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| Status |
Public on May 15, 2023 |
| Title |
R3: Ta_3D7_3dpi_3 |
| Sample type |
SRA |
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| Source name |
Leaves infected with Zymoseptoria tritici
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| Organism |
Triticum aestivum |
| Characteristics |
tissue: Infected leaves
time: Day 3
genotype: Chinese Spring; ST99CH_3D7
treatment: Zymoseptoria tritci infection
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| Extracted molecule |
total RNA |
| Extraction protocol |
Three cm from the tip were discarded, and 6 cm of the adjacent leaf were flash-frozen in liquid N2 and homogenized with zirconium beads (1.4 mm diameter) using the Bead-Rupture equipped with a cooling unit (Omni International, Kennesaw, GA, USA). RNA isolation was performed using GENEzol reagent (Geneaid Biotech, Taipei, Taiwan) following the manufacturer's instructions. RNAeasy Mini Kit (Qiagen GmbH, Hilden, Germany) was used to purify the RNA, and DNA contamination was removed using the on-column DNase treatment of the RNase-Free DNase Set (Qiagen GmbH, Hilden, Germany).
Ribosomal RNA was depleted by poly A enrichment, and DNA libraries were sequenced with Illumina NovaSeq 6000 at Novogene Europe
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| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NovaSeq 6000 |
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| Data processing |
Sequence reads were trimmed for adaptor sequence/low-quality sequence using Trimmomaticv0.35
Trimmed reads were mapped to Triticum aestivum IWGSC transcriptome reference using Kallisto v0.46.1 with default parameters
Read counts were summarized using tximport v1.2.0
Read abundance normalization and differential gene expression analysis were performed with the R package DESeq2
Assembly: Triticum_aestivum.IWGSC.cdna.all
Supplementary files format and content: tab-delimited txi.kallisto abundance counts for all samples
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| Submission date |
May 11, 2023 |
| Last update date |
Jun 16, 2023 |
| Contact name |
Cecile Lorrain |
| E-mail(s) |
clorrain@ethz.ch
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| Organization name |
ETH Zurich
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| Department |
Plant PAthology
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| Lab |
Prof. Bruce McDonald
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| Street address |
Universistätstrasse 2
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| City |
Zurich |
| State/province |
Zurich |
| ZIP/Postal code |
8006 |
| Country |
Switzerland |
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| Platform ID |
GPL25409 |
| Series (1) |
| GSE232243 |
Zymoseptoria tritici suppresses the host immune response and facilitates the success of avirulent strains in mixed infections |
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| Relations |
| BioSample |
SAMN35035582 |
| SRA |
SRX20287381 |
| Supplementary data files not provided |
SRA Run Selector |
| Raw data are available in SRA |
| Processed data are available on Series record |
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