|
| Status |
Public on Aug 31, 2009 |
| Title |
mouse139_vs_female_pool: liver |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
mouse139, liver
|
| Organism |
Mus musculus |
| Characteristics |
strain: CAST/EiJ x C57BL/6J
treatment category: test sample
tissue: liver
sex: female
|
| Treatment protocol |
Mice were fasted overnight before they were killed. Their tissues were collected, flash frozen in liquid nitrogen, and stored in −80 °C prior to RNA isolation. All procedures of housing and treatment of animals were performed in accordance with Institutional Animal Care and Use Committee regulations.
|
| Growth protocol |
All mice were maintained on a 12 h light–12 h dark cycle and fed ad libitum. Mice were fed Purina Chow until 10 wk of age, and then fed western diet (Teklad 88137, Harlan Teklad) for the subsequent 8 wk.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mouse tissues were homogenized, and total RNA extracted using Trizol reagent (Invitrogen) according to manufacturer's protocol.
|
| Label |
Cy5
|
| Label protocol |
Three micrograms of total RNA was reverse transcribed and labeled with either Cy3 or Cy5 fluorochrome. Labeled complementary RNA (cRNA) from each F2 animal was hybridized against a cross-specific pool of labeled cRNAs constructed from equal aliquots of RNA from 150 F2 animals and parental mouse strains for each of the three tissues.
|
| |
|
| Channel 2 |
| Source name |
reference pool (female, liver)
|
| Organism |
Mus musculus |
| Characteristics |
strain: CAST/EiJ x C57BL/6J
treatment category: reference pool
tissue: liver
sex: female
|
| Treatment protocol |
Mice were fasted overnight before they were killed. Their tissues were collected, flash frozen in liquid nitrogen, and stored in −80 °C prior to RNA isolation. All procedures of housing and treatment of animals were performed in accordance with Institutional Animal Care and Use Committee regulations.
|
| Growth protocol |
All mice were maintained on a 12 h light–12 h dark cycle and fed ad libitum. Mice were fed Purina Chow until 10 wk of age, and then fed western diet (Teklad 88137, Harlan Teklad) for the subsequent 8 wk.
|
| Extracted molecule |
polyA RNA |
| Extraction protocol |
Mouse tissues were homogenized, and total RNA extracted using Trizol reagent (Invitrogen) according to manufacturer's protocol.
|
| Label |
Cy3
|
| Label protocol |
Three micrograms of total RNA was reverse transcribed and labeled with either Cy3 or Cy5 fluorochrome. Labeled complementary RNA (cRNA) from each F2 animal was hybridized against a cross-specific pool of labeled cRNAs constructed from equal aliquots of RNA from 150 F2 animals and parental mouse strains for each of the three tissues.
|
| |
|
| |
| Hybridization protocol |
The hybridizations were performed to single arrays (individuals F2 samples labeled with Cy5 and reference pools labeled with Cy3 fluorochromes) for 24 h in a hybridization chamber, washed, and scanned using a confocal laser scanner. Arrays were quantified on the basis of spot intensity relative to background, adjusted for experimental variation between arrays using average intensity over multiple channels, and fitted to a previously described error model to determine significance21 (type I error)
|
| Scan protocol |
Standard dual-channel Agilent scanner with manufacturer provided software.
|
| Description |
ID369
|
| Data processing |
See Rosetta Error Model (PMID: 16522673)
|
| |
|
| Submission date |
May 26, 2009 |
| Last update date |
May 29, 2009 |
| Contact name |
Tomas Babak |
| E-mail(s) |
tomas_babak@merck.com, tomas.babak@utoronto.ca
|
| Phone |
416-978-1839
|
| Fax |
416-978-8528
|
| Organization name |
Best Institute
|
| Department |
Banting and Best Department of Medical Research
|
| Lab |
Timothy Hughes
|
| Street address |
112 College St
|
| City |
Toronto |
| State/province |
ON |
| ZIP/Postal code |
M5G1L6 |
| Country |
Canada |
| |
|
| Platform ID |
GPL8591 |
| Series (1) |
|
