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| Status |
Public on Mar 07, 2013 |
| Title |
Deep Sequencing of the Porcine Endometrial Transcriptome on Day 14 of Pregnancy |
| Organism |
Sus scrofa |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
In pigs, conceptus attachment to the uterine surface epithelium starts around day 14 of pregnancy preceded by a pronounced vascularization at the implantation zones, initiating the epitheliochorial placentation. To characterize the complex transcriptome changes in the endometrium in the course of initial conceptus attachment deep sequencing of endometrial RNA samples of pregnant animals (n=4) and corresponding cyclic controls (n=4) was performed using Illumina RNA-Seq. The obtained sequence reads were mapped to the porcine genome and relative expression values were calculated for the analysis of differential gene expression. Statistical analysis revealed 1,933 differentially expressed genes (FDR 1%), 1,229 with higher and 704 with lower mRNA concentration in the samples from pregnant animals. Expression of selected genes was validated by the use of quantitative real-time RT-PCR. The RNA-Seq data were compared to results of a microarray study of bovine endometrium on day 18 of pregnancy and additional related data sets. Bioinformatics analysis revealed for the genes with higher mRNA concentration in pregnant samples strong overrepresentation particularly for immune-related functional terms but also for apoptosis and cell adhesion. Overrepresented terms for the genes with lower mRNA concentration in pregnant samples were related to extracellular region, ion transport, cell adhesion and lipid and steroid metabolic process. In conclusion, RNA-Seq analysis revealed comprehensive transcriptome differences in porcine endometrium between day 14 of pregnancy and corresponding cyclic endometrium and highlighted new processes and pathways probably involved in regulation of non-invasive implantation in the pig.
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| Overall design |
In total, 8 samples were analyzed, 4 biological replicates for pregnant animals (samples from 4 different animals) and 4 biological replicates for cyclic controls (samples from 4 different animals)
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| Contributor(s) |
Samborski A, Graf A, Krebs S, Kessler B, Bauersachs S |
| Citation(s) |
23426436 |
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| Submission date |
Jan 22, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Stefan Michael Bauersachs |
| E-mail(s) |
[email protected]
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| Organization name |
University of Zurich
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| Department |
Department for Farm Animals
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| Lab |
Genetics and Functional Genomics
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| Street address |
Eschikon 27 EHB 23.1
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| City |
Lindau |
| State/province |
Zurich |
| ZIP/Postal code |
8315 |
| Country |
Switzerland |
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| Platforms (1) |
| GPL15064 |
Illumina Genome Analyzer IIx (Sus scrofa) |
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| Samples (8)
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| GSM1067871 |
Day 14 non-pregnant control, biological replicate 1 |
| GSM1067872 |
Day 14 non-pregnant control, biological replicate 2 |
| GSM1067873 |
Day 14 non-pregnant control, biological replicate 3 |
| GSM1067874 |
Day 14 non-pregnant control, biological replicate 4 |
| GSM1067875 |
Day 14 pregnant, biological replicate 1 |
| GSM1067876 |
Day 14 pregnant, biological replicate 2 |
| GSM1067877 |
Day 14 pregnant, biological replicate 3 |
| GSM1067878 |
Day 14 pregnant, biological replicate 4 |
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| Relations |
| BioProject |
PRJNA186961 |
| SRA |
SRP018102 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE43667_Cuffmerge_merged_transcripts.gtf.gz |
3.1 Mb |
(ftp)(http) |
GTF |
| GSE43667_RAW.tar |
2.5 Mb |
(http)(custom) |
TAR (of TXT) |
| GSE43667_Ssc10_2_EntrezGene.gtf.gz |
1.9 Mb |
(ftp)(http) |
GTF |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
| Processed data are available on Series record |
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