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Sample GSM465028 Query DataSets for GSM465028
Status Public on Jan 12, 2010
Title 7169
Sample type genomic
 
Channel 1
Source name AML blast cells
Organism Homo sapiens
Characteristics digestion: Msp1
age: 54
gender: male
fab: M2
cytogenetic_class: NA
cytogenetic_risk: ND
11q23: 5
3q: 5
7q: 5
5q: 5
t(15;17): Neg
t(8;21): Neg
inv(16): Neg
tri 8: 5
t(6;9): 5
t(9;22): 5
complex: 5
other: 5
normal karyotype: 5
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: 54
gender: male
fab: M2
cytogenetic_class: NA
cytogenetic_risk: ND
11q23: 5
3q: 5
7q: 5
5q: 5
t(15;17): Neg
t(8;21): Neg
inv(16): Neg
tri 8: 5
t(6;9): 5
t(9;22): 5
complex: 5
other: 5
normal karyotype: 5
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

Data table header descriptions
ID_REF
VALUE log2 Ratio (HpaII/MspI)

Data table
ID_REF VALUE
MSPI0406S00000183 -2.150419216
MSPI0406S00000238 -1.724916339
MSPI0406S00000239 -0.142836763
MSPI0406S00000300 2.677254595
MSPI0406S00000301 2.331636718
MSPI0406S00000321 2.001088095
MSPI0406S00000352 1.836524362
MSPI0406S00000353 3.109970949
MSPI0406S00000354 0.539940366
MSPI0406S00000360 0.642209645
MSPI0406S00000361 0.724409378
MSPI0406S00000384 1.864265176
MSPI0406S00000385 2.269845623
MSPI0406S00000410 0.367994415
MSPI0406S00000433 2.873628134
MSPI0406S00000434 0.986380631
MSPI0406S00000435 0.875221172
MSPI0406S00000479 -1.016727446
MSPI0406S00000480 -0.669193087
MSPI0406S00000492 -0.098819888

Total number of rows: 25626

Table truncated, full table size 757 Kbytes.




Supplementary file Size Download File type/resource
GSM465028_221504_532.pair.gz 6.3 Mb (ftp)(http) PAIR
GSM465028_221504_635.pair.gz 6.1 Mb (ftp)(http) PAIR
Processed data included within Sample table

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