|
Status |
Public on Apr 09, 2015 |
Title |
P2396 |
Sample type |
SRA |
|
|
Source name |
Pregnant_endometrium2396
|
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 |
SAMN03246810 |
SRA |
SRX791950 |