|
| Status |
Public on Sep 14, 2021 |
| Title |
root, HI2 |
| Sample type |
SRA |
| |
|
| Source name |
42 hours after inoculation with Phytophthora nicotianae suspension
|
| Organism |
Nicotiana tabacum |
| Characteristics |
cultivar: Hicks
genotype: Hicks
treatment: Phytophthora nicotianae suspension
tissue: Root
|
| Treatment protocol |
The roots of each of eighteen 33-day old plants of each genotype were inoculated with 10 mL of a 1×103 zoospores mL-1 suspension of a P. nicotianae race 0 isolate maintained at N.C. State University. A separate set of eighteen plants of each plant genotype was treated with 10 mL of the suspension buffer (without zoospores) and maintained as uninoculated control plants. All plants were maintained with sub-irrigation for 42 hours post-inoculation, at which time roots were carefully rinsed to remove growth media, excised, transferred to liquid nitrogen for rapid freezing, and eventually stored at -80°C until RNA purification.
|
| Growth protocol |
Plants of each genotype were grown in sub-irrigated 8.3 cm square pots filled with calcined clay (Turface Athletics All Sport, Profile Products, Buffalo Grove, IL, USA) and maintained at 27C in a plant growth room with a 18 hours light: 6 hours dark photoperiod.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Root samples were collected and frozen and ground in liquid nitrogen, and RNA was purified using Plant Rneasy mini kit of Qiagen.
100 ng total RNA samples was used for RNA-seq library construction using NEBNext® UltraTM Directional RNA Library Prep Kit for Illumina (New England BioLabs, Ipswich, MA, USA) followed the protocol for long size insertions.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
Reads were mapped against tobacco K326 genome assembly Nitab4.5 using hisat2 version 2.1.0
Reads mapped to gene assembly were manipulated using samtools for sorting/indexing
Raw count of reads mapped to annotated tobacco gene model (Nitab4.5 version) were extracted using bedtools version 2.25.0
Genome_build: Tobacco K326 genome assembly Nitab4.5
Supplementary_files_format_and_content: tab-delimited text file includes raw count values for each sample (geneIDs can be searched at https://solgenomics.net/jbrowse_solgenomics/?data=data/json/NitabEd17)
|
| |
|
| Submission date |
Mar 14, 2021 |
| Last update date |
Sep 15, 2021 |
| Contact name |
Ramsey Lewis |
| E-mail(s) |
[email protected]
|
| Phone |
(919)-513-4802
|
| Organization name |
North Carolina State University
|
| Department |
Crop and Soil Sciences Department
|
| Lab |
Tobacco Breeding & Genetics
|
| Street address |
101 Derieux PI
|
| City |
Raleigh |
| State/province |
NC |
| ZIP/Postal code |
27695 |
| Country |
USA |
| |
|
| Platform ID |
GPL25653 |
| Series (1) |
| GSE168854 |
Homoeologous Chromosome Exchange Explains the Creation of a QTL Affecting Soil‐Borne Pathogen Resistance in Tobacco |
|
| Relations |
| BioSample |
SAMN18306350 |
| SRA |
SRX10338448 |
