Background
Materials and Methods
Animals and sample collection
Sample RNA preparation
RNA extraction
T7-based linear amplification
cDNA microarray
Bovine utero-placental cDNA microarray
cDNA microarray hybridization
Data normalization of the cDNA microarray
Cluster analysis of the cDNA microarray data
Real-time RT-PCR analysis
Gene | Primer or TaqMan probe | Sequence | Position |
---|---|---|---|
PL-Ala (J02840) | Forward | 5' GCAACATTGGTGGCTAGCAA 3' | 262-281 |
Reverse | 5' GCCCTCGCCAAACTGTTTATTA 3' | 339-317 | |
Probe | 5' CTATAGGCTCGCCAGGGAAATGTTCAATGA 3' | 285-314 | |
PRP-I (J02944) | Forward | 5' CAGACAGGTTTATGAATGCCGC 3' | 458-479 |
Reverse | 5' CGCAGGCAGTAGAACAGGTTAT 3' | 541-520 | |
Probe | 5' TCCTCTGCATCATCTAGTCACGGAGCTG 3' | 483-511 | |
AW464053 | Forward | 5' AATATGCCCAGGGCAAACTG 3' | 296-315 |
Reverse | 5' TCGGGAGTTTGGAGGGAATT 3' | 368-349 | |
Probe | 5' TCAATGCCATCAAGAGCTGCCACAC 3' | 323-347 | |
AW465434 | Forward | 5' ACATCTCCCTGAAAGTGAACCC 3' | 287-308 |
Reverse | 5' TCCATCCTTGCAGAAGTCTCCT 3' | 369-348 | |
Probe | 5' CCCTGGAAGCTCATCTGCAATGTAAAGC 3' | 316-343 | |
AW462349 | Forward | 5' GCGTGGATGGTGTCCTACTTCTA 3' | 216-238 |
Reverse | 5' GCCACAACGAGAAACAGGAAA 3' | 301-281 | |
Probe | 5' TGTCTGTTTGCCTTTACTGGTGAGCCCT 3' | 240-267 | |
AW485575 | Forward | 5' CCTCTGATGAAAGATTGGGAACAG 3' | 195-218 |
Reverse | 5' AAGTGCCAGAGATCTTGGCCT 3' | 285-265 | |
Probe | 5' TTCTCCAAACCAACCACCACCAGCTG 3' | 230-255 | |
GAPDH (U85042) | Forward | 5' AAGGCCATCACCATCTTCCA 3' | 178-197 |
Reverse | 5' CCACTACATACTCAGCACCAGCAT 3' | 253-230 | |
Probe | 5' AGCGAGATCCTGCCAACATCAAGTGG 3' | 200-225 |
Results
T7-based linear amplification
Differential gene expression profiles determined by cluster analysis
Temporal specific gene expression in extra-embryonic membranes
Accession No. | Gene name | D14E/D7E | K-means | Classification |
---|---|---|---|---|
Day 14E/Day 7E down-regulated genes (<0.5)
| ||||
L07872 | Homo sapiens Jk-recombination signal binding protein | 0.19 | 8 | Apoptosis & Cell cycle |
NM_001294 | Homo sapiens CLPTM1 | 0.23 | 4 | Cytokine family |
NM_001021 | Homo sapiens ribosomal protein S17 (RPS17) | 0.25 | 8 | Ribosomal |
M20866 | Sus scrofa cofilin | 0.25 | 1 | Cytoskeleton |
M21683 | Sus scrofa nonhistone protein HMG1 | 0.30 | 8 | DNA binding protein |
AF020508 | Bos taurus PAG-6 | 0.36 | 11 | Cytokine family |
AF020507 | Bos taurus PAG-5 | 0.39 | 11 | Cytokine family |
X91755 | Bos taurus cathepsin L | 0.42 | 8 | Oncogene & Tumor inhibitor |
NM_005722 | Homo sapiens ARP2 actin-related protein 2 homolog (yeast) | 0.43 | 8 | Cytoskeleton |
AF210381 | Bos taurus DDVit1 | 0.44 | 4 | ECM & related |
AF020506 | Bos taurus PAG-4 | 0.46 | 1 | Cytokine family |
U21660 | Bos taurus phosphatidylcholine transfer protein | 0.47 | 4 | |
L02897 | Dog nonerythroid beta-spectrin | 0.47 | 9 | |
AF166124 | Homo sapiens selenoprotein X | 0.49 | 8 | |
Day 14E/Day 7E up-regulated genes (2<)
| ||||
X14926 | Mus musculus calreticulin | 24.00 | 12 | |
AB009282 | Homo sapiens cytochrome b5 | 16.48 | 12 | |
NM_004494 | Homo sapiens hepatoma-derived growth factor (HDGF) | 13.52 | 12 | Oncogene & Tumor inhibitor |
AF000137 | Bos taurus connective tissue growth factor precursor (CTGF) | 12.18 | 12 | Cytokine family |
NM_000365 | Homo sapiens triosephosphate isomerase 1 (TPI1) | 10.52 | 12 | |
X89984 | Homo sapiens BCL7A protein | 10.31 | 12 | Cytoskeleton |
AF217197 | Homo sapiens FBP interacting repressor (FIR) | 9.80 | 12 | Transcriptional regulator |
NM_005720 | Homo sapiens ARPC1B | 9.45 | 3 | Cytoskeleton |
NM_001404 | Homo sapiens EEF1G | 9.43 | 12 | Transcriptional regulator |
AB003094 | Bos taurus ferritin L subunit | 9.38 | 12 | |
X56503 | Sus scrofa casein kinase II beta subunit (CKII beta) | 8.55 | 12 | Enzyme |
X13684 | Bos taurus glutathione peroxidase (gpx1) | 8.39 | 3 | Enzyme |
NM_002436 | Homo sapiens membrane protein, palmitoylated 1 (55 kD) | 8.33 | 12 | Membrane protein |
NM_005022 | Homo sapiens profilin 1 (PFN1) | 8.09 | 12 | Cytoskelton |
X01809 | Bos taurus cathepsin 3' terminus | 8.08 | 12 | Oncogene & Tumor inhibitor |
AF207664 | Homo sapiens matrix metalloprotease (ADAMTS1) | 8.03 | 3 | ECM & related |
X56597 | Homo sapiens humFib fibrillarin | 7.97 | 12 | |
AF182001 | Bos taurus D4-GDP-dissociation inhibitor (D4-GDI) | 7.82 | 3 | |
NM_007317 | Homo sapiens kinesin-like 4 (KNSL4) | 7.66 | 2 | |
M21044 | Bos taurus MHC class I BoLA | 7.65 | 2 | Cytokine family |
Accession No. | Gene name | D21E/D14E | K-means | Classification |
---|---|---|---|---|
Day 21E/Day 14E down-regulated genes (<0.5)
| ||||
U21661 | Rattus norvegicus myotrophin | 0.28 | 2 | Cytokine family |
Day 21E/Day 14E up-regulated genes (2<)
| ||||
AF004877 | Homo sapiens pro-alpha 2(I) collagen (COL1A2) | 16.08 | 4 | ECM & related |
U21660 | Bos taurus phosphatidylcholine transfer protein | 10.13 | 4 | |
X15112 | Bos taurus cytochrome c oxidase subunit VIb (AED) | 10.01 | 4 | |
X59504 | Bos taurus prolactin-like protein (PRP-VI) | 9.62 | 11 | Cytokine family |
AB008683 | Bos taurus alpha2(I) collagen (COL1A2) | 9.27 | 4 | ECM & related |
AF105429 | Ovis aries H19 | 7.81 | 4 | |
X65210 | Bos taurus microsatellite DNA | 7.62 | 11 | |
X15975 | Bos taurus PRP-V | 7.59 | 11 | Cytokine family |
S74761 | Bos taurus water channel protein CHIP29 | 7.44 | 9 | Membrane protein |
AF196320 | Bos taurus Interferon-tau1C | 7.39 | 2 | Cytokine family |
NM_001613 | Homo sapiens actin, alpha 2 (ACTA2) | 6.98 | 4 | Cytoskeleton |
L06151 | Bos taurus PAG-2 | 6.86 | 11 | Cytokine family |
M32303 | Bos taurus metalloproteinase inhibitor | 6.82 | 11 | ECM & related |
NM_001553 | Homo sapiens IGFBP7 | 6.62 | 9 | Cytokine family |
M21683 | Sus scrofa nonhistone protein HMG1 | 6.58 | 8 | DNA binding protein |
AF020508 | Bos taurus PAG-6 | 6.54 | 11 | Cytokine family |
AF125041 | Ovis aries decorin | 6.42 | 4 | |
J02944 | Bos taurus PRP-1 | 6.40 | 11 | Cytokine family |
AB004800 | Sus scrofa S100C protein | 5.68 | 9 | Cytokine family |
AF192336 | Bos taurus PAG-19 | 5.47 | 11 | Cytokine family |
Accession No. | Gene name | D28EEM/D21E | K-means | Classification |
---|---|---|---|---|
Day 28EEM/Day 21E down-regulated genes (<0.5)
| ||||
AF196320 | Bos taurus Interferon-tau1C | 0.07 | 2 | Cytokine family |
AF033096 | Avena sativa nonphototropic hypocotyl 1 (NPH1-1) | 0.22 | 12 | |
L10240 | Homo sapiens EMMPRIN | 0.24 | 7 | ECM & related |
U21660 | Bos taurus phosphatidylcholine transfer protein | 0.27 | 4 | |
X15112 | Bos taurus cytochrome c oxidase subunit VIb (AED) | 0.28 | 4 | |
L34261 | Bos taurus palmitoyl-protein thioesterase | 0.29 | 6 | Enzyme |
M26576 | Homo sapiens alpha-1 collagen type IV | 0.29 | 6 | ECM & related |
NM_001747 | Homo sapiens capping protein, gelsolin-like (CAPG) | 0.32 | 2 | Cytoskeleton |
U46064 | Sus scrofa aldehyde reductase (ALR1) | 0.33 | 3 | Enzyme |
AF020513 | Bos taurus PAG-11 | 0.33 | 12 | Cytokine family |
M11120 | Rat 28S rRNA | 0.33 | 2 | |
NM_004718 | Homo sapiens COX7A2L | 0.34 | 8 | Enzyme |
AF144763 | Bos taurus TIMP-1 | 0.35 | 3 | ECM & related |
AF034607 | Homo sapiens chloride channel ABP | 0.36 | 8 | Membrane protein |
NM_005556 | Homo sapiens keratin 7 (KRT7) | 0.36 | 2 | Cytoskeleton |
AJ243656 | Methanobacterium thermoautotrophicum ehbA-Q | 0.37 | 2 | |
M83104 | Bos taurus cytochrome b5 reductase | 0.37 | 2 | Enzyme |
X59693 | Bos taurus ubiquinol-cytrochrome-c reductase (subunit II) | 0.38 | 6 | Enzyme |
D84557 | Homo sapiens HsMcm6 | 0.38 | 12 | |
M77234 | Homo sapiens ribosomal protein S3a | 0.38 | 6 | Ribosomal |
Day 28EEM/Day 21E up-regulated genes (2 <)
| ||||
AF020508 | Bos taurus PAG-6 | 3.45 | 11 | Cytokine family |
X01912 | Goat epsilon I beta-globin | 3.00 | 9 | |
AF004133 | Sus scrofa adipocyte membrane protein | 2.66 | 1 | Membrane protein |
M73961 | Ovis aries PAG-1 | 2.35 | 6 | Cytokine family |
J02840 | Bos taurus placental lactogen (PL-Ala) | 2.21 | 5 | Cytokine family |
AF192336 | Bos taurus PAG-19 | 2.17 | 11 | Cytokine family |
AB005148 | Bos taurus interleukin 1 (IL-1) receptor antagonist | 2.13 | 1 | Cytokine family |
D10989 | Bos taurus endothelin ETB receptor | 2.12 | 1 | |
X59504 | Bos taurus PRP-VI | 2.08 | 11 | Cytokine family |
M80328 | Bos taurus PL-Val | 2.01 | 5 | Cytokine family |
Z11742 | Bos taurus annexin XI | 2.00 | 5 | Apoptosis & Cell cycle |
Accession No. | Gene name | D28F/D28EEM | K-means | Classification |
---|---|---|---|---|
Day 28F/Day 28EEM down-regulated genes (<0.5)
| ||||
M73961 | Ovis aries PAG-1 | 0.14 | 6 | Cytokine family |
X89984 | Homo sapiens BCL7A protein | 0.14 | 12 | Cytoskeleton |
X15975 | Bos taurus PRP-V | 0.15 | 11 | Cytokine family |
AF079545 | Ovis aries placental lactogen precursor (PL) | 0.16 | 8 | Cytokine family |
AF020509 | Bos taurus PAG-7 | 0.19 | 11 | Cytokine family |
J02840 | Bos taurus placental lactogen (bPL-Ala) | 0.20 | 5 | Cytokine family |
X59504 | Bos taurus PRP-VI | 0.20 | 11 | Cytokine family |
S72871 | Homo sapiens GATA-2 transcription factor | 0.20 | 8 | Transcriptional regulator |
AF192336 | Bos taurus PAG-19 | 0.22 | 11 | Cytokine family |
AF020508 | Bos taurus PAG-6 | 0.23 | 11 | Cytokine family |
J02944 | Bos taurus PRP-I | 0.24 | 11 | Cytokine family |
L06151 | Bos taurus PAG-2 | 0.25 | 11 | Cytokine family |
AF020512 | Bos taurus PAG-10 | 0.27 | 5 | Cytokine family |
AF020514 | Bos taurus PAG-12 | 0.28 | 11 | Cytokine family |
AF192334 | Bos taurus PAG-17 | 0.30 | 11 | Cytokine family |
AL133034 | Homo sapiens clone DKFZp727K171 | 0.31 | 11 | |
Z11742 | Bos taurus annexin XI | 0.31 | 5 | Apoptosis & Cell cycle |
U89321 | Homo sapiens nucleophosmin phosphoprotein (NPM) | 0.32 | 5 | |
X17614 | Bos taurus 3 beta hydroxy-5-ene steroid dehydrogenase/delta 5-delta4 isomerase | 0.32 | 5 | Enzyme |
AF192333 | Bos taurus PAG-16 | 0.32 | 11 | Cytokine family |
Day 28F/Day 28EEM up-regulated genes (2<)
| ||||
L34261 | Bos taurus palmitoyl-protein thioesterase | 4.32 | 6 | Enzyme |
AF000137 | Bos taurus connective tissue growth factor precursor (CTGF) | 2.85 | 12 | Cytokine family |
NM_004458 | Homo sapiens FACL4 transcript variant 1 | 2.84 | 7 | Enzyme |
NM_006491 | Homo sapiens NOVA1 transcript variant 3 | 2.82 | 1 | Oncogene & Tumor inhibitor |
NM_006838 | Homo sapiens methionine methionyl aminopeptidase 2 | 2.72 | 4 | Enzyme |
AB028449 | Homo sapiens helicase-MOI | 2.65 | 9 | DNA binding protein |
AL080102 | Homo sapiens clone DKFZp564N1916 | 2.64 | 9 | |
AF057300 | Homo sapiens truncated RAD50 protein | 2.63 | 3 | |
AB043994 | Bos taurus MMP-2 | 2.56 | 7 | ECM & related |
NM_006719 | Homo sapiens transcript variant ABLIM-m | 2.53 | 1 | Cytoskeleton |
AF195417 | Homo sapiens DEAD-box protein abstrakt (ABS) | 2.51 | 2 | |
Z25531 | Bos taurus repeat region DNA | 2.41 | 3 | |
AF113682 | Homo sapiens clone FLB3436 PRO0868 | 2.40 | 4 | |
S76474 | Homo sapiens trkB | 2.39 | 1 | Cytokine family |
Y16533 | Ovis aries IGF-II | 2.39 | 7 | Cytokine family |
M86739 | Bos taurus neuropeptide Y receptor | 2.38 | 7 | Cytokine family |
AF043937 | Homo sapiens DHAPAT | 2.37 | 9 | Enzyme |
AF144763 | Bos taurus TIMP-1 protein | 2.36 | 3 | ECM & related |
NM_005563 | Homo sapiens stathmin 1/oncoprotein 18 (STMN1) | 2.36 | 4 | Oncogene & Tumor inhibitor |
AF198487 | Homo sapiens transcription factor LBP-1b | 2.34 | 4 | Transcriptional regulator |