Article Figures & Data
Figures
- Figure 1
Diagrammatic representation of the morphological changes that occur in the gastrointestinal tract of a sheep during the transition from (A) pre-ruminant to (B) ruminant. The 14 regions sampled for this study are numbered (12 samples from each of the lambs and 2 from the adult animals only – esophagus and rectum). The esophageal groove is indicated with dotted lines.
- Figure 2
Gene-to-gene network graph of sheep GI tract tissues alongside alveolar macrophages, esophageal tissue and liver with the nodes collapsed by class to illustrate the relative size of each cluster. The top 20 largest clusters are annotated by function. Created using Graphia Professional with parameters Pearson’s R = 0.85, MCLi = 2.2, Minimum Component Size = 2, Minimum Cluster Size = 2.
- Figure 3
Comparative analysis of the expression of five C-type lectin genes, measured as transcripts per million (TPM), across three GI tract tissues (large colon, ileum and rumen) and alveolar macrophages in sheep and goats.
- Figure 4
Sample-to-sample network graph of sheep GI tract samples colored according to developmental stage. Created using Graphia Professional with parameters Pearson’s R = 0.85, MCLi = 2.2, Minimum Component Size = 2, Minimum Cluster Size = 2.
- Figure 5
Principal Component Analysis of macrophage associated signatures in the sheep GI tract illustrating separation by tissue (A & B) and developmental stage (C & D) in three and four components, respectively. The mean of each group was used as the center of the circle colored-by-group with a confidence interval of 0.95 as the ellipse size.
- Figure 6
The top 25 differentially expressed genes up-regulated and top 25 down-regulated genes between goat and sheep in the rumen, ileum and colon of age-matched one-week old animals.
Tables
- Table 1 Details of animals and samples from the GI tract and other tissues included in this study
Species Breed Developmental Stage Sex GI Tract Tissues Reference & ENA Study Accession Sheep Texel x Scottish Blackface Birth (neonate/ pre-ruminant) 1 male, 2 females Stomach Clark et al. 2017 (PRJEB19199) Abomasum, Pylorus Sheep Texel x Scottish Blackface One Week (transition from pre-ruminant to ruminant) 1 male, 2 females Large Intestine Cecum, Colon Spiral, Colon Large Sheep Texel x Scottish Blackface 8 Weeks (ruminant) 2 males, 1 female Small Intestine Duodenum, Ileum, Jejunum, Peyer’s Patch Sheep Texel x Scottish Blackface Adult (GI tract) (2 years) 3 males, 3 females Rumen Complex Omasum, Reticulum, Rumen Sheep Texel x Scottish Blackface Adult (2 years) 3 males, 3 females Esophageal Mucosa, Esophageal Muscle, Rectum, Liver, Alveolar Macrophages Clark et al. 2017 (PRJEB19199) Sheep Texel 8 – 9 Months 1 female Abomasum, Colon, Cecum, Rectum, Rumen, Omentum, Peyer’s Patch Jiang et al. 2014 (PRJEB6169) Sheep Texel Adult (>2 years) 1 male, 1 female Goat Crossbred One Week 3 male Ileum, Rumen, Colon Large, Alveolar Macrophages This Study (PRJEB23196) - Table 2 Examples of differentially expressed genes identified using pairwise comparison of abomasum, rumen and ileum samples from sheep at one-week vs. newborn and 8 weeks vs. 1 week. The gene expression estimate (as TPM) at the earliest developmental stage in each comparison is included as TPM 1 and at the later developmental stage as TPM 2
Gene Tissue Developmental Stage Fold Change P-Value Direction TPM 1 TPM 2 COL1A1 Rumen 8 Weeks vs. 1 Week 2.1 3.3x10−5 Up 29,269 92,501 Ileum 8 Weeks vs. 1 Week −2.3 8.5x10−15 Down 35,506 6919 COL1A2 Rumen 8 Weeks vs. 1 Week 2.1 7.3x10−5 Up 25,919 80,206 Ileum 8 Weeks vs. 1 Week −2.1 5.6x10−14 Down 33,384 7541 KRT36 Rumen 8 Weeks vs. 1 Week 3.9 6.5x10−8 Up 6384 69,503 HMGCS2 Rumen One Week vs. Newborn 8.4 2.3x10−50 Up 66 19,467 SLC14A1 Rumen One Week vs. Newborn 2.4 9.3x10−16 Up 2181 10,158 IL36A Rumen 8 Weeks vs. 1 Week 3.7 1.4x10−5 Up 275 2647 CLEC4E Ileum 8 Weeks vs. 1 Week 2.4 2.7x10−4 Up 15 76 PIP Rumen 8 Weeks vs. 1 Week 3.1 5.1x10−7 Up 375 2113 IFIT2 Ileum One Week vs. Newborn 2.0 1.8x10−6 Up 76 275 IFIT3 Abomasum 8 Weeks vs. 1 Week 3.1 7.7x10−31 Up 337 439 MX1 Abomasum 8 Weeks vs. 1 Week 2.1 5.5x10−21 Up 1048 1307 Rumen One Week vs. Newborn 3.6 1.2x10−5 Up 220 2256 DUOXA2 Rumen One Week vs. Newborn 4.1 3.2x10−5 Up 12 168 IDO1 Ileum One Week vs. Newborn 4.2 2.0x10−8 Up 88 1467
