|
| Status |
Public on Apr 01, 2008 |
| Title |
ALL1_H3K9acetyl_replicate2 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
ALL1_replicate2
|
| Organism |
Homo sapiens |
| Characteristics |
Acute lymphoblastic leukemia with t(9;22)(q34;q11); BCR-ABL p190 (e1a2). Female. Early Pre-B ALL with co-expression of CD33 and CD13
|
| 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 |
ALL1_Replicate2
|
| Organism |
Homo sapiens |
| Characteristics |
Acute lymphoblastic leukemia with t(9;22)(q34;q11); BCR-ABL p190 (e1a2). Female. Early Pre-B ALL with co-expression of CD33 and CD13
|
| 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 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.
|
| 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.
|
| |
|
| 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 |
|
