|
| Status |
Public on Jul 29, 2009 |
| Title |
ML-DmBG3-c2-R1 extraction1_array1_origin |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
ML-DmBG3-c2-R1 extraction1_array1 channel_1
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: ML-DmBG3-c2
tissue: CNS-derived cell-line
genotype: y v f mal
sex: Unknown
|
| Growth protocol |
The general growth protocol for growing Drosophila cell lines in culture.
Protocol to label early activating origins that initiate before the intra-S phase checkpoint. Label refers to 'brdu' or 'mock'
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation from Drosophila cell lines.
An immunoprecipitation procedure in which anti-BrdU is used to enrich for BrdU labeled DNA.
|
| Label |
Cy3
|
| Label protocol |
Labeling of DNA extracts using Sequenase and Cy3/Cy5 dUTP.
|
| |
|
| Channel 2 |
| Source name |
ML-DmBG3-c2-R1 extraction1_array1 channel_2
|
| Organism |
Drosophila melanogaster |
| Characteristics |
cell line: ML-DmBG3-c2
tissue: CNS-derived cell-line
genotype: y v f mal
sex: Unknown
|
| Growth protocol |
The general growth protocol for growing Drosophila cell lines in culture.
Protocol to label early activating origins that initiate before the intra-S phase checkpoint. Label refers to 'brdu' or 'mock'
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation from Drosophila cell lines.
An immunoprecipitation procedure in which anti-BrdU is used to enrich for BrdU labeled DNA.
|
| Label |
Cy5
|
| Label protocol |
Labeling of DNA extracts using Sequenase and Cy3/Cy5 dUTP.
|
| |
|
| |
| Hybridization protocol |
The application of the isolated DNA samples to a specific set of 1 or more microarray slides, including the washing steps.
|
| Scan protocol |
This scanning protocol outputs raw images of intensity values resulting from the hybridization of the DNA sample to the microarray slide. The raw tiffs are quantified and output in an Agilent text format. The agilent data for each slide is loess normalized, corrected for dye-swap and quantile normalization is applied across the multiple array set. We then mangle the data into a single meta slide and convert to a pseudo nimblegen format. We then mangle the Agilent data into a pseudo nimblegen format.
|
| Description |
N/A
|
| Data processing |
We convert agilent data format to a pseudo nimblegen format for processing by MA2C. This will generate the normalized data Processed data are obtained using following parameters: genome version is r5
|
| |
|
| Submission date |
Jul 23, 2009 |
| Last update date |
Jul 29, 2009 |
| Contact name |
DCC modENCODE |
| E-mail(s) |
help@modencode.org
|
| Phone |
416-673-8579
|
| Organization name |
Ontario Institute for Cancer Research
|
| Lab |
modENCODE DCC
|
| Street address |
MaRS Centre, South Tower, 101 College Street, Suite 800
|
| City |
Toronto |
| State/province |
Ontario |
| ZIP/Postal code |
M5G 0A3 |
| Country |
Canada |
| |
|
| Platform ID |
GPL7787 |
| Series (2) |
| GSE17287 |
ML-DmBG3-c2 Replication Origins |
| GSE27981 |
Early Origins Meta-peak generation |
|
