|
| Status |
Public on Apr 09, 2015 |
| Title |
P1541 |
| Sample type |
SRA |
| |
|
| Source name |
Pregnant_endometrium1541
|
| Organism |
Bos indicus |
| Characteristics |
developmental stage: multiparous cows
health status: Healthy
breed: Nelore
pregnancy status: Pregnant
tissue: endometrial biopsy
|
| Treatment protocol |
Therefore, beef cows were synchronized and artificially inseminated at detected estrus. Six days after AI, jugular blood samples and a biopsy from the uterine horn contralateral to the ovary containing the corpus luteum were collected. Based on pregnancy outcome on day 30, samples were retrospectively allocated to the following groups: Pregnant and Non-Pregnant.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from frozen biopsy samples using the AlLrep® DNA/RNA/Protein Mini kit (No. 80004, Qiagen), as recommended by manufacturer’s instructions. cDNA was generated by a routine RNA library preparation TruSeq protocol developed by Illumina Technologies (San Diego, CA) using 1 μg of total RNA as input.
RNA libraries were prepared for sequencing using standard Illumina protocols
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiScanSQ |
| |
|
| Data processing |
CASAVA v1.8.2
The paired end (PE) reads were filtered using the Seqyclean v1.4.13 package (https://bitbucket.org/izhbannikov/seqyclean) which removed all reads with a mean quality under 26 and removed the primer and vector contaminants using the UniVec database (http://www.ncbi.nlm.nih.gov/tools/vecscreen/univec/).
The reads were mapped using the local alignment with Bowtie2 v2.1.0 against the masked Bos taurus genome masked assembly (Bos taurus UMD3.1) and read counts were obtained using HTSeq-count v0.5.4p2 (http://www-huber.embl.de/users/anders/HTSeq/doc/count.html).
The differential expression analysis of the RNA-Seq data was performed with package DESEq2 v1.12.1, from R. The normalized counts were then obtained for each annotated gene.
After normalization, the log2foldchange was obtained through a general linear model approach, the significance test was followed by the FDR-Benjamini-Hochberg correction for multiple tests.
Genome_build: Bos_taurus_UMD_3.1.1
Supplementary_files_format_and_content: P_vs_NP.txt reports abundance measurements
|
| |
|
| Submission date |
Jan 20, 2015 |
| Last update date |
May 15, 2019 |
| Contact name |
Mario Binelli |
| E-mail(s) |
binelli@usp.br
|
| Phone |
19998591388
|
| Organization name |
University of Sao Paulo (USP)
|
| Department |
department of animal reproduction
|
| Lab |
Molecular Physiology and Endocrinology
|
| Street address |
Rua Duque de Caxias Norte, 255
|
| City |
Pirassununga |
| State/province |
SP |
| ZIP/Postal code |
13635-900 |
| Country |
Brazil |
| |
|
| Platform ID |
GPL19671 |
| Series (1) |
| GSE65117 |
Transcriptome profile form endometrial biopsy samples of pregnant and non-pregnant cows |
|
| Relations |
| BioSample |
SAMN03246807 |
| SRA |
SRX790896 |
