|
| Status |
Public on Dec 04, 2008 |
| Title |
H12_bioRep2_dyeSwap |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
12hNoDrug2
|
| Organism |
Mus musculus |
| Characteristics |
C57/Bl6J, female embryo, urogenital sinus harvested after 6 hours from vehicle (Triolein) pulse in the pregnant mother at 16.0 days post conception.
|
| Treatment protocol |
Paired pregnant females were pulsed with 50mg/kg dihydrotestosterone at 16.0 days post conceptionand; urogenital sinus tissue from female embryos were compaired to vehicle after 6 and 12 hr. For the 48 hr (MvsF) time point tissue from unmanipulated male and female littermates were harvested at 17.5 dpc
|
| Growth protocol |
C57/Bl6J (Jackson) pregnancies were timed according to scheduled 4-hour male-female pairings. Embryos were dissected at specified time points with the sex determined by inspection of gonads under a dissecting microscope. UGS tissue was carefully dissected to remove accessory ducts and immediately snap frozen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from homogenized frozen tissue using the Rneasy system (Qiagen). RNA quality was assessed using a Bioanalyzer 2100 (Agilent Technologies)
|
| Label |
Cy5
|
| Label protocol |
250 ng of total RNA input was reverse transcribed into by oligo dT primer incorporating a T7 promoter sequence, and labelled cRNA was obtained by T7 RNA polymerase transcription (Low RNA Input Fluorescent Linear Amplification Kit, Agilent Technologies). cRNA was purified using RNeasy mini kit (Qiagen).
|
| |
|
| Channel 2 |
| Source name |
12hDHT2
|
| Organism |
Mus musculus |
| Characteristics |
C57/Bl6J, female embryo, urogenital sinus harvested after 6 hours from 50mg/kg dihydrotestosterone pulse in the pregnant mother at 16.0 days post conception.
|
| Treatment protocol |
Paired pregnant females were pulsed with 50mg/kg dihydrotestosterone at 16.0 days post conceptionand; urogenital sinus tissue from female embryos were compaired to vehicle after 6 and 12 hr. For the 48 hr (MvsF) time point tissue from unmanipulated male and female littermates were harvested at 17.5 dpc
|
| Growth protocol |
C57/Bl6J (Jackson) pregnancies were timed according to scheduled 4-hour male-female pairings. Embryos were dissected at specified time points with the sex determined by inspection of gonads under a dissecting microscope. UGS tissue was carefully dissected to remove accessory ducts and immediately snap frozen
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was prepared from homogenized frozen tissue using the Rneasy system (Qiagen). RNA quality was assessed using a Bioanalyzer 2100 (Agilent Technologies)
|
| Label |
Cy3
|
| Label protocol |
250 ng of total RNA input was reverse transcribed into by oligo dT primer incorporating a T7 promoter sequence, and labelled cRNA was obtained by T7 RNA polymerase transcription (Low RNA Input Fluorescent Linear Amplification Kit, Agilent Technologies). cRNA was purified using RNeasy mini kit (Qiagen).
|
| |
|
| |
| Hybridization protocol |
1.5 microgram of each of fragmented labeled sample was incubated at 65 Celsius in hybridization chambers for 17 hours. Slides were washed and dried according to the Agilent microarray processing protocols.
|
| Scan protocol |
Images were obtained using the Agilen scanner (Version A.7.5.1, Jun 1 2004). Data were extracted with Agilent Feature Extraction software (version 9.5.3.1).
|
| Description |
Hybridizations on October 25 2005.
|
| Data processing |
Within-array ”loess” normalization and beetwen-arrays ”scale” normalization were applied. No background subtraction was performed. Positive and negative controls features were not used to compute the ”loess” smoothing and in subsequent analyses. For each individual array M-values corresponding to sequence-identical features were averaged after preprocessing.
Data table VALUE column represents log2 (drug/no drug) ratios or log2 (male/female) ratios.
|
| |
|
| Submission date |
Jul 10, 2008 |
| Last update date |
Dec 04, 2008 |
| Contact name |
Luigi Marchionni |
| E-mail(s) |
marchion@jhu.edu
|
| Phone |
410-502-8179
|
| Organization name |
Johns Hopkins University
|
| Department |
Oncology
|
| Lab |
Cancer Biology Program
|
| Street address |
1550 Orleans St., CRB2, Room 1M52
|
| City |
Baltimore |
| State/province |
MD |
| ZIP/Postal code |
21231 |
| Country |
USA |
| |
|
| Platform ID |
GPL7042 |
| Series (1) |
| GSE12077 |
Androgen dependent gene expression profiling of the urogenital sinus |
|
