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Sample GSM858035 Query DataSets for GSM858035
Status Public on Nov 27, 2012
Title 267001
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: 62
gender: female
white blood count (wbc, 10^9/l): 16.7
%blasts: 84%
imatinib: Pos
overall_survival (days): 1337
code_os (dead_1): 0
hyperdiploid: neg
cd25: 95
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: 62
gender: female
white blood count (wbc, 10^9/l): 16.7
%blasts: 84%
imatinib: Pos
overall_survival (days): 1337
code_os (dead_1): 0
hyperdiploid: neg
cd25: 95
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: 17682
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 -3.291361429
MSPI0406S00000238 -2.750401967
MSPI0406S00000239 -1.015052428
MSPI0406S00000300 1.582822499
MSPI0406S00000301 2.423492765
MSPI0406S00000321 3.411327074
MSPI0406S00000352 3.009733734
MSPI0406S00000353 0.656513476
MSPI0406S00000354
MSPI0406S00000360 1.655022546
MSPI0406S00000361 2.668228871
MSPI0406S00000384 1.137283516
MSPI0406S00000385 0.950704677
MSPI0406S00000410 1.084162848
MSPI0406S00000433 2.334926428
MSPI0406S00000434 1.232526365
MSPI0406S00000435 1.109393215
MSPI0406S00000479 0.525289678
MSPI0406S00000480 0.205899248
MSPI0406S00000492 0.616460605

Total number of rows: 25626

Table truncated, full table size 733 Kbytes.




Supplementary file Size Download File type/resource
GSM858035_267001-H-ALL-77-090202_532.pair.gz 6.4 Mb (ftp)(http) PAIR
GSM858035_267001-H-ALL-77-090202_635.pair.gz 6.2 Mb (ftp)(http) PAIR
Processed data included within Sample table

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