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| Status |
Public on Nov 10, 2013 |
| Title |
mRNAs from Fusarium graminearum Z-3639 wetA deletion mutant after 12 h after induction of conidiogenesis |
| Sample type |
SRA |
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| Source name |
Fungi culture
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| Organism |
Fusarium graminearum |
| Characteristics |
genotype/variation: wetA deletion mutant
strain background: Z-3639
time point: 12 h after induction of conidiogenesis
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| Growth protocol |
Each fungal strain was grown on YMA medium for induction of condiogensis for 0h, 6h, and 12h
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| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNAs were extracted with Easy Spin Total RNA Extraction Kit (Intron Biotech, Seongnam, Korea).
Illumina TruSeqTM RNA sample prep kit with standard low throughput (LT) protocol
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
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| Data processing |
BWA software was used for basecalling and genome alignment.
Sequenced reads were mapped to MIPS FGDB_v32 genome (obtained from ftp://ftpmips.gsf.de/fungi/FGDB/v32/) using bwa with parameters aln -q 20 and paired-end results were generated by sampe option.
Reads within exon were counted by the HTSEQ package of Python.
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009. In short, exons from all isoforms of a gene were merged to create one meta-transcript. The number of reads falling in the exons of this meta-transcript was counted and normalized by the size of the meta-transcript and by the size of the library.
RPK100M = 100 x RPKM
Genome_build: FGDB_v32 (ftp://ftpmips.gsf.de/fungi/FGDB/v32/)
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample …
Genome Build:
wetA_12h_processed.txt: FGDB_v32
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| Submission date |
Aug 14, 2013 |
| Last update date |
May 15, 2019 |
| Contact name |
Hokyoung Son |
| E-mail(s) |
hogongi@gmail.com
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| Organization name |
Seoul National University
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| Department |
Center for Food and Bioconvergence
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| Street address |
Daehak-dong, Gwanak-gu
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| City |
Seoul |
| ZIP/Postal code |
151-921 |
| Country |
South Korea |
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| Platform ID |
GPL17573 |
| Series (1) |
| GSE46133 |
RNA-seq Analysis of FlbD-, AbaA-, and WetA-dependent Genes in Fusarium graminearum Z-3639 |
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| Relations |
| BioSample |
SAMN02316795 |
| SRA |
SRX335076 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1208342_wetA_12h_processed.txt.gz |
392.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Processed data provided as supplementary file |
| Raw data are available in SRA |
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