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| Status |
Public on Jun 20, 2019 |
| Title |
sexual_stage3 rep3-1_WT |
| Sample type |
SRA |
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| Source name |
carrot agar culture
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| Organism |
Fusarium neocosmosporiellum |
| Characteristics |
strain: NRRL_22166
tissue: paraphyses
genotype: wild-type
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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 2500 |
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| Description |
Neo_3-3
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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 genome, using the HISAT2 program v2.0.4, 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 RPKM values were computed after normalization by effective library size estimated by trimmed mean of M values, using the edgeR R package v3.14.0.
Genome_build: Fusarium neocosmosporiellum str. NRRL_22166 version spades_s14
Supplementary_files_format_and_content: tab-delimited text file include a matrix of RPKM values for all samples and the associated GFF3 file
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| Submission date |
Jan 02, 2019 |
| Last update date |
Jun 20, 2019 |
| 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 |
GPL25997 |
| Series (1) |
| GSE124553 |
Comparative transcriptomics analyses of fruiting body development in Fusarium species |
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| Relations |
| BioSample |
SAMN10679261 |
| SRA |
SRX5193083 |
| 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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