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| Status |
Public on Dec 19, 2017 |
| Title |
Differential expression analysis of a hyperthermophilic archeaon Thermococcus paralvinellae upon hydrogen stress |
| Organism |
Thermococcus paralvinellae |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
Purpose: Compare the transcriptomes of T. paralvinellae using RNA-Seq gene expression analyses to understand the physiology of this organism when it is grown on different carbon sources, under optimal and hydrogen stress conditions.
Methods: T. paralvinellae was grown in triplicate at with either 0.5% maltose or 0.5% tryptone to investigate its catabolic pathways when grown on a sugar and peptides, respectively. It was also grown on 1% formate to determine the effect of formate on cell growth, metabolite production, and gene expression. It was also grown separately on maltose or tryptone media as before, except with hydrogen in the media to examine the effects of hydrogen inhibition. The cells remaining in the 2-liter bioreactor were concentrated by centrifugation. The resulting cell pellets were resuspended in TRIzol (Invitrogen) and total RNA was extracted using a Direct-zol RNA extraction kit (Zymo). RNA quantity was determined with Qubit fluorometry. RNA integrity was checked by a bioanalyzer and a Nanodrop spectrometer. Genewiz sequencing facilities performed rRNA removal, library construction, multiplexing and sequence the RNA with HiSeq2500, 2×100 Paired-End. We aligned the RNAseq reads to T. paralvinellae genome (STAR) and assigned aligned sequence reads to genomic features (featureCounts). We then quantified transcriptome and reported pairwise significant genes that are differentially expressed by DESeq available under Bioconductor (www.bioconductor.org) on Galaxy platform and in R.
Results: Sequencing depths ranged from 29,974,378 to 45,240,342 sequences, with a mean of 38,990,002 and a median of 38,951,352 reads per sample. Of 2,138 genes annotated in the T. paralvinellae genome, 2084 transcripts were detected by RNA-Seq.Of the 2084 genes detected by transcriptomics, hydrogen stress caused only 48 genes to be differentially regulated (log2FC > 1, P < 0.05) with maltose and tryptone carbon sources. These included mostly genes associated with formate-dependent metabolism and transporters. The upregulated genes upon growth under H2 stress conditions indicate intrinsic formate production via formate hydrogen lyase and format secretion.
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| Overall design |
mRNA profiles of T. paralvinellae grown on 5 different conditions in triplicates were generated by Illumina RNAseq
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| Contributor(s) |
Meydan C |
| Citation(s) |
29235714 |
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| Submission date |
Jul 10, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Begum D. Topcuoglu |
| E-mail(s) |
topcuoglu.begum@gmail.com
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| Organization name |
University of Massachusetts
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| Department |
Microbiology
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| Lab |
James F. Holden Lab
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| Street address |
336 North Pleasant St., Apt:3B
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| City |
Amherst |
| State/province |
MA |
| ZIP/Postal code |
01002 |
| Country |
USA |
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| Platforms (1) |
| GPL23684 |
Illumina HiSeq 2500 (Thermococcus paralvinellae) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA393686 |
| SRA |
SRP111462 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSE101078_TP_2016.11.05_count.txt.gz |
74.4 Kb |
(ftp)(http) |
TXT |
| GSE101078_TP_2016.11.05_tpm.txt.gz |
261.4 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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