|
| Status |
Public on Oct 31, 2023 |
| Title |
Ovaries-TCDD-miRNAs |
| Sample type |
RNA |
| |
|
| Source name |
Ovaries
|
| Organism |
Mus musculus |
| Characteristics |
cell type: Ovaries cells
|
| Treatment protocol |
Both Male and female Mice were either treated with TCDD (10µg/kg body weight) or Vehicle, the latter consisting of an equal amount of DMSO in corn oil, On day 3, ovaries and testes were harvested and single cell suspensions were prepared. miRNA arrays were performed using total RNAs including microRNA and using Affymetrix microarray platform
|
| Growth protocol |
Both ovaries and testes cells were cultured in complete medium for 6 hrs at 37C.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Trizol extraction of total RNA was performed according to the manufacturer's instructions.
|
| Label |
biotin
|
| Label protocol |
Purified miRNA samples isolated from testes and ovaries harvested from mice 72h post-exposure to TCDD were labeled using the Affymetrix® FlashTag™ Biotin HSR RNA Labeling Kit using the manufacturer's specifications for 100 format miRNA 4.0 arrays. GeneChip™ Hybridization, Wash, and Stain kit was used in conjunction with the Affymetrix® Hybridization Oven and Affymetrix® Fluidics Station on the 450 protocol to prepare Affymetrix® GeneChip® miRNA 4.0 arrays. Prepared arrays were then analyzed using the GeneChip™ Scanner 3000 7G (All products in this section are sourced from ThermoFisher Scientific, Waltham, MA, USA 02451). Microarray intensity was quantified, and differential expression was analyzed using Applied Biosystems Transcription Analysis Console (TAC) 4.0 software. Expression data were analyzed using Ingenuity Pathway Analysis (IPA) and miRNA targets were determined using the current target prediction database miRDB (Chen and Wang, 2020), and target prediction algorithm, MirTarget (Liu and Wang, 2019) as well as web-based TargetScan.
|
| |
|
| Hybridization protocol |
Following fragmentation, 10 ug of cRNA were hybridized for 16 hr at 45C on GeneChip Drosophila Genome Array. GeneChips were washed and stained in the Affymetrix Fluidics Station 400.
|
| Scan protocol |
GeneChips were scanned using the Hewlett-Packard GeneArray Scanner G2500A.
|
| Description |
Female mice were treated with TCDD (t 10µg/kg body weight). On day 3, ovaries and testes were harvested and single cell suspensions were prepared. miRNA arrays were performed using total RNAs including microRNA and using Affymetrix microarray platform
|
| Data processing |
The data were analyzed with Microarray Suite version 5.0 (MAS 5.0) using Affymetrix default analysis settings and global scaling as normalization method. The trimmed mean target intensity of each array was arbitrarily set to 100.
More than 1.5 fold increase or decrease
|
| |
|
| Submission date |
Aug 23, 2023 |
| Last update date |
Oct 31, 2023 |
| Contact name |
Narendra P Singh |
| E-mail(s) |
narendra.singh@uscmed.sc.edu
|
| Phone |
8032163422
|
| Organization name |
University of South Carolina
|
| Department |
Pathology, Microbiology, and Immunology
|
| Street address |
6439 Garners Ferry Road,
|
| City |
Columbia |
| State/province |
South Carolina |
| ZIP/Postal code |
29208 |
| Country |
USA |
| |
|
| Platform ID |
GPL21572 |
| Series (1) |
| GSE241576 |
Effect of TCDD exposure in adult female and male mice on the expression of miRNA in the ovaries and testes and associated reproductive functions |
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