|
Status |
Public on Apr 01, 2008 |
Title |
AML2_H3K9acetyl_Replicate1 |
Sample type |
genomic |
|
|
Channel 1 |
Source name |
AML2_Replicate1
|
Organism |
Homo sapiens |
Characteristics |
Acute Myeloid Leukemia with negative by RT-PCR for BCR/ABL, AML1/ETO, CBFbeta/MYH11, MLL-TD and FLT3-ITD. Female. CD11b Positive, co-expression of CD7
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Chromatin immunoprecipitation using rabbit polyclonal antibody H3K9 acetyl from Upsate (Cat # 07-352)
|
Label |
Cy5
|
Label protocol |
Random 9mers pre-labeled with Cy5
|
|
|
Channel 2 |
Source name |
AML2_Replicate1
|
Organism |
Homo sapiens |
Characteristics |
Acute Myeloid Leukemia with negative by RT-PCR for BCR/ABL, AML1/ETO, CBFbeta/MYH11, MLL-TD and FLT3-ITD. Female. CD11b Positive, co-expression of CD7
|
Extracted molecule |
genomic DNA |
Extraction protocol |
Chromatin immunoprecipitation total input control
|
Label |
Cy3
|
Label protocol |
Random 9mers pre-labeled with Cy3
|
|
|
|
Hybridization protocol |
See Roche NimbleGen website and See 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.
|
Scan protocol |
GenePix 4000B scanner (Axon Instruments) - See 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 more details
|
Description |
All samples for microarray hybridization were processed at the Roche NimbleGen Service Laboratory.
|
Data processing |
The H3K9 acetylation status at each promoter was computed by taking the log-ratio between the probe intensities of the ChIP product and input chromatin, which were co-hybridized on the same assay. For each of the 24,134 promoter regions, we computed the moving average of the log-ratio along its 15 probes with a window size of 3 probes, and found the maximum value of the moving averages of over each region covered by 15 probes. All chips that passed primary quality control showed a bimodal distribution with a distinct lower mode. We took these lower modes to indicate non-enriched fragments, and normalized across arrays by lining up these modes.
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|
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Submission date |
Mar 18, 2008 |
Last update date |
Mar 26, 2008 |
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 |
GPL6603 |
Series (1) |
GSE10887 |
H3K9acetyl ChIP on chip for integrative epigenomic study in leukemia samples |
|