MOESM1 of The proteome of IVF-induced aberrant embryo-maternal crosstalk by implantation stage in ewes
Creators: name: Yang, Qianying
name: Fu, Wei
name: Wang, Yue
name: Miao, Kai
name: Zhao, Haichao
name: Wang, Rui
name: Guo, Min
name: Wang, Zhilong
name: Tian, Jianhui
name: An, Lei
Publisher: name: figshare
Year: 2020
Subjects: subject: Cell Biology
subject: Genetics
subject: FOS: Biological sciences
subject: Molecular Biology
subject: Immunology
subject: FOS: Clinical medicine
subject: Biological Sciences not elsewhere classified
subject: Developmental Biology
subject: Cancer

description: Additional file 1: Figure S1. (a) Strategy for samples pooling. Conceptuses are presented as an example. In the IVO (or IVF) group, the samples of 36 (or 18) conceptuses were equally and randomly divided into three pools as independent biological replicates, each pooled sample was detected twice as technical replicates. (b) Pearson’s Correlation coefficient between the randomly selected two biological replicates using the summed peptide intensity values for each protein in the conceptus, C area and IC area samples to confirm the reliability of the processes of sample collection, LC-ESI-MS/MS detection and proteomic analysis. (c) Unsupervised clustering of the protein expression patterns of each biological replicate of the conceptus, C area and IC area samples from the IVO and IVF groups. (d) Volcano plot of DEPs in the C areas, IC areas and conceptuses between the IVO and IVF groups. The red and green dots represent upregulated or downregulated DEPs, respectively (−Log10(P-value) &gt; 1; mean fold change &gt; 2 or &lt; 0.5). Figure S2. (a) Graph visualization of biological processes (BPs) enriched in the IVF conceptuses based on REVIGO analysis. The bigger circle represents the more clustered genes. The gradation of color represents the significance level. Functionally associated BPs are linked. (b) Interaction networks of DEPs between the IVO and IVF conceptuses were created by a web-based search of the STRING database. Boxed regions represent tightly interconnected functional clusters. (c-d) The representative MGI phenotypes associated with embryonic development annotated with DEPs related to metabolism and cell cycle (c) and methyl metabolism (d). (e) Heat map of DEPs related to redox homeostasis in the IVO and IVF conceptuses. Normalized protein abundance is represented in red (relatively high) and green (relatively low). The table shows the representative MGI phenotypes of DEPs in redox homeostasis. Figure S3. (a) Interaction networks of DEPs between IVO and IVF conceptuses were created by a web-based search of the STRING database. Boxed regions represent tightly interconnected functional clusters (b). Graphical visualization of biological processes (BPs) enriched in IVF C areas based on REVIGO analysis. The bigger circle represents the more clustered genes. The gradation of the color represents the significance level. Functionally associated BPs are linked. (c) The representative MGI phenotypes associated with embryonic development annotated with DEPs related to metabolism and translation. Figure S4. (a) Graphical visualization of biological processes (BPs) enriched in IVF IC areas based on REVIGO analysis The bigger circle represents the more clustered genes. The gradation of the color represents the significance level. Functionally associated BPs are linked. (b) Interaction networks of DEPs between the IVO and IVF IC areas are created by a web-based search of the STRING database. Boxed regions represent tightly interconnected functional clusters. (c) Heat map of DEPs involved in Glycolysis/Gluconeogenesis in the IC areas. The level of Log2(IVF/IVO) is represented in red (relatively high) and green (relatively low).