|
| Status |
Public on Nov 27, 2012 |
| Title |
27479402 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
ALL, MspI representation of genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
pathology: ALL
cytogenetics: Neg
immunophenotype: Early-Pre-B
site (pb: peripheral blood; BM: bone marrow): BM
age: 43
gender: female
white blood count (wbc, 10^9/l): 20.5
%blasts: 90%
imatinib: neg
overall_survival (days): 394
code_os (dead_1): 1
hyperdiploid: neg
cd25: 1
cd25(pos >=5%,_neg_<5%): 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 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: Neg
immunophenotype: Early-Pre-B
site (pb: peripheral blood; BM: bone marrow): BM
age: 43
gender: female
white blood count (wbc, 10^9/l): 20.5
%blasts: 90%
imatinib: neg
overall_survival (days): 394
code_os (dead_1): 1
hyperdiploid: neg
cd25: 1
cd25(pos >=5%,_neg_<5%): 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 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: 10176
|
| 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 |
|
