|
| Status |
Public on Apr 30, 2019 |
| Title |
Harrington-Uninoculated-Rep2 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf tissues
|
| Organism |
Hordeum vulgare |
| Characteristics |
host cultivar: Harrington
pathogen isolate: (Not applicable)
isolate virulence profile: (Not applicable)
tissue: Leaf
|
| Treatment protocol |
Barley variety Harrington was swab inoculated with different isolates of fungal pathogen Puccinia graminis f.sp. tritici at two leaf stage
|
| Growth protocol |
Barley variety Harrington were grown for seven days in 6 inch cone
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Total RNA was extracted using Qiagen RNeasy mini kit
Libraries were prepared using the TruSeq RNA Library Prep Kit v2 following the manufactures standard protocol
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina NextSeq 500 |
| |
|
| Data processing |
The Illumina bcl2fastq2 Conversion Software was used to convert basecall (BCL) to FASTQ files and demultiples the reads to each barcodes
Sequnenced reads were trimmed for quality score and ambigious calls using default parameters in CLCgenomics Workbench v8.0
Reads Per Kilobase of exon per Megabase of library size (RPKM) eads Per Kilobase of exon model per Million mapped reads were calculated for reads mapped to pathogen and host gene models in CLC genomics Workbench v8.0
Supplementary_files_format_and_content: tab-delimited text files include total gene reads and RPKM values of host and pathogen genes for each sample
|
| |
|
| Submission date |
Apr 29, 2019 |
| Last update date |
Apr 30, 2019 |
| Contact name |
Robert Brueggeman |
| Organization name |
North Dakota State University
|
| Department |
Plant Pathology
|
| Lab |
Brueggeman Lab
|
| Street address |
306 Walster Hall, North Dakota State University
|
| City |
Fargo |
| State/province |
ND |
| ZIP/Postal code |
58108 |
| Country |
USA |
| |
|
| Platform ID |
GPL26320 |
| Series (1) |
| GSE130423 |
Transcriptome-wide Association study identifies putative Elicitors/Suppressor of Puccinia graminis f. sp. tritici that Modulate Barley rpg4-mediated Stem Rust Resistance |
|
| Relations |
| BioSample |
SAMN11525995 |
| SRA |
SRX5763427 |
