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| Status |
Public on Feb 22, 2016 |
| Title |
fhs1-1 |
| Sample type |
SRA |
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| Source name |
Fungi culture
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| Organism |
Fusarium graminearum |
| Characteristics |
genotype/variation: fhs1 deletion mutant
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| Growth protocol |
Each fungal strain was grown in complete medium (CM) for 24 hour
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| Extracted molecule |
total RNA |
| Extraction protocol |
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
Supplementary_files_format_and_content: tab-delimited text files include gene information and raw counts, RPK100M, RPKM values for each Sample …
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| Submission date |
Oct 09, 2015 |
| 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) |
| GSE73891 |
RNA-seq analysis of FHS1-dependent genes in Fusarium graminearum Z-3639 |
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| Relations |
| BioSample |
SAMN04158530 |
| SRA |
SRX1322831 |
| Supplementary file |
Size |
Download |
File type/resource |
| GSM1905072_fhs1-1_processed.txt.gz |
381.6 Kb |
(ftp)(http) |
TXT |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data provided as supplementary file |
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