Introduction
Materials and methods
Characterization of beta-glucan preparations from oat
Animals and treatment
Microarrays
RNA isolation, validation, labeling, and hybridization
Signal detection and statistical analysis
Real-time RT-PCR
Forward primer (5′–3′) | Reverse primer (5′–3′) | |
---|---|---|
Target gene (LPS-G0 vs. C-G0) | ||
Prodh | GCTGCAGAGGATGGATGTG | GTAGCACTGGAACGTGTTGA |
Camsap2 | AGCCAGTCCAGTCCTGATAA | GAGTCCTCGTCCATGGTTTC |
Hmcn2 | GCGGATTCAGGGTCTACAAG | CTCCAGCTGTGTTGCTAACT |
Serp2 | GAGGGGAAACGTAGCCAAAAC | TTATGTGGCCAACCTGCAAAC |
Gzmc | GCTTCCTGGTGAGAGACAAC | AGTCCTCTTGGCACTTCTCA |
Target gene (LPS-G1 vs. LPS-G0) | ||
Slc27a2 | CTACAACATCCGTGCCAAGT | GTGTCCACGCCATTAGTGTT |
Tpx2 | GAAGAGCAGAAGCAGCAGAA | GCCTCCATCTCAGCCATTTT |
Flt1 | TGGCTCCACGACCTTAGAC | GGCACCTATAGACACCCTCAT |
Serpini2 | CAGCAGCAGATCATGCAAAC | CCAAGACCAGACGAGTCAAG |
Clcn3 | CCTAGATGGAGCAGGTGCTAT | GATCCGTCTGTGCCTTTCTC |
Fat2 | GGAATTTCAGGGTGGCATGA | GAACGAGTATCGGCCATGAG |
Target gene (LPS-G2 vs. LPS-G0) | ||
Kcnk2 | ATGAACCCACGGGCGAAAA | AGTTCTGAGCAGCAGACTTG |
Mcm2 | AGAGACTACCGTCCCATTCC | TCAGCTCCTCCACATCTTCA |
Mtss1l | GACAAGGACCATGCGAAAGA | CAGGTCTCCTTTCCCTTTGC |
Gas7 | ATGGCAACGGCACTTCAG | ACATTCCCAGGTGGTCTCAT |
Usp6nl | TCCGGATCTGGGACATCTAC | GCCCGCTTTAACTCTGTCAT |
Efr3b | AGATGTGGGTCGCCATAGAT | GCTTTCCACGAAGAGGTTGA |
Reference gene | ||
GAPDH (glyceraldehyde 3-phosphate dehydrogenase) | GCTGGGGCTCACCTGAAGG | GGATGACCTTGCCCACAGCC |
Results
Groups | LPS-G0 | LPS-G1 | LPS-G2 |
---|---|---|---|
C-G0 | 138 | – | – |
LPS-G0 | – | 533 | 97 |
Validation of microarray data
Genes commonly regulated in peripheral blood of rats from both dietary groups supplemented with beta-glucans (LPS-G1 and LPS-G2)
Gene symbol | LPS-G0 vs. C-G0 | LPS-G1 vs. LPS-G0 | LPS-G2 vs. LPS-G0 | ||||
---|---|---|---|---|---|---|---|
Fold change | Direction of changes in expression | Fold change | Direction of changes in expression | Fold change | Direction of change in expression | ||
1 |
Dmtn
| 2.047 | Up | 3.041 | Down | Unchanged | |
2 |
Gpr52
| 2.156 | Up | 2.304 | Down | Unchanged | |
3 |
Gtsf1
| 2.233 | Up | 2.171 | Down | Unchanged | |
4 |
Krtap3-1
| 2.183 | Up | 2.304 | Down | Unchanged | |
5 |
Olr1406
| 3.577 | Up | 3.281 | Down | Unchanged | |
6 |
Pced1b
| 2.187 | Up | 2.348 | Down | Unchanged | |
7 |
RGD1563451
| 3.131 | Up | 2.526 | Down | 2.688 | Down |
8 |
RGD1564836
| 2.113 | Up | 2.373 | Down | 2.268 | Down |
9 |
RGD1566248
| 2.230 | Up | Unchanged | 2.271 | Down | |
10 |
Serp2
| 3.388 | Up | 12.594 | Down | Unchanged | |
11 |
Vom1r8
| 2.127 | Up | 2.305 | Down | Unchanged | |
12 |
Brpf1
| 2.357 | Down | 2.278 | Up | Unchanged | |
13 |
Cars
| 2.225 | Down | 2.097 | Up | Unchanged | |
14 |
Ccdc38
| 2.342 | Down | 4.115 | Up | Unchanged | |
15 |
Dppa3l1
| 2.018 | Down | 2.096 | Up | Unchanged | |
16 |
Epm2aip1
| 2.230 | Down | 2.040 | Up | Unchanged | |
17 |
Fam172a
| 2.721 | Down | 3.233 | Up | Unchanged | |
18 |
Lysmd4
| 2.168 | Down | Unchanged | 2.222 | Up | |
19 |
Mbp
| 2.325 | Down | 2.647 | Up | Unchanged | |
20 |
Mpp5
| 2.067 | Down | 2.020 | Up | Unchanged | |
21 |
Phf20l1
| 2.140 | Down | 2.563 | Up | Unchanged | |
22 |
Pip5k1a
| 4.299 | Down | 2.047 | Up | Unchanged | |
23 |
Pptc7
| 2.179 | Down | 2.014 | Up | Unchanged | |
24 |
Prodh
| 3.859 | Down | 2.777 | Up | 8.065 | Up |
25 |
Rab11fip1
| 2.152 | Down | 2.463 | Up | 2.119 | Up |
26 |
RGD1559908
| 2.357 | Down | 2.777 | Up | Unchanged | |
27 |
Scai
| 2.367 | Down | 2.033 | Up | Unchanged | |
28 |
Sft2d3
| 2.845 | Down | 2.470 | Up | Unchanged | |
29 |
Sik1
| 3.268 | Down | 2.838 | Up | Unchanged | |
30 |
Ssbp2
| 2.088 | Down | 2.380 | Up | Unchanged | |
31 |
Syap1
| 2.316 | Down | 2.289 | Up | Unchanged | |
32 |
Twistnb
| 2.122 | Down | 2.296 | Up | Unchanged | |
33 |
Usp6nl
| 2.605 | Down | Unchanged | 2.835 | Up | |
34 |
Uvssa
| 2.079 | Down | Unchanged | 2.273 | Up |
Gene symbol | LPS-G1 vs. LPS-G0 | LPS-G2 vs. LPS-G0 | |||
---|---|---|---|---|---|
Fold change | Direction of changes in expression | Fold change | Direction of change in expression | ||
1 |
Atg10
| 2.319 | Up | 2.023 | Up |
2 |
Ddx25
| 2.750 | Up | 2.517 | Up |
3 |
Efr3b
| 2.155 | Up | 2.328 | Up |
4 |
Fam83c
| 2.529 | Up | 2.187 | Up |
5 |
Fut4
| 2.700 | Up | 2.161 | Up |
6 |
Guf1
| 2.546 | Up | 2.122 | Up |
7 |
Mtus1
| 2.964 | Up | 3.259 | Up |
8 |
Olr1239
| 2.373 | Up | 2.349 | Up |
9 |
Rgsl1
| 2.684 | Up | 2.426 | Up |
10 |
She
| 2.545 | Up | 2.538 | Up |
11 |
Spetex-2F
| 2.138 | Up | 2.353 | Up |
12 |
Spg20
| 3.397 | Up | 3.077 | Up |
13 |
Zbtb48
| 2.654 | Up | 2.150 | Up |
14 |
Clybl
| 2.602 | Down | 2.357 | Down |
15 |
Cst12
| 2.380 | Down | 2.730 | Down |
16 |
Itga7
| 2.277 | Down | 2.409 | Down |
17 |
Olr1486
| 2.517 | Down | 2.905 | Down |
18 |
Spink14
| 2.057 | Down | 2.215 | Down |
19 |
Ube2c
| 5.648 | Down | 3.550 | Down |
Signaling pathways involving the proteins encoded by differentially expressed genes
Pathway | p value | Number of genes |
---|---|---|
NLR_Proteins_WP1294_71833 | 0.012 | 2 |
p53_pathway_WP655_78065 | 0.018 | 4 |
Cholesterol_Biosynthesis_WP461_71765 | 0.042 | 2 |
Toll-like_receptor_signaling_pathway_WP1309_72183 | 0.046 | 5 |
Nucleotide_Metabolism_WP146_71804 | 0.052 | 2 |
Pathway | p value | Number of genes |
---|---|---|
Prostaglandin_Synthesis_and_Regulation_WP303_71789 | 0.024 | 1 |
G1_to_S_cell_cycle_control_WP348_71777 | 0.030 | 2 |
Non-homologous_end_joining_WP1277_69423 | 0.033 | 1 |
Cell_cycle_WP429_71805 | 0.048 | 2 |