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| Status |
Public on Aug 16, 2018 |
| Title |
germination_stage0 rep1 |
| Sample type |
SRA |
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| Source name |
germination_stage0
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| Organism |
Fusarium graminearum |
| Characteristics |
strain: PH-1
tissue: fresh spore
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| Extracted molecule |
total RNA |
| Extraction protocol |
Asexual spores (macro conidia) were spread on Bird agar media (Metzenberg, 2004 Fungal Genet Newsl 51: Article 8) overlaid with a cellophane membrane, and sampled at the indicated spore germination stages and frozen in liquid nitrogen. 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 1 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 2500 |
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| Description |
G0R1
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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
Reads Per Kilobase of transcript per Million mapped reads (RPKM) values were calculated using the StringTie program v1.3.0, and transcripts with a variance of RPKM values less than one were removed, using the Ballgown R package v2.4.2.
Genome_build: Fusarium graminearum str. PH-1 Ensembl Genomes 32
Supplementary_files_format_and_content: tab-delimited text file include a matrix of RPKM 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 |
GPL24501 |
| Series (2) |
| GSE109088 |
Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum [II] |
| GSE109095 |
Sexual stage-induced long noncoding RNAs in the filamentous fungus Fusarium graminearum |
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| Relations |
| BioSample |
SAMN08354628 |
| SRA |
SRX3554195 |
| 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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