|
| Status |
Public on May 19, 2023 |
| Title |
D2- Dro141TX |
| Sample type |
SRA |
| |
|
| Source name |
Scion Leaf
|
| Organism |
Nicotiana benthamiana |
| Characteristics |
cell type: Scion Leaf
treatment: Grafted to tomato rootstock
tomato rootstock: Dro141TX
|
| Treatment protocol |
Scion transcripts of Nicotiana benthamiana grafted to Maxifort and Dro141TX were compared
Unmapped reads to Nicotiana benthamiana genome were mapped to Solanum lycopersicum genome (SL3.0) to identify graft transmissible transcripts from rootstock to scion
|
| Growth protocol |
2 to 3 week old tomato rootstock seedlings of Maxifort and DRO141TX were grafted to similarly cut 3-5 week old N. benthamiana scions. Grafted plants were maintained under a humidity dome for one week before being transferred to a growth chambers at 25°C under a 12 hr light cycle
|
| Extracted molecule |
total RNA |
| Extraction protocol |
RNA was isolated from scion leaves using Rneasy plant mini kit (Qiagen)
RNA libraries for RNA-seq were prepared using NEB NEXT ultra Prep Kit following manufacturer's protocols.
|
| |
|
| Library strategy |
RNA-Seq |
| Library source |
transcriptomic |
| Library selection |
cDNA |
| Instrument model |
Illumina HiSeq 4000 |
| |
|
| Data processing |
CLC Genomics Workbench v 10.0.1
Sequence reads were trimmed for adaptor sequence/low-quality sequence using CLC genomic benchwork (parameter- Quality limit: 0.05)
Trimmed reads were mapped to Nicotiana benthamiana genome Niben 1.0.1 and unmapped reads are collected (match score =1, mismatch cost =2, insertion cost =3, deletion cost =3, length fraction =0.5, similarity fraction =0.8, global alignment =No)
Read not matched with Nicotiana benthamiana genome (Niben1.0.1) were mapped to Solanum lycopersicum genome (SL3.0) using CLC genomic benchwork (parameters- mismath cost: 2 insertion cost: 3 deletion cost: 3 length fraction: 0.8 similarity fraction: 0.8)
Read count extraction and normalization were performed using CLC genomic benchwork
Assembly: SL3.0
Supplementary files format and content: Excel file include RPKM values for all six samples
|
| |
|
| Submission date |
Aug 17, 2022 |
| Last update date |
May 19, 2023 |
| Contact name |
Madhu Kappagantu |
| E-mail(s) |
[email protected], [email protected]
|
| Organization name |
University of Maryland
|
| Street address |
4291 Fieldhouse drive
|
| City |
College Park |
| State/province |
MD |
| ZIP/Postal code |
20742 |
| Country |
USA |
| |
|
| Platform ID |
GPL29766 |
| Series (1) |
| GSE211493 |
Rootstock induced scion resistance against tobacco mosaic virus is associated with the induction of defense related transcripts and graft transmissible mRNAs |
|
| Relations |
| BioSample |
SAMN30377996 |
| SRA |
SRX17124391 |
