|
| Status |
Public on Apr 25, 2018 |
| Title |
Zt09_Ta_C_01 |
| Sample type |
SRA |
| |
|
| Source name |
Z. tritici infection of Triticum aestivum Obelisk leaves
|
| Organisms |
Triticum aestivum; Zymoseptoria tritici |
| Characteristics |
t. aestivum cultivar: Obelisk
age: 14-day-old seedlings
z. tritici isolate: Zt09 / IPO323<delta>chr 18
days post infection (dpi): 13
infection stage: C
|
| Treatment protocol |
14-day-old seedlings of Triticum aestivum Obelisk were brush-inoculated with fungal inoculum adjusted to 1 x 10^8 cells/ml in 0.1 %Tween 20
|
| Growth protocol |
To produce fungal inoculum, cells of Zymoseptoria tritici isolates were inoculated from glycerol stocks onto YMS agar and grown at 18 °C. Single cells were grown in liquid YMS (200 rpm, 18 °C) and harvested at 3500 rpm for 10 min.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
total RNA from Z. tritici-infected wheat material was isolated using the TRIzol™ reagent according to the manufacturer’s instructions
NEBNext UltraTM Directional RNA Library Prep Kit
strand-specific RNA-seq libraries including polyA enrichment
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2500 |
| |
|
| Data processing |
Removal of residual TruSeq adapter sequences, Trimmomatic version 0.33
Trimming of 12 nucleotides at 5' end of all reads, Trimmomatic version 0.33
Filtering of reads based on quality scores: At least 80 % of bases must have a quality score ≥ 20 or read was dropped. FASTX-toolkit version 0.0.14
Masking of low quality bases: Nucleotides with quality score < 20 were masked with ‘N’. FASTX-toolkit version 0.0.14
Mapping of reads to genomes of Z. tritici isolates, TopHat2 version 2.0.9
Manipulation of RNA-seq read alignments: SAMtools version 0.1.19
Counting of mapped sequencing reads per gene: HTSeq version 0.6.1p1
Genome_build: reference assembly Zt05 (Zt05 = MgDk09_U34) available through NCBI BioProject PRJNA312067
Genome_build: reference assembly Zt09 / IPO323Δchr 19 is available at: http://genome.jgi.doe.gov/Mycgr3/Mycgr3.home.html
Genome_build: reference assembly Zt10 (Zt10 = STIR01_A26b) is available at GenBank GCA_000223645.2
Supplementary_files_format_and_content: comma separated text file including raw counts of sequencing reads for all Z. tritici genes shared between the three isolates
|
| |
|
| Submission date |
Oct 25, 2017 |
| Last update date |
May 15, 2019 |
| Contact name |
Janine Haueisen |
| E-mail(s) |
[email protected]
|
| Organization name |
Christian-Albrechts University of Kiel
|
| Department |
Botanical Institute
|
| Lab |
Environmental Genomics
|
| Street address |
Am Botanischen Garten 1-9
|
| City |
Kiel |
| ZIP/Postal code |
24118 |
| Country |
Germany |
| |
|
| Platform ID |
GPL24181 |
| Series (1) |
| GSE106136 |
Transcriptome analyses of three Zymoseptoria tritici isolates during infection of Triticum aestivum |
|
| Relations |
| BioSample |
SAMN07833715 |
| SRA |
SRX3324158 |
