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| Status |
Public on Jan 14, 2020 |
| Title |
RNA-Seq Analysis to confirm Different Transcriptomic Profiles of Soil-Derived Functional Module Consortia. |
| Organism |
soil metagenome |
| Experiment type |
Expression profiling by high throughput sequencing
|
| Summary |
Purpose: Deconstructing the soil microbiome into reduced-complexity functional modules represents a novel method of microbiome analysis. The goals of this study are to confirm differences in transcriptomic patterns among five functional module consortia.
Methods: mRNA profiles of 3 replicates each of functional module enrichments of soil inoculum in M9 media with either 1) xylose, 2) n-acetylglucosamine, 3) glucose and gentamycin, 4) xylan, or 5) pectin were generated by sequencing using an Illumina platform (GENEWIZ performed sequencing). Sequence reads that passed quality filters were aligned to a soil metagenome using Burrows Wheeler Aligner. Resulting SAM files were converted to raw reads using HTSeq, and annotated using Uniref90 or EGGNOG databases.
Results: To reduce the size of the RNA-Seq counts table and increase its computational tractability, transcripts containing a minimum of 75 total counts, but no more than 3 zero counts, across the 15 samples were removed. The subsequent dataset was normalized using DESeq2, resulting in a dataset consisting of 6947 unique transcripts across the 15 samples, and 185,920,068 reads. We identified gene categories that were enriched in a sample type relative to the overall dataset using Fisher’s exact test.
Conclusions: our dataset confirms that the functional module consortia generated from targeted enrichments of a starting soil inoculum had distinct functional trends by enrichment type.
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| Overall design |
mRNA profiles of enriched functional consortia were sequenced using an Illumina HiSeq platform.
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| Contributor(s) |
Naylor D, McClue R |
| Citation(s) |
32636252 |
| |
| Submission date |
Jan 13, 2020 |
| Last update date |
Jul 13, 2020 |
| Contact name |
Daniel Torres Naylor |
| E-mail(s) |
dtnaylor@berkeley.edu, dtnaylor@pnnl.gov
|
| Organization name |
Pacific Northwest National Laboratory
|
| Department |
Biological Systems Division
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| Street address |
3300 Stevens Drive, MSIN. J4-18
|
| City |
Richland |
| State/province |
WA |
| ZIP/Postal code |
99354 |
| Country |
USA |
| |
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| Platforms (1) |
| GPL20780 |
Illumina HiSeq 2000 (soil metagenome) |
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| Samples (15)
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| Relations |
| BioProject |
PRJNA600987 |
| SRA |
SRP241826 |
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