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Sample GSM857862 Query DataSets for GSM857862
Status Public on Nov 27, 2012
Title 264472
Sample type genomic
 
Channel 1
Source name ALL, MspI representation of genomic DNA
Organism Homo sapiens
Characteristics pathology: ALL
cytogenetics: BCR/ABL
immunophenotype: Early-Pre-B
site (pb: peripheral blood; BM: bone marrow): BM
age: 50
gender: male
white blood count (wbc, 10^9/l): 38.6
%blasts: 88%
imatinib: neg
overall_survival (days): 242
code_os (dead_1): 1
hyperdiploid: neg
cd25: 11
cd25(pos >=5%,_neg_<5%): Pos
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 # 06370381001)
 
Channel 2
Source name ALL, HpaII representation of genomic DNA
Organism Homo sapiens
Characteristics pathology: ALL
cytogenetics: BCR/ABL
immunophenotype: Early-Pre-B
site (pb: peripheral blood; BM: bone marrow): BM
age: 50
gender: male
white blood count (wbc, 10^9/l): 38.6
%blasts: 88%
imatinib: neg
overall_survival (days): 242
code_os (dead_1): 1
hyperdiploid: neg
cd25: 11
cd25(pos >=5%,_neg_<5%): Pos
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 # 06370381001)
 
 
Hybridization protocol See Roche NimbleGen website for the detailed manufacturers protocol.
Scan protocol Scanning was performed using NimbleGen MS 200 scanner
Description HELP DNA methylation array for ALL primary sample
Sample name: 9696
Data processing Raw data (.pair) files generated using NimbleScan software. Signal intensities at each HpaII amplifiable fragment were calculated as a robust (20% trimmed) mean of their component probe-level signal intensities (as described in Khulan et al. Genome Research 2006). 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 considered as “failed” probes and marked as NA values. After QC processing for each array, a median normalization was performed on each array by subtracting the median log-ratio (HpaII/MspI) of that array (resulting in median log-ratio of 0 for each array).
 
Submission date Jan 09, 2012
Last update date Nov 27, 2012
Contact name Huimin Geng
E-mail(s) huimin.geng@ucsf.edu
Organization name UCSF
Department Department of Laboratory Medicine
Street address 513 Parnassus Ave., MSB S-1480
City San Francisco
State/province CA
ZIP/Postal code 94143
Country USA
 
Platform ID GPL6604
Series (2)
GSE34937 Integrative Epigenomic Analysis Identifies Biomarkers and Therapeutic Targets in Adult B-Acute Lymphoblastic Leukemia [methylation profiling]
GSE34941 Integrative Epigenomic Analysis Identifies Biomarkers and Therapeutic Targets in Adult B-Acute Lymphoblastic Leukemia

Data table header descriptions
ID_REF
VALUE log2 (HpsII/MspI) ratio

Data table
ID_REF VALUE
MSPI0406S00000183 -3.460528443
MSPI0406S00000238 -2.610679985
MSPI0406S00000239 -0.802842937
MSPI0406S00000300 1.784923139
MSPI0406S00000301 2.111253725
MSPI0406S00000321 2.759833402
MSPI0406S00000352 1.455251835
MSPI0406S00000353 -0.725242159
MSPI0406S00000354
MSPI0406S00000360 -1.254456072
MSPI0406S00000361 -1.344295157
MSPI0406S00000384
MSPI0406S00000385 -0.576141111
MSPI0406S00000410
MSPI0406S00000433 0.132061265
MSPI0406S00000434 -0.353545281
MSPI0406S00000435 -0.744946982
MSPI0406S00000479 -2.664039717
MSPI0406S00000480
MSPI0406S00000492 -1.137372953

Total number of rows: 25626

Table truncated, full table size 702 Kbytes.




Supplementary file Size Download File type/resource
GSM857862_264472-H-ALL-20-090126_532.pair.gz 6.3 Mb (ftp)(http) PAIR
GSM857862_264472-H-ALL-20-090126_635.pair.gz 6.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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