GEO DataSets

(Submitter supplied) Heterosis has greatly improved the yield and quality of crops. However, previous studies often focused on improving the yield and quality of the shoot system, while research on the root system was neglected. We determined the root numbers of 12 F1 hybrids, all of which showed strong heterosis, indicating that tobacco F1 hybrids have general heterosis. To understand its molecular mechanism, we selected two hybrids with strong heterosis, GJ (G70 × Jiucaiping No.2) and KJ (K326 × Jiucaiping No.2), and their parents for transcriptome analysis. more...

Organism:

Nicotiana tabacum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29390

30 Samples

Download data: TXT

(Submitter supplied) Here, we compile valuable insights gathered over years of generating Ribo-seq datasets from different plant species and experimental setups. We tested the effects of variable ribonuclease treatments for the generation of ribosome protected fragments (RPFs). We tested rRNA depletion strategies designed specifically for Arabidopsis and Tobacco. We also compare ligation-free to ligation-based library preparation strategies for generating Ribo-seq libraries.

Organism:

Arabidopsis thaliana; Nicotiana tabacum

Type:

Other

4 related Platforms

16 Samples

Download data: XLSX

(Submitter supplied) This SuperSeries is composed of the SubSeries listed below.

Organism:

Arabidopsis thaliana; Nicotiana tabacum

Type:

Non-coding RNA profiling by high throughput sequencing; Expression profiling by high throughput sequencing

Platforms:

GPL23495 GPL29390 GPL26208

48 Samples

Download data: BED

(Submitter supplied) Small RNAs (sRNAs) are essential for normal plant development and range in size classes of 21-24 nucleotides. The 22nt small interfering RNAs (siRNAs) and miRNAs are processed by Dicer-like 2 (DCL2) and DCL1 respectively and can initiate secondary siRNA production from the target transcript amplifying the silencing signal in plants. 22nt siRNAs are under-represented due to competition with DCL4, while only a small number of 22nt miRNAs exist due to the rare occurrence of an asymmetric bulge in the precursor miRNA stem. more...

Organism:

Nicotiana tabacum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29390

19 Samples

Download data: BED

(Submitter supplied) Heterochromatic condensates (chromocenters) are critical for maintaining the silencing of heterochromatin. However, it is a riddle why the presence of chromocenters is variable across species. Here, we reveal that variations in the plant heterochromatin protein ADCP1 confer a diversity in chromocenter formation via phase separation. ADCP1 physically interacts with the high mobility group protein HMGA to form a complex and mediates heterochromatin condensation by multivalent interactions. more...

Organism:

Nicotiana tabacum; Nicotiana benthamiana; Arabidopsis thaliana; Solanum lycopersicum

Type:

Genome binding/occupancy profiling by high throughput sequencing

4 related Platforms

50 Samples

Download data: BW

(Submitter supplied) This RNA-seq is a part of the paper describing the role of PIN5 in generating auxin sinks. https://www.biorxiv.org/content/10.1101/2024.01.24.576992v1

Organism:

Nicotiana tabacum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29390

6 Samples

Download data: SF

(Submitter supplied) Heterosis, a phenomenon where hybrids exhibit superior performance in various traits such as yield, quality, and resistance compared to their parents, has long been a focus of agricultural research. Although tobacco biomass significantly affects tobacco yield and economic profitability, the underlying reasons for the dominance of tobacco biomass hybrids and their formation remain unclear. To address this, we selected 5 tobacco varieties (lines) with large differences in tobacco biomass as the parents and formulated F1 hybrids to analyze the expression of tobacco biomass heterosis. more...

Organism:

Nicotiana tabacum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29390

18 Samples

Download data: TXT

(Submitter supplied) Tobacco (Nicotiana tabacum L.) is an important cash crop, and the size of its leaves significantly influences both yield and quality. However, the upper part of tobacco leaves, due to its dense tissue structure, often faces issues such as narrow and thick leaves during the production of roasted cigarettes. These problems have a severe impact on the yield and quality of the upper leaf. Although the mechanism of leaf size regulation in Arabidopsis thaliana has been extensively studied, it remains unclear for tobacco. more...

Organism:

Nicotiana tabacum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29390

9 Samples

Download data: TXT

(Submitter supplied) We used two hybrid combinations and their 4 parents as materials. One week after topping the tobacco plant, samples were taken, including three tissues: root, stalk, and leaf. The RNA of these samples was extracted, and transcriptome sequencing analysis was carried out to explore the transcriptional profile differences between hybrids and their parents, and to analyze the gene differential expression between different tissues.

Organism:

Nicotiana tabacum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29390

54 Samples

Download data: TXT

(Submitter supplied) Heterosis has greatly improved the yield and quality of crops. However, previous studies often focused on improving the yield and quality of the shoot system, while research on the root system was neglected. We determined the root numbers of 12 F1 hybrids, all of which showed strong heterosis, indicating that tobacco F1 hybrids have general heterosis. To understand its molecular mechanism, we selected two hybrids with strong heterosis, GJ (G70 × Jiucaiping No.2) and KJ (K326 × Jiucaiping No.2), and their parents for transcriptome analysis. more...

Organism:

Nicotiana tabacum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29390

15 Samples

Download data: TXT

(Submitter supplied) In this study, we have used the comparative transcriptomic and proteomic approaches to decipher the changes in genes and protein abundances in cigar tobacco leaves under LL. In this study, DEGs and DEPs related to glycolysis, starch and sucrose metabolism, tyrosine metabolism, photosynthesis-antenna proteins, and photosynthesis pathways are significantly enriched. This study offers novel insights into both transcriptome and proteome levels response mechanisms under different light intensities.

Organism:

Nicotiana tabacum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29390

9 Samples

Download data: XLSX

(Submitter supplied) Through a two-year field experiment, G70×GDH11 with strong heterosis and K326×GDH11 with weak heterosis were screened out. Transcriptome analyses revealed that 80.89% and 57.28% of the differentially expressed genes (DEGs) in the strong and weak heterosis combinations exhibited an overdominant expression pattern, respectively. The genes that up-regulated the overdominant expression in the strong heterosis hybrids were significantly enriched in the ion homeostasis. more...

Organism:

Nicotiana tabacum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29390

18 Samples

Download data: TXT

(Submitter supplied) Cell proliferation and division are fundamental processes of plant development and homeostasis. With the feature of high homogeneity, tobacco Bright Yellow-2 (BY-2) cells, a so-called “HeLa” cell line in plants, provide a useful system for study the cell cycle of plants, particularly when in combination with the latest high-throughput single-cell RNA sequencing (scRNA-seq) technology. Here, we generated both scRNA-seq and bulk RNA-seq data from the BY-2 cells and found that the enzymatic hydrolysis during protoplasting was the major factor contributing to cell clustering noise. more...

Organism:

Nicotiana tabacum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29390

8 Samples

Download data: CSV, TXT

(Submitter supplied) Purpose: To further identify the genes and pathways involved in the necrotic phenotype of NtCBL5A-OE lines, the leaf transcriptome profiling of WT and OE-2 lines grown under control conditions and salt stress (100 mM NaCl) at 4 DAT were sequenced and compared. Methods: Two datasets of differentially expressed genes (DEGs) were made in which we identified the genes that were differentially expressed as a result of the overexpression of NtCBL5A: Control-WT vs Control-OE2 (C-WT/C-OE2), Salt-WT vs Salt-OE2 (S-WT/S-OE2). more...

Organism:

Nicotiana tabacum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29390

8 Samples

Download data: TXT

(Submitter supplied) We compared the level of methylated cytosines between hydrogen peroxide overproducing (L8) and azygotes (L1) tobacco plants. We generated single base resolution maps of DNA methylation by whole genome bisulfite sequencing for 6-week-old plants from both transgenic tobacco lines. In total, we found 4,765 and 4,667 hyper and hypomethylated cytosines, respectively. These DmCs were associated with different regions of the genome, resulting in 1034 genes with at less one DMCs. more...

Organism:

Nicotiana tabacum

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL29390

6 Samples

Download data: BEDGRAPH