|
| Status |
Public on Nov 10, 2014 |
| Title |
6X-SuUR |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
stage 13 egg chamber
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: 6X-SUUR
developmental stage: stage 13 egg chamber
|
| Treatment protocol |
Ovaries were hand dissected from females fattened for 2 days on wet yeast in EBR. Stage 13 egg chambers were isolated and transferred to EBR on ice until 100 egg chambers were collected. Egg chambers were stored at -20oC until all egg chambers from each genotype were collected.
|
| Growth protocol |
Drosophila were grown on standard cornmeal, molasses agar media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Egg chambers were resupended in genomic DNA extraction buffer (10mM Tris pH8.0, 1mM EDTA, 100mM NaCl, 0.5% SDS), dounced and sonicated in a Bioruptor 300 (Diagenode). Standard phenol/chloroform extraction followed by isopropanol precipitation was used to isolate total genomic DNA.
|
| Label |
Cy5
|
| Label protocol |
DNA was labeled by random priming and purified with an Amicon Ultra 30K column (Millipore)
|
| |
|
| Channel 2 |
| Source name |
Oregon R (Wild-type) embryonic 0-2h diploid gDNA
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Wild-type (Oregon R)
developmental stage: embryonic 0-2h
|
| Treatment protocol |
Ovaries were hand dissected from females fattened for 2 days on wet yeast in EBR. Stage 13 egg chambers were isolated and transferred to EBR on ice until 100 egg chambers were collected. Egg chambers were stored at -20oC until all egg chambers from each genotype were collected.
|
| Growth protocol |
Drosophila were grown on standard cornmeal, molasses agar media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Egg chambers were resupended in genomic DNA extraction buffer (10mM Tris pH8.0, 1mM EDTA, 100mM NaCl, 0.5% SDS), dounced and sonicated in a Bioruptor 300 (Diagenode). Standard phenol/chloroform extraction followed by isopropanol precipitation was used to isolate total genomic DNA.
|
| Label |
Cy3
|
| Label protocol |
DNA was labeled by random priming and purified with an Amicon Ultra 30K column (Millipore)
|
| |
|
| |
| Hybridization protocol |
Slides were hybridized to custom Agilent tiling arrays and washed as per Agilent recommendations
|
| Scan protocol |
Arrays were scanned on an Agilent scanner per manufacturer's protocol
|
| Description |
AMAID:027763
|
| Data processing |
Raw data was normailized LOESS normalized using the Ringo package in R.
|
| |
|
| Submission date |
Mar 20, 2014 |
| Last update date |
Nov 10, 2014 |
| Contact name |
Terry L. Orr-Weaver |
| E-mail(s) |
[email protected]
|
| Phone |
617-258-5251
|
| Organization name |
Whitehead Institute for Biomedical Research
|
| Lab |
Orr-Weaver
|
| Street address |
9 Cambridge Center
|
| City |
Cambridge |
| State/province |
MA |
| ZIP/Postal code |
02142 |
| Country |
USA |
| |
|
| Platform ID |
GPL18443 |
| Series (2) |
| GSE56054 |
CGH of stages 10B and 13 amplifying follicle cells to determine the effect SuUR has on replication fork progression |
| GSE56056 |
SuUR role in regulation of DNA replication |
|
