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|
| Status |
Public on Oct 24, 2011 |
| Title |
LE:K-562 (60043) |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
LE:K-562
|
| Organism |
Homo sapiens |
| Characteristics |
cell line: LE:K-562
tissue of origin: Leukemia
age: 53
Sex: F
prior treatment: Bisulfan/PiBr
epithelial: no
source: Pleural effusion
ploidy: 3n-, Hypotriploid (58-68)
p53 mutation: MT
doubling time: 19.6
sample description: CML
|
| Treatment protocol |
Untreated
|
| Growth protocol |
As described previously (Pubmed ID: 17272646) using conditions based on those adopted by DTP for their drug screen and harvested at ~80% confluence.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified from cells using either the QIAamp DNA Blood Maxi Kit, or the Blood & Cell Culture DNA Maxi Kit (Qiagen Inc., Valencia, CA) according to manufacturer's instructions. Quality was assessed by optical density 260/280 ratio using a spectrophotometer (Beckman-Coulter, Fullerton, CA) and by 0.8% agarose (SeaKem GTG, FMC BioProducts, Rockland, ME) gel electrophoresis in 1x TAE (Roche, Indianapolis, IN).
|
| Label |
Cy3
|
| Label protocol |
Purified genomic DNA (1 ug) was fragmented and labeled by random priming with Cy3- or Cy5-labeled random 9mer oligos.
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| |
|
| Channel 2 |
| Source name |
Male human reference
|
| Organism |
Homo sapiens |
| Characteristics |
Sex: M
sample description: Pool of six normal male samples
|
| Treatment protocol |
Untreated
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Genomic DNA was purified from cells using either the QIAamp DNA Blood Maxi Kit, or the Blood & Cell Culture DNA Maxi Kit (Qiagen Inc., Valencia, CA) according to manufacturer's instructions. Quality was assessed by optical density 260/280 ratio using a spectrophotometer (Beckman-Coulter, Fullerton, CA) and by 0.8% agarose (SeaKem GTG, FMC BioProducts, Rockland, ME) gel electrophoresis in 1x TAE (Roche, Indianapolis, IN).
|
| Label |
Cy5
|
| Label protocol |
Purified genomic DNA (1 ug) was fragmented and labeled by random priming with Cy3- or Cy5-labeled random 9mer oligos.
|
| |
|
| |
| Hybridization protocol |
Hybridization was carried out at NimbleGen. In brief, the Cy3-labeled test sample and Cy5-labeled reference sample were combined and hybridized overnight at 42°C in NimbleGen Hybridization Buffer (NimbleGen Systems). Arrays were washed with the NimbleGen Wash Buffer System (NimbleGen Systems) and immediately dried down by centrifugation.
|
| Scan protocol |
Arrays were scanned (at NimbleGen) at 5 um resolution using the GenePix4000B scanner (Axon Instruments). Data was extracted from scanned images using NimbleScan 2.0 software (NimbleGen Systems) and the extracted intensity for each spot was saved as raw data.
|
| Description |
Leukemia cancer cell line LE:K-562 compared to Male human reference
|
| Data processing |
Probes were mapped to human genome reference HG19 (NCBI 37) to provide chromosome and position annotations. After taking ratio of sample/reference, log to the base 2 was taken. Dye bias was calculated using the one sample (LC:A549) with dye flips and subtracted from all arrays. Probe bias was calculated as described in article and subtracted from all probes. R (64-bit ver. 2.13.0) was used to do log2 transformation of the ratio (sample/reference). The log ratio was corrected for dye and probe bias (as described in article).
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| |
|
| Submission date |
Jun 29, 2011 |
| Last update date |
Oct 24, 2011 |
| Contact name |
Sudhir Varma |
| E-mail(s) |
sudhirv4rma@gmail.com
|
| Organization name |
HiThru Analytics
|
| Street address |
1215 Wessex Pl
|
| City |
Princeton |
| State/province |
NJ |
| ZIP/Postal code |
08540 |
| Country |
USA |
| |
|
| Platform ID |
GPL13786 |
| Series (1) |
| GSE30291 |
Nimblegen 385K array CGH on NCI-60 cancer cell lines |
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