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| Status |
Public on Jul 28, 2022 |
| Title |
Uterine infection-induced transcriptomic changes in the bovine endometrium |
| Organism |
Bos taurus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Perform RNA-seq study on infectious bovine endometrial tissues to reveal important genes and biological pathways regulating uterine physiology following uterine infections
Methods:RNA sequencings were done using Illumina platform. Single-end reads in the FASTQ format were explored using FastQC, low-quality reads were trimmed from both 3’ and 5’ ends until a base pair of Phred quality score of 30 (99.9% accurate) or greater was found, reads having a mean quality score less than 30 and length below 30 nucleotides were filtered out. Cleaned reads were aligned against the bovine reference genome (Bos_taurus.ARS-UCD1.2) using HiSAT2. The resulting SAM files were sorted, converted to BAM files using SAMtools. Read counts mapped to bovine gene models were generated using htseq-count script from HTSeq package. Bioconductor DESeq2 was used to get the differentially expressed genes among infectious vs normal uterine tract groups
Conclusions: The study demonstrated that uterine infections altered several genes and pathways related to inflammatory response, immune response, uterine physiology, uterine enviroment and fertility in the intercaruncular region of bovine endometrium.
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| Overall design |
There are 4 normal uterine tract and 5 infectious uterine tract samples. Differential gene expression between each group (Infectious vs. Normal) are compared.
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| Contributor(s) |
Mishra B, Khadka V, Mahfuz Rahman A |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
| Submission date |
Jul 25, 2022 |
| Last update date |
Jul 28, 2022 |
| Contact name |
MAHFUZ RAHMAN ADNAN |
| E-mail(s) |
mahfuzradnan@gmail.com
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| Organization name |
University of Hawaii at Manoa
|
| Department |
Human Nutrition, Food and Animal Sciences
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| Lab |
Reproduction Lab
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| Street address |
1955 East-West Road
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| City |
Honolulu |
| State/province |
HI |
| ZIP/Postal code |
96822 |
| Country |
USA |
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| Platforms (1) |
| GPL23055 |
Illumina NextSeq 500 (Bos taurus) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA862118 |
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