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| Status |
Public on Jul 13, 2022 |
| Title |
RNA-Sequencing based analysis of bovine endometrium during the maternal recognition of pregnancy |
| Organism |
Bos taurus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Perform RNA-seq study on bovine endometrial tissues during the peri-implantation period (Day16-17 of gestation) to reveal important genes and biological pathways required for conceptus growth and development
Methods:RNA sequencing was done using Illumina NextSeq500. 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 not 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 pregnant vs. non-pregnant (P vs. NP), pregnant vs. cyclic (P vs. C), and non-pregnant vs. cyclic (NP vs. C) groups.
Conclusions: The study demonstrated that the presence of conceptus at Day 15-17 of gestation affects the endometrial gene expression related to endometrial remodeling, immune response, nutrients and ion transporters, and relevant signaling pathways in the caruncular region of bovine endometrium during the maternal recognition of pregnancy.
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| Overall design |
There are 4 Cyclic, 4 Pregnant, 4 Non-Pregnant samples. Differential gene expression between each group (pregnant vs. non-pregnant, pregnant vs. cyclic, and non-pregnant vs. cyclic) are compared.
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| Contributor(s) |
Mishra B, Khadka V, Adhikari B |
| Citation(s) |
35799127 |
| |
| Submission date |
Feb 15, 2022 |
| Last update date |
Jul 13, 2022 |
| Contact name |
Vedbar S Khadka |
| E-mail(s) |
[email protected]
|
| Phone |
8086921462
|
| Organization name |
JABSOM Bioinformatics Core, University of Hawaii
|
| Lab |
Vedbar S Khadka
|
| Street address |
651 IIalo Street
|
| City |
Honolulu |
| State/province |
HI |
| ZIP/Postal code |
96813 |
| Country |
USA |
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| Platforms (1) |
| GPL23055 |
Illumina NextSeq 500 (Bos taurus) |
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| Samples (12)
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| Relations |
| BioProject |
PRJNA807310 |
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