|
| Status |
Public on Jul 05, 2023 |
| Title |
P2.4a.1 |
| Sample type |
SRA |
| |
|
| Source name |
Leaf
|
| Organism |
Nicotiana tabacum |
| Characteristics |
tissue: Leaf
cultivar: TN90
line: P2.4a
genotype: Transgenic plant with overexpressed of NtYb1
genetic modification: Transformed with NtYb1 (EGY2) transgene driven by 35S CMV promoter
|
| Treatment protocol |
Prior to leaf maturity in the Oxford field experiment, frozen top leaf samples were collected from three biological replicates of TN 90LC and green stem segregants derived from primary transformants TN 90LC + 35S:Yb1 P2 4a, TN 90LC + 35S:Yb1 P9 10a, and TN 90LC + 35S:Yb1 P3 4a. 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 field in Oxford, North Carolina State, USA.
|
| Extracted molecule |
total RNA |
| Extraction protocol |
Leaf 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 2000 |
| |
|
| Data processing |
RNAseq reads were trimmed to remove poor quality bases using fastq-mcf with parameters of q=30, l=50 and P=30.
Reads were mapped against tobacco TN90 genome assembly Nitab-TN90 (GCF_000715135.1_Ntab-TN90_genomic.fna) 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 (GCF_protein_coding_gene) were extracted using bedtools version 2.25.0
Assembly: Tobacco TN90 enome assembly Nitab4.5 (GCF_000715135.1_Ntab-TN90_genomic.fna)
Supplementary files format and content: tab-delimited text files include raw count values for each sample
|
| |
|
| Submission date |
Jun 30, 2023 |
| Last update date |
Jul 05, 2023 |
| Contact name |
Ramsey Lewis |
| E-mail(s) |
rslewis@ncsu.edu
|
| 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 |
GPL13760 |
| Series (1) |
| GSE236277 |
Changes in Physiology of Burley Tobacco Plants Genetically Engineered to Express a Functional NtEGY2 Gene |
|
| Relations |
| BioSample |
SAMN36176696 |
| SRA |
SRX20852342 |
