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Status |
Public on Dec 10, 2019 |
Title |
Transcriptional analysis effect of excess sugar and lipid on the growth and development of Caenorhabditis elegan |
Organism |
Caenorhabditis elegans |
Experiment type |
Expression profiling by high throughput sequencing
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Summary |
Purpose:We used transcriptome sequencing to study the mechanism of sugar and lipid excesses on nematode growth and development. Methods:Nematodes grew to L4 phase and collected nematodes from different treatment groups, including control group without any treatment, 400 mM sucrose, 500 ug/ml stearic acid, co-treatment with sucrose and stearic acid, and co-treatment with resveratrol-sucrose-stearic acid, 3 replicates per group. Extract total RNA, detect RNA quality, library preparation, sequencing, and analyze data Results:Reads were obtained for each sample using Illumina Hiseq X Ten sequencing. After discarding the low-quality reads, corresponding to 48 million clean reads obtained from sequencing were mapped on the reference genome of C. elegans (GCF_000002985.6). High Pearson's correlation coefficients of FPKM distribution between the three biological replicates for each sample were detected (R2 = 0.93-0.99, P < 0.001) , reflecting the robustness of our library preparation from nematodes’ RNA samples.Compared with control group, there were 905 DEGs in the sucrose group , of which 387 genes were upregulated and 518 genes were downregulated. Similarly, there were 698 DEGs in the stearic acid group , including 367 upregulated and 331 downregulated DEGs. Compared with control group, there were 1014 DEGs in group SUC-STE, including 476 upregulated DEGs, and 538 downregulated DEGs. Moreover, in contrast to the sucrose-stearic acid group, there were 10 DEGs after treated with resveratrol, including 5 upregulated DEGs and 5 downregulated DEGs.
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Overall design |
Deep-sequencing using Illumina, in triplicate, yielded L4 stage nematode mRNA expression profiles without treatment, sugar and lipid treatment alone, sugar and lipid co-treatment, and resveratrol-sugar-lipid co-treatment.
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Contributor(s) |
Wang X, Zhang L |
Citation(s) |
32015763 |
Submission date |
Dec 09, 2019 |
Last update date |
Feb 10, 2020 |
Contact name |
Xiong Wang |
E-mail(s) |
Nobita_Wang@aliyun.com
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Phone |
18379141626
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Organization name |
China Agricultural University
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Department |
College of Food Science and Nutritional Engineering
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Street address |
No. 17, Qinghua East Road, Haidian District, Beijing
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City |
Beijing |
ZIP/Postal code |
100083 |
Country |
China |
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Platforms (1) |
GPL13657 |
Illumina HiSeq 2000 (Caenorhabditis elegans) |
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Samples (15)
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Relations |
BioProject |
PRJNA594361 |
SRA |
SRP235274 |
Supplementary file |
Size |
Download |
File type/resource |
GSE141668_Gene_full_table.xls.gz |
3.5 Mb |
(ftp)(http) |
XLS |
GSE141668_control_vs_ste.annotation.xls.gz |
87.0 Kb |
(ftp)(http) |
XLS |
GSE141668_control_vs_suc-ste.annotation.xls.gz |
127.4 Kb |
(ftp)(http) |
XLS |
GSE141668_control_vs_suc.annotation.xls.gz |
113.9 Kb |
(ftp)(http) |
XLS |
SRA Run Selector |
Raw data are available in SRA |
Processed data are available on Series record |
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