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| Status |
Public on Jan 05, 2018 |
| Title |
Gloeophyllum trabeum 0-5 mm_rep2 |
| Sample type |
SRA |
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| Source name |
brown rot decayed wood
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| Organism |
Gloeophyllum trabeum |
| Characteristics |
strain: ATCC 11539
wafer locus: 0-5 mm
decay stage: early decay
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| Growth protocol |
Directional growth of fungi on wood wafers was used to segregate fungal wood decay stages (space-for-time) in modified ASTM soil-block microcosms, described in detail, previously (Zhang et al., 2016). Sterilized wood wafers (length × width × thickness = 60 × 25 × 2.5 mm) cut from aspen (Populus sp.) lumber were propped in microcosms with the 25-mm edge resting on the soil surface, colonized from the base by one of four test fungi. Soil medium was a 1:1:1 mixture of soil, peat, and vermiculite hydrated to 40–45% (wt/vol) moisture content. Two brown rot fungi Postia placenta ATCC 44394 and Gloeophyllum trabeum ATCC 11539 and two white rot fungi Trametes versicolor A1-ATF (Minnesota Forest Pathology culture collection, University of Minnesota, USA) and Pleurotus ostreatus ATCC 32237 were maintained on 1.5% (wt/vol) malt extract agar prior to inoculating microcosms. Wafers were harvested when fungi had progressed 50 mm up the length of a wafer. By defining the visible hyphal front as a benchmark (0 mm), four 5-mm sections (5 x 25 x 2.5 mm) were extracted, one from 5 mm above the hyphal front (no fungus), one that included the hyphal front (0-5 mm), and two from further behind the hyphal front (15-20, 30-35 mm).
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total fungal RNA was extracted from fresh wood sections with TRIzol (Life Technologies) and cleaned up with a Qiagen RNeasy Mini Kit (Qiagen, Inc.) prior to RNA sequencing or quantitative RT-PCR (qRT-PCR), a method validated in Zhang et al. (2016).
For RNA sequencing, TruSeq RNA v2 libraries were prepared and sequenced on a HiSeq 2500 System (Illumina Inc., San Diego, CA) by using the standard protocols from Illumina.
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
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| Description |
Temporal seperation of brown rot was sptially acomplished by wafer design
UMN_augustus_GtrATCC11539.aa
UMN_augustus_GtrATCC11539.gtf
Dataset_1_All_genes_expression_profiles_during_wood_decay_in_brown_and_white_rot_fungi.xlsx
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| Data processing |
Raw RNA-seq reads were trimmed for Truseq2 adapters and for low-quality sequence with Trimmomatic (v0.33) and quality control was integrated using FastQC (v0.11.5). Remaining reads were mapped to the respective reference genome using Genomic Short-read Nucleotide Alignment Program (GSNAP) (Wu and Nacu, 2010). Beaker (v1.8) was used to annotate the genome by incorporating the above RNA-seq mapping data. These newly annotated genomes (AA files and GTF files) were compared with JGI’s (Joint Genome Institute, http://jgi.doe.gov/) genome annotation by testing the location of RNA-seq reads relative to exons, and this generated significantly improved annotations for all four fungi. The aligned read counts were computed using the “featureCounts” function of the Rsubread package (v1.22.2), and normalized as Reads Per Kilobase of transcript per Million mapped reads (RPKM) as gene expression level. The test of differential expression was made using edgeR's (v3.14) “glmQLFit” routine on the design matrix. The profiling data for whole-genome transcripts and DEGs are available in Dataset 1 (Excel file).
Genome_build: Postia placenta MAD-698-R-SB12 v1.0, Gloeophyllum trabeum v1.0, Trametes versicolor v1.0 and Pleurotus ostreatus PC15 v2.0 from JGI (https://genome.jgi.doe.gov/programs/fungi/index.jsf)
Supplementary_files_format_and_content: AA files include amino acid sequences; GTF files include genome annotations; Excel file (.xlsx) includes pairwise comparison and RPKM levels.
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| Submission date |
Dec 18, 2017 |
| Last update date |
May 21, 2020 |
| Contact name |
Jonathan Schilling |
| E-mail(s) |
schillin@umn.edu
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| Phone |
612-624-1761
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| Organization name |
University of Minnesota
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| Street address |
2004 folwell ave
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| City |
saint paul |
| State/province |
minnesota |
| ZIP/Postal code |
55108 |
| Country |
USA |
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| Platform ID |
GPL24400 |
| Series (1) |
| GSE108189 |
Comparing gene expression timing and amplitude to delineate the unique pathways of brown and white rot wood-degrading fungi |
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| Relations |
| Reanalyzed by |
GSM4564507 |
| BioSample |
SAMN08196648 |
| SRA |
SRX3478320 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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