|
| Status |
Public on Jun 04, 2012 |
| Title |
orr_weaver_fat_body_rep1 extraction1_array1 |
| Sample type |
genomic |
| |
|
| Channel 1 |
| Source name |
orr_weaver_fat_body_rep1 channel_1
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Oregon-R Orr-Weaver(genotype : TBA outcross : TBA description : Wild-type Oregon-R population maintained by Terry Orr-Weaver. made_by : wt population )
tissue: Fatbody
developmental stage: cleavage stage
genotype: TBA
Sex: Unknown
|
| Growth protocol |
Adult fat body:Newly hatched (0-24hours) female and male Oregon R flies from the modENCODE strain were dissected into an Eppendorf tube full of unsupplemented Grace?s media on ice. Holding each fly by the thorax with forceps, the abdomen was opened with another pair of forceps, and the layer of fat cells permitted to stream into the tube.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation:All tissues were homogenized with a pestle in an Eppendorf tube in 500ul SDS lysis buffer. 5ul RNAse was added to each sample and incubated for one hour at room temperature.5 ul proteinase K was added and samples were incubated at 50oC for two hours.The samples were phenol/chloroform extracted and ethanol precipitated.The pellets were washed 70% ethanol and air dried then dissolved in 1X NEB buffer 4.The DNA was digested with RsaII and AluI for two hours at 37oCLabeling was done according to the Invitrogen protocol.
|
| Label |
Cy3
|
| Label protocol |
Labeling of isolated DNA with cy5 or cy3
|
| |
|
| Channel 2 |
| Source name |
orr_weaver_embryo_rep1 channel_2
|
| Organism |
Drosophila melanogaster |
| Characteristics |
strain: Oregon-R Orr-Weaver(genotype : TBA outcross : TBA description : Wild-type Oregon-R population maintained by Terry Orr-Weaver. made_by : wt population )
tissue: Fatbody
developmental stage: cleavage stage
genotype: TBA
Sex: Unknown
|
| Growth protocol |
Oregon R (TO-W strain) embryos were collected from a population cage for one hour, dechorionated with 50% bleach, and washed three times in PBS with 0.1% triton.
|
| Extracted molecule |
genomic DNA |
| Extraction protocol |
DNA isolation:All tissues were homogenized with a pestle in an Eppendorf tube in 500ul SDS lysis buffer. 5ul RNAse was added to each sample and incubated for one hour at room temperature.5 ul proteinase K was added and samples were incubated at 50oC for two hours.The samples were phenol/chloroform extracted and ethanol precipitated.The pellets were washed 70% ethanol and air dried then dissolved in 1X NEB buffer 4.The DNA was digested with RsaII and AluI for two hours at 37oCLabeling was done according to the Invitrogen protocol.
|
| Label |
Cy5
|
| Label protocol |
Labeling of isolated DNA with cy5 or cy3
|
| |
|
| |
| 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.
|
| Data processing |
Normalization_and_smoothing_of_log2_ratios:DM:1 protocol. Two-color Agilent tiling arrays were processed by Bioconductor primarily with the Ringo package (Toedling et al., 2007, PMID: 17594472). Briefly, each array was loess normalized and then probe log2 ratios were smoothed by running medians across windows of 10kb along the genome, requiring at least 3 probes within a window.
|
| |
|
| Submission date |
Jun 04, 2012 |
| Last update date |
Feb 02, 2015 |
| 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 |
GPL11290 |
| Series (1) |
|
| Relations |
| Named Annotation |
GSM942057_Norm_smoothed_log2_ratios.252532110032_201201251329_S01_CGH-v4_10_Apr08_1_1.wig.gz |
