|
| Status |
Public on Jan 10, 2018 |
| Title |
CS_96224_1_2dpi |
| Sample type |
SRA |
| |
|
| Source name |
Wheat leaves (cv. Chinese spring) infected with B.g. tritici 96224, 48h post infection
|
| Organisms |
Triticum aestivum; Blumeria graminis f. sp. tritici |
| Characteristics |
host_plant_tissue: leaves
host_cultivar: Chinese Spring
blumeria_isolate: 96224
|
| Treatment protocol |
Leaf segments of each of the replicates were collected at 2 days after infection and directly frozen in liquid nitrogen
|
| Growth protocol |
Ten days old detached leaf segments were infected with fresh spores and the infected leaf segments were kept on benzimidazole agar plates at 20°C and 70% humidity with a 16 hours light/8 hours dark cycle (Parlange et al., 2011).
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using the miRNeasy mini kit from Qiagen according to the manufacturer’s instructions.
RNA libraries were prepared for sequencing using standard Illumina protocols, Illumina sequencing Hi-Seq 2000
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 2000 |
| |
|
| Data processing |
MAPPING: The RNA sequencing reads were mapped on the reference genome with STAR (Dobin et al. 2013) allowing one mismatch per 100 bp and no multimapper with the following command: STAR –outFilterMultiMapNmax 1 – outFilterMismatchNoverLmax 0.01 – alignIntronMax 500
COUNT: Read counts were determined from the mapping files with featureCounts 1.4.6.
Genome_build: The Blumeria graminis subsp. f.sp. tritici genome with accession number PRJEB23548 was used.
Supplementary_files_format_and_content: The processed data files are count table obtained from featureCount. The first column is the gene ID and the last column is the read count. Other columns are explained in the header of the files.
|
| |
|
| Submission date |
Dec 21, 2017 |
| Last update date |
Jan 24, 2018 |
| Contact name |
Coraline Rosalie Praz |
| E-mail(s) |
coraline.praz@botinst.uzh.ch
|
| Organization name |
University of Zürich
|
| Department |
Institute of Plant and Microbial Biology
|
| Street address |
Zollikerstrasse 107
|
| City |
Zürich |
| ZIP/Postal code |
8008 |
| Country |
Switzerland |
| |
|
| Platform ID |
GPL24424 |
| Series (1) |
| GSE108405 |
Transcriptomics study of three Blumeria graminis formae speciales |
|
| Relations |
| BioSample |
SAMN08225134 |
| SRA |
SRX3503528 |
