|
| Status |
Public on Oct 18, 2011 |
| Title |
3SG orc2 mut (Exel6288Df) CGH |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
third instar salivary gland from orc2 mut
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: orc2k43/Df(3R)Exel6288
|
| Treatment protocol |
Salivary glands were hand dissected from committed wandering third instar larvae directly into EBR medium. Immediately before freezing at -80C, EBR was removed. Control channel gDNA was from collection plates of 0-2h staged eggs from WT (OrR) Drosophila
|
| Growth protocol |
Drosophila were grown on standard cornmeal, molasses agar media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Salivary glands were sonicated in in 0.5 mL of ChIP lysis buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate) and phenol-chloroform extracted and ethanol precipitated.
|
| Label |
Cy3
|
| Label protocol |
DNA was labeled using Invitrogen's BioPrime Total for Agilent aCGH labeling kit
|
| |
|
| Channel 2 |
| Source name |
OrR (WT) embryonic 0-2h diploid gDNA
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: OrR (WT)
|
| Treatment protocol |
Salivary glands were hand dissected from committed wandering third instar larvae directly into EBR medium. Immediately before freezing at -80C, EBR was removed. Control channel gDNA was from collection plates of 0-2h staged eggs from WT (OrR) Drosophila
|
| Growth protocol |
Drosophila were grown on standard cornmeal, molasses agar media.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
Salivary glands were sonicated in in 0.5 mL of ChIP lysis buffer (50 mM HEPES/KOH pH 7.5, 140 mM NaCl, 1 mM EDTA, 1% Triton X-100, 0.1% Na-Deoxycholate) and phenol-chloroform extracted and ethanol precipitated.
|
| Label |
Cy5
|
| Label protocol |
DNA was labeled using Invitrogen's BioPrime Total for Agilent aCGH labeling kit
|
| |
|
| |
| 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
|
| Data processing |
Raw data was median normalized using the Ringo package in R in order to generate .wig files containing smoothed log ratios.
|
| |
|
| Submission date |
Sep 06, 2011 |
| Last update date |
Oct 18, 2011 |
| Contact name |
Terry L. Orr-Weaver |
| E-mail(s) |
weaver@wi.mit.edu
|
| 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 |
GPL11290 |
| Series (2) |
| GSE31898 |
CGH to ascertain levels of gDNA in third instar salivary glands of various mutant Drosophila |
| GSE31900 |
Developmental Control of Gene Copy Number by Repression of Replication Initiation and Fork Progression |
|
