Transcriptome Analysis of Landrace Pig Subcutaneous Preadipocytes during Adipogenic Differentiation
Abstract
:1. Introduction
2. Materials and Methods
2.1. Ethics Statement
2.2. Animals and Isolation of Preadipocytes
2.3. Induction of Subcutaneous Preadipocytes
2.4. Oil Red O staining
2.5. RNA Isolation, Sequencing, and Sequence Data Processing
2.6. Short Time-Series Expression Miner Analysis
2.7. Gene Ontology and Pathway Analyses
2.8. Validation of DEGs Using Reverse Transcription Quantitative PCR
2.9. Availability of Data and Material
3. Results
3.1. Phenotypic Changes during Preadipocyte Differentiation
3.2. Sequencing Results and Quality Control
3.3. Differential Expression of mRNAs during Preadipocyte Differentiation
3.4. Functions of Differentially Expressed Genes
3.5. STEM Analysis
3.6. Functions of Differentially Expressed Genes Involved in Significant Gene Expression Profiles
3.7. Validation of RNA-Seq-Based Gene Expression
3.8. Expression Patterns of Key Genes in Preadipocyte Differentiation
4. Discussion
4.1. Differentially Expressed Genes during Preadipocyte Differentiation
4.2. Differentially Expressed Genes and Pathways in Profile 21
4.3. Differentially Expressed Genes and Pathways in Profile 22
4.4. Other Important Differentially Expressed Genes and Pathways
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Sample | Before Filtering | After Filtering | Unique Mapped Reads | Multiple Mapped Reads | Mapping Ratio | ||
---|---|---|---|---|---|---|---|
Clean Reads Number | Clean Q30 Bases (%) | HQ Clean Reads Number | Clean Q30 Bases (%) | ||||
A0d | 36,419,702 | 33,808,409 (92.83%) | 35,253,720 | 33,364,121 (94.64%) | 32,064,753 (90.95%) | 274,708 (0.78%) | 91.73% |
B0d | 31,200,494 | 29,172,462 (93.50%) | 30,099,248 | 28,606,325 (95.04%) | 27,329,518 (90.80%) | 174,318 (0.58%) | 91.38% |
C0d | 26,486,876 | 24,717,553 (93.32%) | 25,638,168 | 24,333,185 (94.91%) | 23,365,096 (91.13%) | 190,142 (0.74%) | 91.88% |
A2d | 28,087,146 | 26,264,290 (93.51%) | 27,127,016 | 25,784,229 (95.05%) | 24,631,732 (90.80%) | 214,138 (0.79%) | 91.59% |
B2d | 27,412,180 | 25,644,094 (93.55%) | 26,554,122 | 25,234,382 (95.03%) | 24,196,924 (91.12%) | 151,568 (0.57%) | 91.69% |
C2d | 26,603,022 | 24,828,600 (93.33%) | 25,547,810 | 24,262,755 (94.97%) | 23,048,014 (90.22%) | 146,522 (0.57%) | 90.79% |
A4d | 30,269,944 | 28,196,453 (93.15%) | 29,243,938 | 27,734,951 (94.84%) | 26,631,402 (91.07%) | 215,232 (0.74%) | 91.80% |
B4d | 28,011,286 | 26,212,961 (93.58%) | 27,141,124 | 25,808,495 (95.09%) | 24,797,742 (91.37%) | 167,664 (0.62%) | 91.98% |
C4d | 33,020,078 | 30,497,344 (92.36%) | 30,913,550 | 29,185,483 (94.41%) | 46,107,395 (90.56%) | 416,494 (0.82%) | 91.38% |
A8d | 29,540,224 | 27,590,569 (93.40%) | 28,581,192 | 27,146,416 (94.98%) | 25,946,229 (90.78%) | 196,022 (0.69%) | 91.47% |
B8d | 38,772,832 | 36,198,316 (93.36%) | 37,484,166 | 35,598,712 (94.97%) | 34,076,825 (90.91%) | 274,396 (0.73%) | 91.64% |
C8d | 26,907,478 | 25,118,131 (93.35%) | 26,004,832 | 24,696,789 (94.97%) | 23,582,654 (90.69%) | 206,442 (0.79%) | 91.48% |
Gene ID | Gene Symbol | 2d vs. 0d | 4d vs. 0d | 8d vs. 0d | |||
---|---|---|---|---|---|---|---|
Log2(FC) | FDR | Log2(FC) | FDR | Log2(FC) | FDR | ||
ENSSSCG00000002777 | HSD11B2 | 3.036220 | 2.88 × 10−3 | 3.036220 | 2.88 × 10−3 | 3.292283 | 1.19 × 10−7 |
ENSSSCG00000003894 | CYP4B1 | 2.178599 | 5.92 × 10−6 | 2.178599 | 5.92 × 10−6 | 2.290617 | 4.15 × 10−15 |
ENSSSCG00000006474 | NES | −2.321415 | 9.39 × 10−9 | −2.321415 | 9.39 × 10−9 | −1.585476 | 4.76 × 10−4 |
ENSSSCG00000010450 | LIPA | 1.014733 | 3.90 × 10−3 | 1.014733 | 3.90 × 10−3 | 1.052272 | 1.48 × 10−5 |
ENSSSCG00000013599 | ANGPTL4 | 1.517481 | 2.04 × 10−3 | 1.517481 | 2.04 × 10−3 | 2.361101 | 3.22 × 10−12 |
ENSSSCG00000015396 | SEMA3D | −1.735399 | 8.38 × 10−4 | −1.735399 | 8.38 × 10−4 | −1.620849 | 4.72 × 10−3 |
ENSSSCG00000016634 | CAV1 | −1.864162 | 5.15 × 10−8 | −1.864162 | 5.15 × 10−8 | −1.566771 | 9.61 × 10−5 |
ENSSSCG00000021646 | KLF9 | 1.326810 | 2.95 × 10−5 | 1.326810 | 2.95 × 10−5 | 1.523982 | 1.62 × 10−8 |
ENSSSCG00000023760 | CLEC14A | −1.274697 | 9.98 × 10−3 | −1.274697 | 9.98 × 10−3 | −1.801044 | 7.92 × 10−8 |
ENSSSCG00000027550 | PLCD1 | 1.203787 | 6.90 × 10−4 | 1.203787 | 6.90 × 10−4 | 1.260086 | 1.73 × 10−6 |
ENSSSCG00000033922 | ALKAL1 | −3.057428 | 8.46 × 10−4 | −3.057428 | 8.46 × 10−4 | −3.117238 | 2.35 × 10−4 |
ENSSSCG00000034943 | GDF6 | −2.768335 | 3.54 × 10−3 | −2.768335 | 3.54 × 10−3 | −2.175725 | 1.52 × 10−2 |
ENSSSCG00000035863 | PLIN2 | 1.320747 | 3.95 × 10−4 | 1.320747 | 3.95 × 10−4 | 1.577466 | 4.80 × 10−5 |
ENSSSCG00000038783 | IGFBP3 | −2.894488 | 3.73 ×10−11 | −2.894488 | 3.73 × 10−11 | −2.872955 | 1.14 × 10−21 |
ENSSSCG00000039244 | PHYH | 1.429808 | 3.98 × 10−3 | 1.429808 | 3.98 × 10−3 | 1.278978 | 1.16 × 10−3 |
ENSSSCG00000040631 | LPL | 2.462269 | 3.44 × 10−6 | 2.462269 | 3.44 × 10−6 | 2.391050 | 2.09 × 10−7 |
GO ID | Description | p-Value | Genes | |
---|---|---|---|---|
2d vs. 0d | GO:0030154 | Cell differentiation | 0.046435 | ANGPTL4, CAV1, ALKAL1, GDF6, IGFBP3, LPL |
GO:0008283 | Cell proliferation | 0.001630 | KLF9, LIPA, NES, CAV1, PLCD1, IGFBP3 | |
GO:0006629 | Lipid metabolic process | 0.000184 | LIPA, CAV1, PLCD1, PHYH, LPL | |
4d vs. 0d | GO:0030154 | Cell differentiation | 0.000001 | ADGRF1, MYOM1, CDH2, CDC20, RORA, IVL, S100A10, COL11A1, LFNG, SFRP2, CPT1A, ANGPTL4, ICAM1, KIF20A, AGR2, RELN, COL3A1, CAV1, ANLN, FST, BATF2, CTSB, SLC2A4, KRT4 CCNB1, MMP8, ZBTB16 SNAI1, ALKAL1, CDKN2B, GDF6, INHBA, COL1A1, PTHLH, RGS2, TRIB1, CHAC1, RND1, IGFBP3, NPNT, SOD2, IL34, LPL |
GO:0008283 | Cell proliferation | 0.000195 | CDH2, RORA, NES, SFRP2, SPRY1, LIPA, LAMC2, CAV1, KLF9, F3, KRT4, OVOL1, PLCD1, CCNB1, ZBTB16, GPNMB, CDKN2B, INHBA, TRIB1, IGFBP3, HMOX1, SOD2, IL34 | |
GO:0006629 | Lipid metabolic process | 0.008311 | RORA, ABCA1, GPCPD1, AGT, LIPA, SCD, CPT1A, CAV1, PLCD1, SNAI1, PHYH, LPL | |
8d vs. 0d | GO:0030154 | Cell differentiation | 0.000001 | ADGRF1, MYOM1, CDH2, CDC20, RORA, IVL, S100A10, COL11A1LFNG, SFRP2, CPT1A, ANGPTL4, ICAM1, KIF20A, AGR2, RELN, COL3A1, CAV1, ANLN, FST, BATF2, CTSB, SLC2A4, KRT4, CCNB1, MMP8, ZBTB16, SNAI1, ALKAL1, CDKN2B, GDF6, INHBA, COL1A1, PTHLH, RGS2, TRIB1, CHAC1, RND1, IGFBP3, NPNT, SOD2, IL34, LPL |
GO:0008283 | Cell proliferation | 0.000195 | CDH2, RORA, NES, SFRP2, SPRY1, LIPA, LAMC2, CAV1, KLF9, F3, KRT4, OVOL1, PLCD1, CCNB1, ZBTB16, GPNMB, CDKN2B, INHBA, TRIB1, IGFBP3, HMOX1, SOD2, IL34 | |
GO:0006629 | Lipid metabolic process | 0.008311 | RORA, ABCA1, GPCPD1, AGT, LIPA, SCD, CPT1A, CAV1, PLCD1, SNAI1, PHYH, LPL |
Pathway | p-Value | Genes | |
---|---|---|---|
2d vs. 0d | Steroid hormone biosynthesis | 0.00259 | HSD11B2, AKR1C1 |
4d vs. 0d | PPAR signaling pathway | 0.00017 | SCD, ANGPTL4, GK |
Steroid hormone biosynthesis | 0.01279 | HSD11B2, AKR1C1 | |
Cell cycle | 0.01253 | CDC20, CCNB1, WEE1 | |
8d vs. 0d | PPAR signaling pathway | 0.00077 | CD36, ANGPTL4, GK |
Steroid hormone biosynthesis | 0.02929 | HSD11B2, AKR1C1 | |
p53 signaling pathway | 0.04143 | CDK1, CCNB1 | |
PI3K/Akt signaling pathway | 0.03306 | ITGA3, COL6A3, AREG, THBS3, TLR2, HGF, FGF1, ANGPT2, SPP1, MYC | |
Wnt signaling pathway | 0.03833 | SFRP5, SFRP2, PORCN, MYC, WNT2B | |
Cellular senescence | 0.02123 | CDK1, CCNB1, CXCL8, CCNB3, MYC | |
TNF signaling pathway | 0.00215 | CCL2, MAP3K8, CX3CL1, CSF2, FOS |
GO ID | Description | p-Value | Genes | |
---|---|---|---|---|
Profile 9 | GO:0008283 | Cell proliferation | 0.01528 | DPT, ESM1, SERPINF1, AREG, NOV, F2, HGF |
GO:0030154 | Cell differentiation | 0.03364 | SERPINF1, L1CAM, SEMA3C, NEUROG2, NOV, ANKRD1 ITGA3, FLRT2, SLIT2, F2 | |
Profile 21 | GO:0006629 | Lipid metabolic process | 0.00096 | PLCD1, PHYH, CPT1A, PLBD2, LPL, EEF1A2, LIPA |
Profile 22 | GO:0006629 | Lipid metabolic process | 0.00520 | SLC27A1, AGT, ACAA2, CYP1B1, EGR1, PECR |
GO:0008283 | Cell proliferation | 0.04071 | TRIB1, JUNB, JUN, CYP1B1, TXNRD1, KLF4, ATOH8 | |
GO:0030154 | Cell differentiation | 0.00321 | ANGPTL4, MYBPH, TRIB1, JUNB, TXNIP, JUN, KLF4, IL18R1, ZNF365, FOS, ATOH8, EGR1, NCKIPSD, ZFP36 | |
Profile 24 | GO:0030154 | Cell differentiation | 0.00321 | CCL2, RND1, FOXA2, RGS2, PGLYRP1, SOD2 IL34, SLC2A4 |
Pathway | p-Value | Genes | |
---|---|---|---|
Profile 21 | PPAR signaling pathway | 0.00003 | PLIN2, LPL, CPT1A, LIPA |
Fatty acid degradation | 0.01736 | ADH1C, CPT1A, LIPA | |
Profile 22 | TNF signaling pathway | 0.00009 | JUN, IL18R1, CX3CL1 JUNB, FOS |
PPAR signaling pathway | 0.00413 | SLC27A1, ANGPTL4 | |
Fatty acid degradation | 0.01447 | ALDH2, ACAA2 |
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Zhao, X.; Chen, S.; Tan, Z.; Wang, Y.; Zhang, F.; Yang, T.; Liu, Y.; Ao, H.; Xing, K.; Wang, C. Transcriptome Analysis of Landrace Pig Subcutaneous Preadipocytes during Adipogenic Differentiation. Genes 2019, 10, 552. https://doi.org/10.3390/genes10070552
Zhao X, Chen S, Tan Z, Wang Y, Zhang F, Yang T, Liu Y, Ao H, Xing K, Wang C. Transcriptome Analysis of Landrace Pig Subcutaneous Preadipocytes during Adipogenic Differentiation. Genes. 2019; 10(7):552. https://doi.org/10.3390/genes10070552
Chicago/Turabian StyleZhao, Xitong, Shaokang Chen, Zhen Tan, Yuan Wang, Fengxia Zhang, Ting Yang, Yibing Liu, Hong Ao, Kai Xing, and Chuduan Wang. 2019. "Transcriptome Analysis of Landrace Pig Subcutaneous Preadipocytes during Adipogenic Differentiation" Genes 10, no. 7: 552. https://doi.org/10.3390/genes10070552
APA StyleZhao, X., Chen, S., Tan, Z., Wang, Y., Zhang, F., Yang, T., Liu, Y., Ao, H., Xing, K., & Wang, C. (2019). Transcriptome Analysis of Landrace Pig Subcutaneous Preadipocytes during Adipogenic Differentiation. Genes, 10(7), 552. https://doi.org/10.3390/genes10070552