|
| Status |
Public on Feb 20, 2010 |
| Title |
FemaleBody_Rep3 |
| Sample type |
RNA |
| |
|
| Source name |
Female Body (minus ovaries)
|
| Organism |
Danio rerio |
| Characteristics |
strain: AB (wild type)
gender: Female
age: 4-12 months
|
| Biomaterial provider |
Texas A&M Zebrafish Facility
|
| Treatment protocol |
Reproductive males and females (3 each) were paired on day 1, and spawning was confirmed on day 2 by the presence of eggs. Males and females were subsequently separated and housed for five days. On day 7 individuals were sacrificed and dissections were performed.
|
| Growth protocol |
Standard rearing protocols were used, as described in Westerfield, 2000:
Westerfield, M. (2000). The zebrafish book. A guide for the laboratory use of zebrafish (Danio rerio). 4th ed., Univ. of Oregon Press, Eugene.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Standard Trizol (Invitrogen) extraction.
|
| Label |
biotin
|
| Label protocol |
Standard Affymetrix
|
| |
|
| Hybridization protocol |
Standard Affymetrix
|
| Scan protocol |
Standard Affymetrix
|
| Description |
Upon euthanasia the entire reproductive tract from each individual was removed under a dissecting microscope (320X) with sterilized fine-tipped forceps, placed in 200 ul Trizol, and snap-frozen in a dry ice-ethanol bath. At this time the remainder of the body was placed in 4000 ul Trizol, and similarly snap-frozen. All downstream procedures were performed according to standardized manufacturer protocols.
|
| Data processing |
Data were analyzed 4 different ways:
VALUE [GCOS]: Expression values were computed using the MAS5 algorithm in GCOS version 1.2, under suggested settings. All probesets were scaled using a TGT value of 500, and no normalization was applied (i.e., the normalization factor was 1.0).
VALUE2 [GC-RMA]: Expression values were computed using the GC-RMA model-based algorithm in GeneSpring GX 7.3.1 (Agilent Technologies). Default normalization is performed as follows: the raw intensity value for each probe set on a chip is divided by the overall median intensity value for that chip. This “prenormalized” value is then divided by the median “prenormalized” value for that specific probe set across all 12 chips in the experiment.
VALUE3 [PM-Only]: All 12 chips were analyzed simultaneously in dCHIP, which uses a model-based algorithm to estimate expression values. The normalization procedure implemented in dCHIP normalizes all arrays in the analysis against the array with median intensity. This array was analyzed using the PM-Only procedure under default parameters.
VALUE4 [PM-MM]: All 12 chips were analyzed simultaneously in dCHIP, which uses a model-based algorithm to estimate expression values. The normalization procedure implemented in dCHIP normalizes all arrays in the analysis against the array with median intensity. This array was analyzed using the PM-MM procedure under default parameters.
|
| |
|
| Submission date |
Feb 24, 2009 |
| Last update date |
Feb 26, 2009 |
| Contact name |
Clayton M Small |
| E-mail(s) |
csmall@mail.bio.tamu.edu
|
| Phone |
979 845 4342
|
| Organization name |
Texas A&M University
|
| Department |
Biology
|
| Lab |
Dr. Adam Jones
|
| Street address |
3258 TAMU
|
| City |
College Station |
| State/province |
TX |
| ZIP/Postal code |
77843-3258 |
| Country |
USA |
| |
|
| Platform ID |
GPL1319 |
| Series (1) |
| GSE14979 |
Sex- and gonad-biased gene expression in zebrafish |
|
