|
| Status |
Public on Nov 30, 2012 |
| Title |
gastrula 12 degreesBlock_3_DB2_12 |
| Sample type |
RNA |
| |
|
| Source name |
gastrula 12 degrees
|
| Organism |
Strongylocentrotus purpuratus |
| Characteristics |
deveopmental stage: gastrula stage embryo
female: D3
male: B3
replicate: 2
block: 3
temperature ©: 12
sampling,time: 37.13
dasl,plate: TempCross_1
dasl,plate,row: B
dasl,plate,column: 1
culture,stage,mean: 0.350852002346032
culture,stage,sd: 0.0820971016221211
|
| Treatment protocol |
Cultures were grown in a growth chamber at 12C, 15C or 18C
|
| Growth protocol |
Sea urchins spawned, fertilized, washed and cultured in artificial sea water (CoralLife) until the mid-gastrula stage
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Embryos were concentrated and disrupted in Qiagen RLT buffer with 1% BME, and then extracted with the RNeasy kit. All RNA concentrations were above 10ng/ul. RNA concentrations above 200 ng/ul were diluted to this value.
|
| Label |
Cy3/Cy5
|
| Label protocol |
Standard Illumina DASL label protocol
|
| |
|
| Hybridization protocol |
Standard Illumina DASL hybridization protocol
|
| Scan protocol |
Standard Illumina DASL scanning protocol
|
| Description |
Used
|
| Data processing |
Raw, pre-BeadStudio files were processed using tools in the beadarray package in R. Details are in the accompanying manuscript. Briefly, probe measurements from the Cy3 channel were averaged, and then log-transformed. Each probe was first corrected for background effects by regression against data from negative control probes. Then all samples were normalized to the average expression of probes targeting the gene RBM8A.
Normalized intensities for each probe included in the final analysis. Several probes were excluded because they appeared to target other transcripts.
|
| |
|
| Submission date |
May 24, 2011 |
| Last update date |
Dec 01, 2012 |
| Contact name |
Daniel Runcie |
| E-mail(s) |
[email protected]
|
| Organization name |
Duke University
|
| Department |
Biology Department
|
| Street address |
Box 90338
|
| City |
Durham |
| State/province |
NC |
| ZIP/Postal code |
27708 |
| Country |
USA |
| |
|
| Platform ID |
GPL13644 |
| Series (2) |
| GSE29504 |
Genetics of gene expression responses to temperature stress in a sea urchin gene network |
| GSE38644 |
Genetics of gene expression responses to temperature stress in a sea urchin gene network (DASL) |
|
