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Items: 1 to 20 of 1348

1.

The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper

(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
Series
Accession:
GSE240949
ID:
200240949

2.

The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper [PRJNA634831]

(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
Series
Accession:
GSE240948
ID:
200240948

3.

The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper [PRJNA525913]

(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
Series
Accession:
GSE240947
ID:
200240947

4.

The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper [PRJNA223222]

(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
Series
Accession:
GSE240946
ID:
200240946

5.

The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper [PRJNA385363]

(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
Series
Accession:
GSE240945
ID:
200240945

6.

The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper [PRJNA987837]

(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
Series
Accession:
GSE240944
ID:
200240944

7.

The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper [PRJNA973829]

(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
Series
Accession:
GSE240943
ID:
200240943

8.

The landscape of abiotic and biotic stress-responsive splice variants with deep RNA-seq datasets in hot pepper

(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
Series
Accession:
GSE240234
ID:
200240234

9.

effecaps-phytophthora capsici project: Phytophthora capsici Illumina RNAseq transcriptome of two isolates, one adapted to pepper, another non adapted, in two pepper accessions, one partially resistant and one susceptible to Phytophthora capsici

(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
Series
Accession:
GSE206447
ID:
200206447

PubMed Full text in PMC Similar studies

10.

The 3D architecture of the pepper genome and its relationship to function and evolution

(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
Series
Accession:
GSE206031
ID:
200206031

11.

Gene regulatory networks for compatible versus incompatible grafts identify a role for SlWOX4 during junction formation

(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
Series
Accession:
GSE167482
ID:
200167482

PubMed Full text in PMC Similar studies SRA Run Selector

12.

Chiltepin pepper RNA-Seq data of two fruit development stages

(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
Series
Accession:
GSE171889
ID:
200171889

PubMed Full text in PMC Similar studies SRA Run Selector

13.

Graft junction transcriptome between tomato and pepper over time

(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:
GPL16195 GPL26701 GPL16345
58 Samples
Download data: TXT
Series
Accession:
GSE131700
ID:
200131700

SRA Run Selector

14.

Expression data from Capsicum annuum inoculated with Fusarium oxysporum Fo47

(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
Series
Accession:
GSE49432
ID:
200049432

PubMed Full text in PMC Similar studies Analyze with GEO2R

15.

Chili pepper RNA-Seq data for fruit development in a set of accessions

(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
Series
Accession:
GSE165448
ID:
200165448

PubMed Full text in PMC Similar studies SRA Run Selector

16.

A Comprehensive Transcriptional Profiling of Pepper Responses to Root Knot Nematode

(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
Series
Accession:
GSE152857
ID:
200152857

SRA Run Selector

17.

Comprehensive transcriptome profiling for response to phytohormone-induced signaling in Capsicum annuum L.

(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
Series
Accession:
GSE149037
ID:
200149037

PubMed Full text in PMC Similar studies SRA Run Selector

18.

Transcriptome profiling of abiotic responses to heat, cold, salt, and osmotic stress of Capsicum annuum L.

(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
Series
Accession:
GSE132824
ID:
200132824

PubMed Full text in PMC Similar studies SRA Run Selector

19.

Genome-wide comparative analysis in Solanaceae plants reveals evolution of novel miRNAs targeting defense genes in Capsicum spp.

(Submitter supplied) Background: MicroRNAs (miRNAs) play roles in various biological processes including growth, development, and defense in plants. Recent studies revealed that some plant miRNAs could produce secondary small interfering RNAs (siRNAs) such as phased, secondary siRNAs (phasiRNAs) and they regulate cascade of gene expression. Results: We performed genome-wide comparative analysis of miRNAs and their targets in Solanaceae plants in an evolutionary perspective. more...
Organism:
Solanum lycopersicum; Capsicum annuum; Solanum tuberosum
Type:
Other; Non-coding RNA profiling by high throughput sequencing
Platforms:
GPL16195 GPL16436 GPL16345
6 Samples
Download data: XLSX
Series
Accession:
GSE102781
ID:
200102781

PubMed Full text in PMC Similar studies SRA Run Selector

20.

Identification and characterization of conserved microRNAs in pepper by high-throughput sequencing

(Submitter supplied) High-throughput sequencing was employed to identify conserved microRNAs in pepper.
Organism:
Capsicum annuum
Type:
Non-coding RNA profiling by high throughput sequencing
Platform:
GPL15575
1 Sample
Download data: TXT
Series
Accession:
GSE37999
ID:
200037999

SRA Run Selector

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