|
| 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 and MspI signals are aligned across density-dependent sliding windows of fragment size-sorted data (described in detail in Thompson et al, Bioinformatics 2008;24:1161-1167). After intra-array normalization each channel was centered by subtracting background noise (2.5 median absolute deviations from the median of the random probes’ log2 signal for that channel) from its log2-transformed signal intensities. The HpaII/MspI (unmethylated/reference) ratio was then determined for each probe set on array.
|
| |
|
| Submission date |
Oct 23, 2009 |
| Last update date |
Jan 12, 2010 |
| Contact name |
Maria Eugenia Figueroa |
| E-mail(s) |
mef162@miami.edu
|
| Organization name |
University of Miiami
|
| Department |
Human Genetics
|
| Lab |
Maria Figueroa
|
| Street address |
1501 NW 10th Ave, BRB 709A, Locator code C227
|
| City |
Miami |
| State/province |
FL |
| ZIP/Postal code |
33136 |
| Country |
USA |
| |
|
| Platform ID |
GPL6604 |
| Series (1) |
| GSE18700 |
Genome-wide DNA methylation profiling of Acute Myeloid Leukemia |
|
