Data · dataset · 2026
Transcriptome sequencing data of Nicotiana benthamiana after infiltration with six distinct Agrobacterium strains
Listed in ScienceDB
Commonly used laboratory Agrobacterium strains differ in their genetic backgrounds and modified helper Ti plasmids, which may induce varying degrees and durations of host immune responses and transcriptional reprogramming.
Description
However, the differential responses of N. benthamiana, the most commonly used host, to these strains remain unclear. In this study, we for the first time systematically investigated the transcriptional defense responses of N. benthamiana to six common laboratory Agrobacterium strains (Agrobacterium tumefaciens C58C1, GV3101, LBA4404, AGL-1, EHA105, and the Rhizobium rhizogene strain ArA4).
N. benthamiana that were not infiltrated with Agrobacteriumwere used as the control group (0 dpi). Transcriptome profiling of tobacco leaves was conducted at 3 and 7 dpi to clarify the conserved and divergent regulation of tobacco immune pathways and stress responses by different strains. Agroinfiltrated leaves at 3 dpi and 7 dpi were sampled, immediately frozen in liquid nitrogen, and stored at -80 °C in an ultra-low temperature freezer.
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Non-agroinfiltrated leaves were sampled at 0 dpi as the control group. Total RNA was extracted, and genomic DNA was removed using an RNA Easy Fast Kit (DP452; TIANGEN Co. Ltd., Beijing, China) following the manufacturer’s instructions.
After quality control, RNA-seq libraries were constructed using the NEBNext® Ultra™ II RNA Library Prep Kit for Illumina® (NEB, Ipswich, MA, USA). Libraries were sequenced with 150-bp paired-end reads on the Novaseq 6000 system according to the manufacturer’s protocol to generate transcriptome data. Adapter sequences and low-quality reads were removed using FastQC software (v0.12.1) to obtain clean reads.
Links
Where it is published
- DOI doi.org/10.57760/sciencedb.40003 ↗
DOI / persistent id · from scidb cn
Catalogue records · 1
- OAI-PMH record scidb.cn/oai?verb=GetRecord&metadataPrefix=oai_dc&identifier=10.57760%2… ↗
metadata API · from scidb cn
Topics
- From keywords
- Earth & Environmental Science · Engineering · Humanities · Life Sciences · Social Science
- Inferred from text
- Agricultural biotechnology 71% · RNA sequencing 65% · Sequencing 75%
Provenance · 1 source records, 13 field assertions
| Source | Key | Last seen | Raw |
|---|---|---|---|
| ScienceDB | 10.57760/sciencedb.40003 | 12 d ago | JSON v1 |
| Field | Assertion | Extractor | Evidence |
|---|---|---|---|
| access_level | source · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].anzsrc:group:3001 | enrichment · scidb cn | taxonomy-embedding@1.0.0 | title+keywords+description (71%) |
| concepts[field].local:field:earth-environmental | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:engineering | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:humanities | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:life-sciences | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[field].local:field:social-science | mapping · scidb cn | connector:scidb_cn@1.0.0 | |
| concepts[modality].local:modality:rna-seq | enrichment · scidb cn | keyword-concept-rules@1.0.0 | title+description (65%) |
| concepts[modality].local:modality:sequencing | enrichment · scidb cn | keyword-concept-rules@1.0.0 | title+description (75%) |
| description | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/description |
| license | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/rights |
| publication_date | source · scidb cn | connector:scidb_cn@1.0.0 | |
| title | source · scidb cn | connector:scidb_cn@1.0.0 | /metadata/dc/title |