|
| Status |
Public on Jun 18, 2015 |
| Title |
brca2[KO]_1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
stage 13 egg chambers
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain genotype/variation: brca2[KO]/CyO
developmental stage: stage 13 egg chambers
|
| Treatment protocol |
Ovaries were hand dissected from females fattened for 2 days on wet yeast in Grace’s media. Stage 13 egg chambers were isolated and transferred to Grace’s media on ice until 100 egg chambers were collected. Egg chambers were stored at -80ᵒC 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 ChIP lysis buffer buffer (50mM HEPES/KOH pH 7.5, 140mM NaCl, 1mm EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate), 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 0-2 hour embryonic diploid DNA
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Oregon R
genotype/variation: wild type
developmental stage: 0-2 hour embryos
|
| Treatment protocol |
Ovaries were hand dissected from females fattened for 2 days on wet yeast in Grace’s media. Stage 13 egg chambers were isolated and transferred to Grace’s media on ice until 100 egg chambers were collected. Egg chambers were stored at -80ᵒC 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 |
Embryos were resupended in 1% SDS in TE, 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:049276
|
| Data processing |
Raw data was LOESS normalized using the Ringo package in R. The .bed files contain the normalized log2 ratio (Cy5/Cy3) representing test/reference
|
| |
|
| Submission date |
Mar 09, 2015 |
| Last update date |
Jun 18, 2015 |
| 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 |
GPL19853 |
| Series (2) |
| GSE66690 |
CGH of stage 13 amplifying follicle cells to measure changes in replication fork progression in DNA damage checkpoint and double-strand break repair mutants |
| GSE66691 |
Replication fork progression during re-replication requires the DNA damage checkpoint and double-strand break repair |
|
