|
| Status |
Public on Jun 14, 2007 |
| Title |
Control 1000 vs. DES 1000 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
RNA prepared from uteri of 19 day old female CD-1 mice
|
| Organism |
Mus musculus |
| Characteristics |
Control
|
| Biomaterial provider |
Female CD-1 pups, 19 days of age
|
| Treatment protocol |
Pooled RNA prepared from uteri of 19 day old female CD-1 mice treated on days1-5 with corn oil
|
| Growth protocol |
After birth, pups were separated by sex and female pups were standardized to 8 female pups per litter. Mice were housed in polysulfone ventilated cages and provided NIH-31 laboratory mouse chow and fresh water ad libitum. Mouse chow was tested for estrogenic activity and found to be negative.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Uteri were snap frozen in liquid nitrogen. Frozen tissues were pulverized and RA was prepared using RNeasy Mini kits according to the manufacturer's protocol. The quality of the RNA was assessed by 1% agarose gel with ethidium bromide. RNA was pooled from 10 mice and assayed again for quality using the Agilent 2100 Bioanalyzer.
|
| Label |
Cy3
|
| Label protocol |
Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 1µg of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.
|
| |
|
| Channel 2 |
| Source name |
RNA prepared from uteri of 19 day old female CD-1 mice
|
| Organism |
Mus musculus |
| Characteristics |
DES treated
|
| Biomaterial provider |
Female CD-1 pups, 19 days of age
|
| Treatment protocol |
Pooled RNA prepared from uteri of 19 day old female CD-1 mice treated on days1-5 with 1000 µg/kg/day DES dissolved in corn oil
|
| Growth protocol |
After birth, pups were separated by sex and female pups were standardized to 8 female pups per litter. Mice were housed in polysulfone ventilated cages and provided NIH-31 laboratory mouse chow and fresh water ad libitum. Mouse chow was tested for estrogenic activity and found to be negative.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Uteri were snap frozen in liquid nitrogen. Frozen tissues were pulverized and RA was prepared using RNeasy Mini kits according to the manufacturer's protocol. The quality of the RNA was assessed by 1% agarose gel with ethidium bromide. RNA was pooled from 10 mice and assayed again for quality using the Agilent 2100 Bioanalyzer.
|
| Label |
Cy5
|
| Label protocol |
Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 1µg of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol.
|
| |
|
| |
| Hybridization protocol |
For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol.
|
| Scan protocol |
Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (v7.4).
|
| Description |
Total RNA was amplified using the Agilent Low RNA Input Fluorescent Linear Amplification Kit protocol. Starting with 500ng of total RNA, Cy3 or Cy5 labeled cRNA was produced according to manufacturer's protocol. For each two color comparison, 750ng of each Cy3 and Cy5 labeled cRNAs were mixed and fragmented using the Agilent In Situ Hybridization Kit protocol. Hybridizations were performed for 17 hours in a rotating hybridization oven using the Agilent 60-mer oligo microarray processing protocol. Chips were scanned with an Agilent Scanner and processed with the Agilent Feature Extraction Software (v7.4).
|
| Data processing |
Rosetta Resolver Error Model, values are Cy5/Cy3 in fold change
|
| |
|
| Submission date |
Sep 11, 2006 |
| Last update date |
Jun 15, 2007 |
| Contact name |
NIEHS Microarray Core |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
NIEHS
|
| Department |
DIR
|
| Lab |
Microarray Core
|
| Street address |
111 T.W. Alexander Drive
|
| City |
RTP |
| State/province |
NC |
| ZIP/Postal code |
27709 |
| Country |
USA |
| |
|
| Platform ID |
GPL891 |
| Series (1) |
| GSE5825 |
Developmental Exposure to DES Alters Uterine Gene Expression That Maybe Associated with Neoplasia Later in Life |
|
