GEO DataSets

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

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16195 GPL26789 GPL33654

425 Samples

Download data: TXT

(Submitter supplied) Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA sequencing (RNA-seq) datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. In this study, we report five RNA-seq datasets (350.7 Gb) inoculated with one of three bacteria, one virus, or one oomycete. more...

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26789

78 Samples

Download data

(Submitter supplied) Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA sequencing (RNA-seq) datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. In this study, we report five RNA-seq datasets (350.7 Gb) inoculated with one of three bacteria, one virus, or one oomycete. more...

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26789

78 Samples

Download data

(Submitter supplied) Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA sequencing (RNA-seq) datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. In this study, we report five RNA-seq datasets (350.7 Gb) inoculated with one of three bacteria, one virus, or one oomycete. more...

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26789

98 Samples

Download data

(Submitter supplied) Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA sequencing (RNA-seq) datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. In this study, we report five RNA-seq datasets (350.7 Gb) inoculated with one of three bacteria, one virus, or one oomycete. more...

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26789

39 Samples

Download data

(Submitter supplied) Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA sequencing (RNA-seq) datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. In this study, we report five RNA-seq datasets (350.7 Gb) inoculated with one of three bacteria, one virus, or one oomycete. more...

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26789

15 Samples

Download data

(Submitter supplied) Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA sequencing (RNA-seq) datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. In this study, we report five RNA-seq datasets (350.7 Gb) inoculated with one of three bacteria, one virus, or one oomycete. more...

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26789 GPL16195 GPL33654

117 Samples

Download data

(Submitter supplied) Alternative splicing (AS) is a widely observed phenomenon in eukaryotes that plays a critical role in development and stress responses. In plants, the large number of RNA-seq datasets in response to different environmental stressors can provide clues for identification of condition-specific and/or common AS variants for preferred agronomic traits. We report RNA-seq datasets (350.7 Gb) from Capsicum annuum inoculated with one of three bacteria, one virus, or one oomycete and obtained additional existing transcriptome datasets. more...

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26789 GPL16195 GPL33654

219 Samples

Download data: TXT

(Submitter supplied) ngs2013_07_pcapsici-effecaps-phytophthora capsici-The analysed RNAseq concerned the oomycete Phytophthora capsici in growth on pepper plants. 1/ How the adaptation of a pathogen to a host depends on its gene expression? 2/ How the plant host impacts the expression of pathogen genes at the very beginning of infection?-Two isolates of Phytophthora capsici were used: the Pc107 isolate (called A for adapted to pepper from INRAE GAFL Avignon), and the Pc273 isolate (N for non-adapted to pepper, collected on pumpkin in the USA). more...

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16195

24 Samples

Download data: TXT

(Submitter supplied) The organization of chromatin into self-interacting domains is universal among eukaryotic genomes, though how and why they form varies considerably. Here we report a chromosome-scale reference genome assembly of pepper (Capsicum annuum) and explore its 3D organization through integrating high-resolution Hi-C maps with epigenomic, transcriptomic, and genetic variation data. Chromatin folding domains in pepper are as prominent as TADs in mammals but exhibit unique characteristics. more...

Organism:

Capsicum annuum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29650

12 Samples

Download data: BEDGRAPH, BW, NARROWPEAK

(Submitter supplied) We performed a transcriptome analysis on the graft junction of tomato and pepper self grafts and heterografts.

Organism:

Capsicum annuum; Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL29771 GPL26789

48 Samples

Download data: XLSX

(Submitter supplied) Two fruit development stages of the wild chiltepin pepper (Capsicum annuum var. glabriusculum) were studied. RNA-Seq data was obtained from fruits at 20 and 68 days after anthesis with two biological replicates for a total of 4 samples. 260 million raw reads were sequenced and over 80% of them mapped back to the Capsicum annuum genome.

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29996

4 Samples

Download data: FA, GFF3, TSV

(Submitter supplied) We report transcripts from tomato:tomato and pepper:pepper self-grafts, and tomato:pepper and pepper:tomato hetergrafts over 4 time points: 24 hours after grafting, 3 days after grafting, 5 day after grafting, and 2 weeks after grafting Examination of 4 graft combinations over 4 time points

Organism:

Capsicum annuum; Solanum lycopersicum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL26701 GPL16345 GPL16195

58 Samples

Download data: TXT

(Submitter supplied) Profiling of small RNAs identified a total of 359 and 357 conserved; and 490 and 155 novel miRNAs in C. chinense and C. frutescens, respectively. Based on the sequence similarity observed on alignment with already reported plant miRNAs, conserved and novel miRNAs were identified in both the species. The target prediction analysis reveals vital role of miRNAs in regulating genes involved in transcriptions, protein modification, signal transduction and metabolism. more...

Organism:

Capsicum frutescens; Capsicum chinense

Type:

Non-coding RNA profiling by high throughput sequencing

Platforms:

GPL24847 GPL24848

8 Samples

Download data: XLSX

(Submitter supplied) The colonization of Capsicum annuum roots by Fusarium oxysporum Fo47 induces resistance responses on the plant. Fo47 is a non-pathogenic strain of Fusarium oxysporum. Fo47 colonizes only the most outer layers of the root surface but it does not colonize inner tissues. Pre-treatment of roots with Fo47 reduces the symptom development produced by later pathogen inoculation. The expression of genes in distal tissues was determined by microarray analysis of stems of Fo47-treated plants. more...

Organism:

Solanum lycopersicum; Capsicum annuum

Type:

Expression profiling by array

Platform:

GPL4741

6 Samples

Download data: CEL

(Submitter supplied) Twelve chili pepper accessions, six domesticated, four wild and two F1 crosses were studied. RNA-Seq experiments were performed with fruits from each accession at 7 different times after anthesis. Additionally, samples of seedlings from two accessions were evaluated. The data set is comprised by 179 samples, that in total have more than 3 billion reads map to the Capsicum annuum genome.

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29650

179 Samples

Download data: CSV, FA, GTF

(Submitter supplied) We sequenced the transcriptomes of resistant and susceptible cultivar roots uninoculated and with RKN M. incognita, over three time points; 1-, 4-, and 7-days post inoculation. Over 300 million high quality reads from 36 samples were mapped to the pepper reference genome. Comparing inoculation and resistance profiles revealed generic biotic stress responses and specific nematode resistance responses. more...

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26789

35 Samples

Download data: TXT

(Submitter supplied) We sought to investigate the scope of transcriptome analyses of peppers subjected to four major phytohormones. For this, At the 6-true-leaf stage, pepper plants were sprayed at underside of leaves with 5 mM sodium salicylate (SA), 100 μM methyl jasmonate (JA), 5 mM ethephone (ET), 100 μM (±)-ABA, or distilled water (mock). For RNA-seq library construction, the third or fourth leaves from four plants were harvested per replicate at 0, 1, 3, 6, 12, and 24 h after treatment. more...

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26789

78 Samples

Download data: TXT

(Submitter supplied) We sought to investigate the scope of transcriptome analyses of peppers subjected to four major environment stresses (heat, cold, drought, and salinity). For this, at the six-true-leaf stage, plants were subjected to a temperature of 10°C or 40°C to mimic cold or heat stress, respectively. For salinity stress, plants were treated with 50 mL of a 400 mM NaCl solution; for osmotic stress, the peppers were treated with 50 mL of 400 mM mannitol. more...

Organism:

Capsicum annuum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL26789

78 Samples

Download data: TXT

(Submitter supplied) The Tsw gene conferring Tomato spotted wilt virus (TSWV) resistance in Capsicum chinense breaks down at high temperatures. Here, we performed RNA-Seq analysis under different temperature conditions to uncover the resistance breakdown mechanism using TSWV-resistant C. chinense ‘PI152225’ and susceptible ‘Habanero’. RNA-Seq analysis revealed only a few differentially expressed genes (DEGs) at 1 dpi but 2,096 and 551 DEGs between plants at 25°C and 30°C at 5 dpi. more...

Organism:

Capsicum chinense

Type:

Expression profiling by high throughput sequencing

Platform:

GPL25985

23 Samples

Download data: FA, GFF3, TXT