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| Status |
Public on Aug 16, 2018 |
| Title |
sexual_stage0 rep2_∆xrn1 |
| Sample type |
SRA |
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| Source name |
sexual_stage0 ∆xrn1
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| Organism |
Fusarium graminearum |
| Characteristics |
strain: PH-1
tissue: vegetative hyphae
genotype: delta-xrn1
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| Extracted molecule |
total RNA |
| Extraction protocol |
Fungal hyphae were scraped out from carrot agar culture and frozen in liquid nitrogen, and total RNA was isolated using the standard Trizol extraction protocol with additional extraction steps.
The KAPA Stranded RNA-Seq Library Preparation Kit was used with 2 ug of total RNA for the construction of cDNA libraries.
Stranded RNA-seq with poly-A captured RNA samples
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
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| Data processing |
Sequencing was performed on an Illumina HiSeq 2500 High Output flow cell (v4) using Illumina HiSeq SBS reagents (v4) in a 1x50bp paired end format. Base calling was done by Illumina Real Time Analysis (RTA) v1.18.64 and output of RTA was demultiplexed and converted to FastQ format with Illumina Bcl2fastq v1.8.4.
Poor quality reads were trimmed and/or filtered out, and adapters and homopolymers were trimmed from raw reads, using the ngsShoRT program v2.2, with parameters -lqs 12 -tera_avg 20 -5a_mp 98 -rmHP_ml 10
Filtered reads were mapped to the repeat-masked genome (Ensembl version 32), using the HISAT2 program v2.0.4, with default parameters
De novo transcript assembly was performed using the StringTie program v1.3.0, with default parameters
Read counts for gene loci in the de novo annotations were calculated using the htseq-count program v0.6.1. Gene expression levels in counts-per-million (CPM) value were computed and normalized by effective library size estimated by trimmed mean of M values, using the edgeR R package v3.14.0.
Genome_build: Fusarium graminearum str. PH-1 Ensembl Genomes 32
Supplementary_files_format_and_content: tab-delimited text file include a matrix of log2-CPM values for all samples and the associated GTF file
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| Submission date |
Jan 11, 2018 |
| Last update date |
Aug 16, 2018 |
| Contact name |
Wonyong Kim |
| E-mail(s) |
apbiomol@gmail.com
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| Organization name |
Michigan State University
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| Department |
Plant Biology
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| Lab |
Trail, Frances
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| Street address |
612 Wilson Road, Room 166
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| City |
East Lansing |
| State/province |
Michigan |
| ZIP/Postal code |
48824 |
| Country |
USA |
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| Platform ID |
GPL24502 |
| Series (2) |
| GSE109094 |
Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum [I] |
| GSE109095 |
Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum |
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| Relations |
| BioSample |
SAMN08354644 |
| SRA |
SRX3554190 |
| 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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