|
| Status |
Public on Oct 08, 2007 |
| Title |
1M-89 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
1M-89
|
| Organism |
Homo sapiens |
| Characteristics |
HCT116+chr3, clone 1M-89
|
| Treatment protocol |
control, without methotrexate treatment
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Cell line DNA was isolated by incubation overnight at 55º C in 3 ml of 1x TE buffer (pH=7.5) supplemented with 0.5 % SDS and 0.1 µg/µl proteinase K, followed by ethanol precipitation after 24 hours.
|
| Label |
Cy3
|
| Label protocol |
Genomic DNA (600 ng) was labeled by random priming to incorporate Cy3 dCTP in a 50 µl reaction.
|
| |
|
| Channel 2 |
| Source name |
Reference genomic DNA
|
| Organism |
Homo sapiens |
| Characteristics |
gender: male,
tissue type: blood
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Reference genomic DNA was isolated from whole blood of healthy male doner. DNA was prepared using standard methods ie. cell lysis and proteinase K digestion followed by ETOH precipitation. Detailed protocol can be found at http://cancer.ucsf.edu/array/protocols/index.php.
|
| Label |
Cy5
|
| Label protocol |
Genomic DNA (600 ng) was labeled by random priming to incorporate Cy5 dCTP in a 50 µl reaction.
|
| |
|
| |
| Hybridization protocol |
Labeled test and reference DNAs together with 100 µg human Cot-1 DNA were hybridized for ~48 hrs at 37º C.
|
| Scan protocol |
We acquired 16-bit DAPI, Cy3 and Cy5 images using a custom built CCD camera system (Hamilton et al. 2006. A large field CCD system for quantitative imaging of microarrays. Nuc. Acids Res. 34, e58).
|
| Description |
Used Spot files "HA3.1_clonepos_May04.20060811.txt" & "HA3.1_spotclone.20060807.txt" to analyse the raw images for this sample.
|
| Data processing |
We carried out image and data analysis using UCSF SPOT (Jain AN et al. 2002. Fully automatic quantification of microarray image data. Genome Res. 12:325-332). Ratios for each spot were calculated as the total background-corrected fluorescence intensity ratios for the test and reference channels. In addition, array CGH data were corrected for BAC clone specific GC content and in some hybridizations a geometrical dependence of the ratios on the array. Justification of these procedures is presented in Tokuyasu et al. (in preparation). We used the SPROC software to automatically filter the data based on quality criteria, average the log2 ratios of the replicate spots, and assign genome position. Only clones for which two or more spots passed quality criteria and for which the standard deviation of the replicates was less than 0.2 were included in the subsequent analysis. Data were normalized to set the median log2 ratio to zero. Data were derived from two different versions of arrays: HumArray2.0 and HumArray3.1. For compatibility, data are presented in the HumArray 3.1 format.
|
| |
|
| Submission date |
Nov 10, 2006 |
| Last update date |
Oct 08, 2007 |
| Contact name |
Donna G Albertson |
| E-mail(s) |
[email protected]
|
| Phone |
415-502-8463
|
| Organization name |
University of California San Francisco
|
| Department |
Comprihensive Cancer Center
|
| Street address |
Box 0808
|
| City |
San Francisco |
| State/province |
CA |
| ZIP/Postal code |
94143-0808 |
| Country |
USA |
| |
|
| Platform ID |
GPL4421 |
| Series (1) |
| GSE6262 |
Genome Position and Gene Amplification |
|
