GEO DataSets

(Submitter supplied) Strigolactones (SLs), a class of phytohormones, play a pivotal role in governing critical aspects of plant development, including shoot branching and root development. DWARF53 (D53) is a key repressor in the SL signaling. Nevertheless, its involvement and regulatory mechanisms in cotton fiber development—a representative single-cell model, has remained elusive. In this study, we unveil GhD53 represses the transcription of SL-inducible genes GhFAD3-2 and GhFAD3-4, which are involved in linolenic acid biosynthesis—a stimulant of cell elongation, thus inhibiting cotton fiber elongation. more...

Organism:

Gossypium hirsutum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29713

2 Samples

Download data: TXT

(Submitter supplied) Xanthomonas spp. employ transcription activator-like effectors (TALEs) to promote pathogenicity by activating host susceptibility (S) genes. Cotton GhSWEET10 is an S gene targeted by a TALE in an early isolate of Xanthomonas citri pv. malvacearum (Xcm), but not by recent field Xcm isolates. To understand the pathogenicity shift in Xcm and its adaptation to cotton, we assembled the whole genome and the TALE repertoire of three recent Xcm Texas field isolates. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16485

6 Samples

Download data: XLSX

(Submitter supplied) Clarified the relationship between the photosynthetic performance and photosynthetic pigment metabolism of Yt30.

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30244

6 Samples

Download data: TXT

(Submitter supplied) Histone methylation is one of the most significant epigenetic modifications in plants because it is responsible for regulating and controlling the expression of many important functional genes. Although there have been many studies concerning histone methylation, its specific functions and mechanisms in cotton fiber initiation remain unclear. To determine if the H3K27me3 modification had regulated cotton fiber initiation in upland cotton (Gossypium hirsutum), we performed a comparative analysis on the cleavage under targets and tagmentation (CUT&Tag) between the wild-type cultivar Xu142 and its fibreless mutant Xu142 fl. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29713

18 Samples

Download data: XLS

(Submitter supplied) Roots from 10 independent plants subjected to 300 mg/l PS-COOH treatments and to control conditions were pooled separately to form single biological replicates for RNA-seq analysis. Transcriptomics analyses showed that antioxidant activity-related genes were significantly upregulated after PS-COOH treatments, indicating that oxidative stress was induced in cotton.

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29713

6 Samples

Download data: TXT

(Submitter supplied) Cotton is the main source of natural fiber in the textile industry, making it one of the most economically important fiber crops in the world. Verticillium wilt, caused by the pathogenic fungus Verticillium dahlia, is one of the most damaging biotic factors limiting cotton production. Mechanistic details of cotton defense responses to verticillium wilt remain unclear. In this study, GFP-labeled strain of V. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29713

12 Samples

Download data: XLS

(Submitter supplied) Plants can synthesize a wide range of terpenoids in response to various environmental cues. However, the specific regulatory mechanisms governing terpenoid biosynthesis at the cellular level remain largely elusive. Herein, we employed single-cell RNA sequencing (scRNA-seq) to comprehensively characterize the transcriptome profile of cotton leaves and established a hierarchical transcriptional network regulating cell-specific terpenoid production. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29713

3 Samples

Download data: MTX, TSV

(Submitter supplied) Cotton (Gossypium hirsutum) is widely distributed worldwide, and improving the quality of its fiber is one of the most important tasks in cotton breeding. Cotton fibers are primarily composed of cellulose, which is synthesized and regulated by cellulose synthase (CesAs). However, the molecular mechanism of CesA genes in cotton is unclear. In this study, the cotton transcriptome and metabolome were used to investigate the significant function of CesA genes in fiber development. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29713

6 Samples

Download data: XLSX

(Submitter supplied) ChIP-seq data of 5 dpa fibers from GhBES1-Overexpression cotton plants GHBES1-OE-FIBER-CHIP-SEQ

Organism:

Gossypium hirsutum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29713

2 Samples

Download data: BW

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

Organism:

Zea mays; Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL24163 GPL27127

24 Samples

Download data

(Submitter supplied) Cotton seedlings were subjected to water-deficit stress along with control condition for 24 hours or 48 hours and tissues emcompassing the elongation zone of primary roots were analysed for differential accumulated transcripts compared to control.

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL27127

12 Samples

Download data: XLSX

(Submitter supplied) Meristem maintenance, achieved through the highly conserved CLAVATA-WUSCHEL (CLV-WUS) regulatory circuit, is fundamental in balancing stem cell proliferation with cellular differentiation. Disruptions to meristem homeostasis can alter meristem size, leading to enlarged organs. Cotton, the world’s most important fiber crop, shows inherent variation in fruit size. Leveraging meristem regulation could benefit cotton agriculture and increase yields of high-quality fibers. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL32355

18 Samples

Download data: FPKM_TRACKING, TXT

(Submitter supplied) To investigate the gossypol synthasis between distinct cotton species CKG and CKN We then performed gene expression profiling analysis using data obtained from RNA-seq of 3 organs betweeen two species

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29713

18 Samples

Download data: XLS

(Submitter supplied) Salinity is a major abiotic stress at critical stages of seed germination and seedling establishment. Germination rate (GR) and field emergence rate (FER) are the key traits that determine the basic number of plants stand under field conditions. To explore molecular mechanisms in upland cotton under salt stress, a population of 177 recombinant inbred lines (RILs) and their parents were evaluated for seed germination traits (GP, germination potential; GR; FW, fresh weight; DW, dry weight; GL, germinal length) and seedling traits (FER; SH, seedling height; NL, Number of main stem leaves) in 2016-2018. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16485

27 Samples

Download data: XLSX

(Submitter supplied) As an initial step to explore the cotton (Gossypium hirsutum L.) root transcriptional response to the southern Root-Knot Nematode (RKN) Meloidogyne incognita infestation, conventional heirloom G. hirsutum (Gh) cultivars [susceptible Acala SJ-2 (SJ2), moderately resistant Upland Wild Mexico Jack Jones (WMJJ), and resistant Acala NemX] that have been shown to be useful as an informative genetic model for detecting and introgressing RKN resistance genes into commercial Upland cotton were used to enlighten the molecular mechanisms and gene expression of RKN resistance. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19231 GPL31052

18 Samples

Download data: TXT

(Submitter supplied) Our study provides evidence for the mechanism of Glc regulation of cotton fiber elongation, indicating that Glc not only serves as a nutrient, but also serves as a signal to regulate cotton fiber elongation. We also provided evidence that there is crosstalk between Glc and BR, and that the BR signal is located downstream of the Glc signal in the regulation of cotton fiber elongation

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29713

9 Samples

Download data: XLSX

(Submitter supplied) To explore the mechanisms of cotton response to this alkaline stress, we used next-generation sequencing (NGS) technology to study transcriptional changes of cotton under NaHCO3 alkaline stress. A total of 18,230 and 11,177 differentially expressed genes (DEGs) were identified in cotton roots and leaves, respectively. Gene ontology (GO) analysis indicated the enrichment of DEGs involved in various stimuli or stress responses. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23158

18 Samples

Download data: XLSX

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

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29633

9 Samples

Download data: BED, TXT

(Submitter supplied) Cotton is an excellent model for studying heterosis, crop domestication and bioengineering improvement. Chromatin profiling helps to reveal how histone modifications are involved in controlling differential gene expression between A and D subgenome in allotetraploid cotton. However, the detailed profiling and functional characterization of H3K27me3 and H3K4me3/H3K27me3 bivalent mark are still understudied in cotton. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29633

3 Samples

Download data: TXT

(Submitter supplied) Cotton is an excellent model for studying heterosis, crop domestication and bioengineering improvement. Chromatin profiling helps to reveal how histone modifications are involved in controlling differential gene expression between A and D subgenome in allotetraploid cotton. However, the detailed profiling and functional characterization of H3K27me3 and H3K4me3/H3K27me3 bivalent mark are still understudied in cotton. more...

Organism:

Gossypium hirsutum

Type:

Genome binding/occupancy profiling by high throughput sequencing

Platform:

GPL29633

6 Samples

Download data: BED