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| Status |
Public on Aug 05, 2019 |
| Title |
Expression of target genes in itaconic acid cluster and electron transport chain in Aspergillus terreus NRRL1960 cultivated under low dissolved oxygen |
| Organism |
Aspergillus terreus |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Aim: We aimed to study the differential gene expressions of the target genes encoding H+-ATPase, the mitochondrial respiratory chain complex, and the alternative oxidase (AOX) in Aspergillus terreus NRRL1960 cultivated under low dissolved oxygen
Methods:The fermentation samples were collected for RNA extraction.The barcoded RNA libraries were prepared using Lexogen’s Quant-Seq 3’ mRNA seq kit (Ion Torrent, Lexogen, Vienna, Austria). DNA templates for sequencing were prepared from 200 bp v3 OT2 kit and the Ion One Touch 2 platform. Sequencing was performed on the Ion Proton by Ion Torrent Suite v5.0.4. Raw sequences form each sample were uploaded and the dapter sequences were trimmed. The reads were aligned to A. terreus NIH2624 genome references downloaded from http://fungi.ensembl.org/info/website/ftp/index.html using Star 2.4.1d. The bam index files were generated. The quantification of gene expression was performed by Htseq v0.6.0 with -f and -s options indicating bam inputs and un-stranded reads, respectively. Cuffdiff v.2.1.1 was used to estimate the transcript abundance with the -no-diff and default options to generate the differential analysis for each described comparison.
Results:From the gene expression (FPKM) results, genes in Cytochrome C complex and aoxA had the high expression level compared to pma encoding H+-ATPase. However, the different gene expression analysis results shown that the target genes in the mitochondrial respiratory chain complex were predominantly down regulated as observed from the log2(fold_change) less than -1 and and the gene encoding AOX (aoxA) were down regulated.
Conclusions: In this study, the transcriptomic analysis were performed for better understanding the biosynthesis pathway and the regulation of target genes in itaconic acid cluster and the ATP regeneration pathway.
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| Overall design |
Nine samples were fungal mycelia collected from the fermentation broth at the end of the growth (at 48h) phase and those taken during the production phase (at 72, 96, 120, 144, 168, 192, 216, 240h). Transcription levels (FPKM) of the target genes of all sample were analyzed. The differential gene expression levels were the data of the gene expression during the production phase (at 72, 96, 120, 144, 168, 192, 216, 240h) compared with that at the end of the growth (48 h).
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| Contributor(s) |
Pajareeya S, Piroonporn S, Sitanan T, Somboon T, Suttichai A, Aphichart K, Nuttha T |
| Citation missing |
Has this study been published? Please login to update or notify GEO. |
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| Submission date |
Aug 02, 2019 |
| Last update date |
Aug 07, 2019 |
| Contact name |
Pajareeya Sogserm |
| E-mail(s) |
pajaree_song@hotmail.com
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| Phone |
66848807884
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| Organization name |
Chulalongkorn University
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| Department |
The Institute of Biotechnology and Genetic Engineering
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| Street address |
254 Chulalongkorn University Institute Building 3, Phayathai Road, Pathum Wan
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| City |
Bangkok |
| ZIP/Postal code |
10300 |
| Country |
Thailand |
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| Platforms (1) |
| GPL27003 |
Ion Torrent PGM (Aspergillus terreus) |
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| Samples (9)
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| Relations |
| BioProject |
PRJNA558537 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE135329_RAW.tar |
20.0 Kb |
(http)(custom) |
TAR (of TXT) |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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