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| Status |
Public on Jun 01, 2017 |
| Title |
Rat 47 ovary |
| Sample type |
SRA |
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| Source name |
ovary
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| Organism |
Rattus norvegicus |
| Characteristics |
strain: Sprague-Dawley
diet: control
tissue: ovary
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| Treatment protocol |
After 11 weeks on diet, ovaries were removed from all of animals (OVX) and half were implanted with slow-release estradiol (E2) pellets (OVX+E) a week later. Surgeries were performed under isoflurane/oxygen gas mixture; isoflurane was set at 2.5% and the oxygen flow to 2.0L/min. Before creating the incisions, the animals were given an injection of marcaine on each side based on their diet (0.1 mL for control, 0.15 mL for HFHS, 0.2 mL for HFHS rats over 400 grams) in order to relieve any pain caused the surgery. The surgical area was sterilized and small incisions were made bilaterally to expose and remove the ovaries. The muscle layer was sutured and the skin layer was closed with clips. The surgical area was wiped with antibacterial cream. Ovaries were stored individually in 4% PFA at 4°C for 24 hours. Ovaries were subsequently stored in 30% sucrose at 4°C.
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| Growth protocol |
Female Sprague-Dawley rats (n = 60; P17) were obtained from Charles River and were housed with mothers until weaning at day 23. At weaning, rats were randomly assigned to either a HFHS (n = 32) or control diet (n = 28) group. The control group had ad libitum access to water and standard rat chow (Envigo – LM-485, 3.1 kcal/g, 17% calories from fat). The HFHS diet group had ad libitum access to water, a 32% sucrose solution, and high fat chow (Research Diets – D12492, 5.24 kcal/g, 60% of the calories derived from fat). Animals were housed in pairs in a climate-controlled environment with a 12:12 h light:dark cycle (lights on at 8 am). Animals were weighed and handled every other day. All animal procedures were approved for use by the Washington and Lee University Institutional Animal Care and Use Committee (Protocol # NT0717).
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| Extracted molecule |
polyA RNA |
| Extraction protocol |
Immediately following removal, ovary tissue was flash frozen on liquid nitrogen and stored at -80 oC. To purify total RNA, tissue was thawed in TRIzol and homogenized using mechanical disruption. RNA was then purified using a commercial spin column kit, according to manufacturer’s instructions (Direct-zol RNA MiniPrep, Zymo Research R2053), and flash frozen on liquid nitrogen
Following poly(A) selection, cDNA libraries were prepared using the HiSeq SBS Kit (v. 4) with 4x-mutiplexing and the quality was verified by Bioanalyzer analysis. Sequencing was performed on the HiSeq 2500 platform, in paired-end 125 base-pair mode. All four independent ovary samples were run in a single lane, which generated a total of 47,664 Mbp of sequence across 1.9 x 108 clusters with mean Q-scores all above 35.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Data processing |
Raw sequencing reads in FASTQ format were filtered for quality and adapter sequences removed using Trimmomatic (v. 0.35) with the following parameters: a 4-base sliding window with average quality cutoff of 20, removal of leading and trailing low quality bases below the quality of 20 and a minimum read length of 119 bases.
Surviving reads were aligned to the Rattus norvegicus genome using the RGD gene model version 6.0, retrieved from ncbi.nlm.nih.gov on 03/23/2016, using STAR (v 2.5.1b) with the length of the annotated genome sequence specified as 124.
Gene expression estimation, expressed as fragments per kilobase per million reads (FPKM), was performed using RSEM (v. 1.2.29) with default options.
Genome_build: rn6
Supplementary_files_format_and_content: text files with TPM and FPKM
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| Submission date |
Jun 10, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
Gregg Brooks Whitworth |
| E-mail(s) |
whitworthg@wlu.edu
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| Phone |
(415) 336-3872
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| Organization name |
Washington and Lee Unversity
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| Department |
Biology
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| Street address |
204 West Washington St
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| City |
Lexington |
| State/province |
VA |
| ZIP/Postal code |
24450 |
| Country |
USA |
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| Platform ID |
GPL18694 |
| Series (1) |
| GSE83220 |
High-Fat High-Sugar Diet Induces Polycystic Ovary Syndrome in a Rodent Model |
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| Relations |
| BioSample |
SAMN05226145 |
| SRA |
SRX1837067 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM2196470_F_47_O.genes.results.txt.gz |
421.0 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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