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Sample GSM2830282 Query DataSets for GSM2830282
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) janine.haueisen@gmail.com
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

Supplementary data files not provided
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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