|
| Status |
Public on Jun 10, 2015 |
| Title |
MDR7 strain replicate 1 |
| Sample type |
SRA |
| |
|
| Source name |
wheat
|
| Organism |
Zymoseptoria tritici |
| Characteristics |
strain: 09-CB1
fungicide-phenotype: TriR7 MDR
|
| Growth protocol |
strains were grown in liquid YPD during 60 h at 18°C and 140 rpm
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was extracted using the RNeasy plant mini kit (Qiagen) and verified on 2100 Bioanalyzer (Agilent)
library prep with RNA Truseq Sample prep kit at sequencing provider IGA technologies, Udine, Italy
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
primary bioinformatics analysis for quality metrics control (Illumina pipeline vers. 1.9)
Sequenced reads were trimmed for adaptor sequence, and masked for low-complexity or low-quality sequence, then mapped then mapped to reference genes (Mgraminicolav2.FrozenGeneCatalog20080910.transcripts)
Reads Per Kilobase of exon per Megabase of library size (RPKM) were calculated using a protocol from Chepelev et al., Nucleic Acids Research, 2009.
Genome_build: Mgraminicolav2.FrozenGeneCatalog20080910.transcripts
Supplementary_files_format_and_content: tab-delimited text files include RPKM values for each Sample.
|
| |
|
| Submission date |
Jun 19, 2014 |
| Last update date |
May 15, 2019 |
| Contact name |
Sabine Fillinger |
| E-mail(s) |
sabine.fillinger@versailles.inra.fr
|
| Organization name |
INRA
|
| Department |
UMR1290 BIOGER
|
| Street address |
BP01
|
| City |
Thiverval-Grignon |
| ZIP/Postal code |
78850 |
| Country |
France |
| |
|
| Platform ID |
GPL18273 |
| Series (1) |
| GSE58672 |
Next generation RNA sequencing to identify overexpressed transporter genes in Zymoseptoria tritici field strains |
|
| Relations |
| BioSample |
SAMN02867558 |
| SRA |
SRX612450 |
