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) We performed RNA-seq analysis of the root transcriptional response to Fusarium oxysporum f.sp. vasinfectum (FOV) race 4 (FOV4) infection in Gossypium barbadense, also known as Pima cotton. Susceptible Gossypium barbadense inbred lines Pima S-7 (PI 560140) and Pima 3-79 susceptible to Fusarium wilt [Fusarium oxysporum f.sp. vasinfectum (FOV)] race 4 (FOV4), and Pima S-6 (PI 608346) which is resistant to FOV4 infection, were used for the preparation of cDNA libraries and further RNA-seq analyses. more...

Organism:

Gossypium barbadense

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33440 GPL25504

18 Samples

Download data: TXT

(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) Increasing soil salinization has led to severe losses of plant yield and quality. Researching the formation of plant salt tolerance and the molecular mechanism of the salt stress response is therefore urgent. We here take advantage of recent progress in single-cell transcriptomics technology to systematically analyze plant roots response to salt stress, and 57,185 high-quality cells were totally obtained from 5-day-old lateral root tips of Gossypium arboreum under natural growth and different salt-treatment conditions. more...

Organism:

Gossypium arboreum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33192

8 Samples

Download data: MTX, TSV

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

Organism:

Gossypium bickii

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL33097 GPL33091

19 Samples

Download data: MTX, TSV

(Submitter supplied) Comprehensive utilization of cottonseeds is limited by the presence of pigment gland and its inclusion gossypol. The ideal cotton is glandless-seeds and glanded-plant, a trait found in only few Australian wild cotton species, including Gossypium bickii. Introgressing the trait to cultivated species is proved to be difficult. Understanding the biological processes towards pigment gland morphogenesis and the associated underlying molecular mechanisms will facilitate breeding cultivated cotton varieties with the trait of glandless-seeds and glanded-plant. more...

Organism:

Gossypium bickii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33097

1 Sample

Download data: MTX, TSV

(Submitter supplied) Comprehensive utilization of cottonseeds is limited by the presence of pigment gland and its inclusion gossypol. The ideal cotton is glandless-seeds and glanded-plant, a trait found in only few Australian wild cotton species, including Gossypium bickii. Introgressing the trait to cultivated species is proved to be difficult. Understanding the biological processes towards pigment gland morphogenesis and the associated underlying molecular mechanisms will facilitate breeding cultivated cotton varieties with the trait of glandless-seeds and glanded-plant. more...

Organism:

Gossypium bickii

Type:

Expression profiling by high throughput sequencing

Platform:

GPL33091

18 Samples

Download data: TXT

(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:

Gossypium hirsutum; Zea mays

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) The purpose of this study was to find candidate genes related to fiber strength by comparing the differences in gene expression levels of different samples at different stages of fiber development. Methods: PimaS-7 and 5917, two Gossypium barbadense materials with significant difference in fiber strength, were used as experimental materials. Transcriptome sequencing was performed on the fibers at 0,5,10,15,20,25,30,35 dPA after flowering, with three biological replicates。Sequence reads that were quality-screened were analyzed at the transcriptional subtype level using two methods :Burrows-Wheeler Aligner (BWA), then Aova (Aova) and Tophat, then Cufflinks. more...

Organism:

Gossypium barbadense

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19651

48 Samples

Download data: TXT

(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