|
| Status |
Public on Aug 15, 2023 |
| Title |
GH-treated TXOX rat replicate 4 |
| Sample type |
RNA |
| |
|
| Channel 1 |
| Source name |
GH-treated TXOX rat
|
| Organism |
Rattus norvegicus |
| Characteristics |
gender: male
strain: Sprague Dawley
tissue: Liver
condition: GH-treated TXOX
|
| Treatment protocol |
The goitrogenic drug methimazole (MMI; 0.05%) was added to the drinking water for 5 weeks starting on postnatal day (PND) 59 until sacrifice on PND94. Two weeks after starting MMI administration (TX), rats were orchidectomized (OX) or sham–operated to make TXOX rats or testis-intact controls (TX), respectively. Six rats were not treated with MMI and were subjected to sham-surgery to provide euthyroid testis-intact controls (INTACT). Four days after OX, we began hormonal replacement with TP (50 μg/kg; sc; 5 days per week) (TXOXTP) or vehicle (0.20 ml corn oil) (TXOX) to TXOX rats for 20 days before hormonal replacement with GH for 7 days. GH (0.3 mg/kg/day) (TXOXGH or TXOXTPGH) was administered as two daily sc injections at 12-h intervals (08:00h and 20:00h) to mimic the male-specific GH secretion. Adult hypothyroid control animals received equivalent amounts of the vehicle alone. On PND94, liver was snap frozen in liquid nitrogen and stored at -80ºC until processed for mRNA analysis.
|
| Growth protocol |
A microarray containing 27000 rat 70-mer oligo probe sets produced at the KTH Microarray Center (www.biotech.kth.se) was used to evaluate the effects of hypothyroidism and hormonal replacement in TXOX rats on liver gene expression.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TriReagent (Sigma, St. Louis, MO) according to the protocol supplied by the manufacturer. RNA yields were measured by UV absorbance and the quality of total RNA was analyzed by using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
|
| Label |
Cy5
|
| Label protocol |
Five μg of high-quality total RNA from the liver were reversed-transcribed and labeled with Cy5 (test samples) or Cy3 (TXOX referecence samples)
|
| |
|
| Channel 2 |
| Source name |
hypothyroid-orquidectomized rats
|
| Organism |
Rattus norvegicus |
| Characteristics |
condition: hypothyroid-orquidectomized rats
tissue: liver
|
| Treatment protocol |
The goitrogenic drug methimazole (MMI; 0.05%) was added to the drinking water for 5 weeks starting on postnatal day (PND) 59 until sacrifice on PND94. Two weeks after starting MMI administration (TX), rats were orchidectomized (OX) or sham–operated to make TXOX rats or testis-intact controls (TX), respectively. Six rats were not treated with MMI and were subjected to sham-surgery to provide euthyroid testis-intact controls (INTACT). Four days after OX, we began hormonal replacement with TP (50 μg/kg; sc; 5 days per week) (TXOXTP) or vehicle (0.20 ml corn oil) (TXOX) to TXOX rats for 20 days before hormonal replacement with GH for 7 days. GH (0.3 mg/kg/day) (TXOXGH or TXOXTPGH) was administered as two daily sc injections at 12-h intervals (08:00h and 20:00h) to mimic the male-specific GH secretion. Adult hypothyroid control animals received equivalent amounts of the vehicle alone. On PND94, liver was snap frozen in liquid nitrogen and stored at -80ºC until processed for mRNA analysis.
|
| Growth protocol |
A microarray containing 27000 rat 70-mer oligo probe sets produced at the KTH Microarray Center (www.biotech.kth.se) was used to evaluate the effects of hypothyroidism and hormonal replacement in TXOX rats on liver gene expression.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was isolated with TriReagent (Sigma, St. Louis, MO) according to the protocol supplied by the manufacturer. RNA yields were measured by UV absorbance and the quality of total RNA was analyzed by using a 2100 Bioanalyzer (Agilent Technologies, Palo Alto, CA).
|
| Label |
Cy3
|
| Label protocol |
Five μg of high-quality total RNA from the liver were reversed-transcribed and labeled with Cy5 (test samples) or Cy3 (TXOX referecence samples)
|
| |
|
| |
| Hybridization protocol |
Hybridized following the manufacturer’s protocol (ProntoTM Plus System, Promega).
|
| Scan protocol |
After 16 h of hybridization, the slides were washed and scanned using the GenePix Microarray Scanner (Axon Instruments, CA).
|
| Description |
Biological replicate 4 of 4.GH-treated TXOX rat
|
| Data processing |
Four independent hybridizations were performed comparing individual animals from the different experimental groups (INTACT, TXOXGH, TXOXTP and TXOXTPGH) with the references TXOX for a total of 4 analyses (4 biological replicates). The LOWESS method was used to normalize the raw intensity data. If the measured probe sets were not present in at least 3 of the 4 chips, they were assumed to contain no information and therefore were eliminated to reduce data complexity. Differentially expressed genes were identified by using the SAM statistical technique. A q value was assigned for each of the detectable genes in the array. This value is similar to a P-value, measuring the lowest false discovery rate (FDR) at which differential expression of a gene is considered significant. A minimal FDR of 0.05 was assigned for each gene. An additional selection requirement was added to FDR based on absolute changes in the gene expression ratios. A value of 1.5 (50%) (log2 ratio ≥ |0.57|) was chosen to describe ratios as up- or down-regulated.
|
| |
|
| Submission date |
Mar 12, 2018 |
| Last update date |
Aug 15, 2023 |
| Contact name |
Leandro Fernández-Pérez |
| E-mail(s) |
leandrofco.fernandez@ulpgc.es
|
| Organization name |
University of Las Palmas de Gran Canaria (ULPGC-IUIBS)
|
| Department |
Clinical Sciences
|
| Lab |
Pharmacology
|
| Street address |
Blas Cabrera Felipe s/n
|
| City |
Las Palmas de Gran Canaria |
| State/province |
Las Palmas |
| ZIP/Postal code |
35016 |
| Country |
Spain |
| |
|
| Platform ID |
GPL17592 |
| Series (1) |
| GSE111718 |
Effects of Testosterone and GH on liver transcriptome |
|
