|
| Status |
Public on Jul 09, 2014 |
| Title |
mRNAs from F. graminearum fss1 overexpression mutant after 1 h after incubation in PDB |
| Sample type |
SRA |
| |
|
| Source name |
Fungi culture
|
| Organism |
Fusarium graminearum |
| Characteristics |
strain background: Z-3639
genotype/variation: fss1::gen-Pef1a-fss1; fss1 overexpression mutant
cultured in: potato dextrose broth for 1hr
|
| Growth protocol |
Each fungal strain was grown in potato dextrose broth (PDB) with or wihtout 1 M NaCl supplementation for an hour
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted from mycelia in liquid nitrogen using the Easy-Spin Total RNA Extraction Kit (Intron Biotech, Seongnam, Korea).
Illumina TruSeqTM RNA sample prep kit with standard low throughput (LT) protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Description |
PDB_OEFSS1
|
| 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 (manually proccessed version of 'ASM24013v3' accessible at http://mips.gsf.de/genre/proj/FGDB/)
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample
|
| |
|
| Submission date |
Jul 08, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Hokyoung Son |
| E-mail(s) |
hogongi@gmail.com
|
| Organization name |
Seoul National University
|
| Department |
Center for Food and Bioconvergence
|
| Street address |
Daehak-dong, Gwanak-gu
|
| City |
Seoul |
| ZIP/Postal code |
151-921 |
| Country |
South Korea |
| |
|
| Platform ID |
GPL17573 |
| Series (1) |
| GSE59177 |
RNA-seq analysis of FSS1-dependent genes in Fusarium graminearum Z-3639 |
|
| Relations |
| BioSample |
SAMN02904736 |
| SRA |
SRX647719 |
