 |
 |
GEO help: Mouse over screen elements for information. |
|
| Status |
Public on Jul 08, 2022 |
| Title |
Q110-UREA |
| Sample type |
SRA |
| |
|
| Source name |
Uterus
|
| Organism |
Equus caballus |
| Characteristics |
tissue: Endometrium
treatment: Urea
|
| Treatment protocol |
At the day of ovulation (D0), oral treatment started and continued until D7. Mares received the treatment or control diet in a random order (n= 11 mares/group) in a crossover design, and the intervening estrous cycle served as a washout cycle between two experimental cycles. The treatment group was fed 0.4 g of feed-grade urea (Hallway Feeds, Lexington, KY) per kg of body weight daily, mixed with 2.4 kg of sweet feed (Poize 10% crude protein, Hallway Feeds), molasses and mixed grass hay (8.4% crude protein). The control group received identical sweet feed, molasses and hay. Daily meals were divided in two equal amounts given in the morning and afternoon using individual feeding pens. Mares had ad libitum access to water.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total cellular RNA was extracted from endometrial samples using a RNeasy Mini Kit (Qiagen, Gaithersburg, MD). A total of 1 μg of RNA was treated with DNase I (Ambion Inc., Austin, TX) for 30 minutes at 37℃ to remove genomic DNA according to manufacturer’s instructions. Endometrial samples were processed for RNA extraction using a RNeasy Mini Kit (Qiagen, Gaithersburg, MD) following the manufacturer’s recommendations. After extraction, RNA concentration and quality were analyzed using a Nanodrop 2000 spectrophotometer Thermo Fisher Scientific) and a Bioanalyzer® (Agilent, Santa Clara, CA). Samples had a 260/280 ratio > 2.0, 28S:18S rRNA ratios >1.8 and RNA integrity number (RIN) was 9.78 0.06 (mean SEM).
A TruSeq Stranded mRNA library prep kit (Illumina, San Diego, CA) was used to prepare libraries for mRNA sequencing. Libraries were loaded onto an Agilent DNA 1000 chip and validated on an Agilent 2100 Bioanalyzer (Agilent). Quantitation was performed with the Illumina Library Quantification Kit, ABI Prism qPCR Mix from Kapa Biosystems. Libraries were run on a NextSeq 500 v2 (Illumina) 300cycles High Output kit in a 2x150 base pairs with paired-end reads.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The Fastq files were evaluated for read quality using FastQC 0.11.4
Trim Galore 0.4.1 was used for adapter and read quality trimming (Phred score threshold of 30).
Reads were mapped to the Equus caballus reference genome (EquCab 3.0) using the software STAR 2.5.3a (Dobin, Davis et al. 2013)
Reads were annotated with the equine reference annotation from NCBI using Cufflinks 2.2.1
Fragments per kilobase per million (FPKM) were used to determine the expression level of genes
Cuffdiff 2.2.1 was used to calculate differentially expressed genes (DEG) between samples from the control and urea groups
Significance level was set at FDR-adjusted p-value of the test statistic < 0.1 using a Benjamini-Hochberg correction
Genome_build: EquCab 3.0
Supplementary_files_format_and_content: Normalized abundance measurements- Cufflink Gene.FPKM.Tracking
|
| |
|
| Submission date |
Jul 08, 2019 |
| Last update date |
Jul 08, 2022 |
| Contact name |
Barry A. Ball |
| Organization name |
University of Kentucky
|
| Department |
Veterinary Scinece
|
| Lab |
Reproduction
|
| Street address |
108 Gluck Equine Research Center,
|
| City |
Lexington |
| State/province |
Kentucky |
| ZIP/Postal code |
40546-0099 |
| Country |
USA |
| |
|
| Platform ID |
GPL21401 |
| Series (2) |
| GSE133973 |
EFFECT OF ORAL UREA SUPPLEMENTATION ON THE ENDOMETRIAL TRANSCRIPTOME OF MARES |
| GSE133974 |
EFFECT OF ORAL UREA ADMINISTRATION ON THE TRANSCRIPTOME OF THE EQUINE ENDOMETRIUM AND EMBRYO |
|
| Relations |
| BioSample |
SAMN12232195 |
| SRA |
SRX6415659 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM3931531_Q110.Ure.fpkm_tracking.gz |
889.5 Kb |
(ftp)(http) |
FPKM_TRACKING |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
|
|
|
|
 |
