GEO DataSets

(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) 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) 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) 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) 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

(Submitter supplied) Sea Island cotton (Gossypium barbadense) is the source of the world’s finest fiber-quality cotton, yet relatively little is understood about the genetic variation among diverse germplasm, the genes underlying important traits, and the effects of pedigree selection. Here, we resequenced 336 G. barbadense accessions and identified 16 million SNPs. Phylogenetic and population structure analyses revealed two major gene pools and a third admixed subgroup derived from geographical dissemination and interbreeding. more...

Organism:

Gossypium barbadense

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30678

90 Samples

Download data: TXT

(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) 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) Tetraploid cotton plants serve as prime natural fiber source for the textile industry. Although various omics studies have revealed molecular basis for fiber development, a better understanding of transcriptional regulation mechanism regulating lint fiber initiation is necessary to meet global natural fiber demand. Here, we aimed to perform transcriptome sequencing to identify DEGs (differentially expressed genes) in ovules of the cotton variety Xu142 and its fibreless mutant Xu142fl during early lint fiber initiation period. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30244

6 Samples

Download data: XLS

(Submitter supplied) We compared different days post-anthesis (5DPA, 10DPA, 15DPA and 25DPA) differentially expressed genes (DEGs) in fiber development between G. hirsutum and G. barbadense. In addition, we analysis the differentially expressed genes (DEGs) function using the database for annotation, visualization and integrated discovery (DAVID). Overall, gene expression pattern have significantly difference between G. more...

Organism:

Gossypium barbadense; Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16485 GPL19651

8 Samples

Download data: TXT

(Submitter supplied) ADC2 has a positive regulating effect on fiber elongation, which provides a basis for future cotton fiber development and research.

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL29713

6 Samples

Download data: TXT

(Submitter supplied) To explore the regulation mechanism of GhWRKY16 in fiber development, we performed a transcriptome deep sequencing (RNA-seq) analysis on 9 DPA fibers from wild type and GhWRKY16-RNAi seeds. We identified 2,186 differentially expressed genes (DEGs), consisting of 1,088 upregulated genes and 1,098 downregulated genes Gene ontology (GO) cluster analysis showed that the DEGs regulated by GhWRKY16 are classified in diverse molecular functions, cellular components and biological processes.

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL30129

9 Samples

Download data: TXT

(Submitter supplied) The fibers of cotton (Gossypium spp.) are a key agronomic resource. These fibers are made up of individual epidermal cells on the surface of the cotton seed which undergo a dramatic developmental shift, elongating into cells that are up to several centimeters long. Efforts to understand the causes of this shift has been hampered by the difficulty of isolating fiber cells from epidermal cells at the earliest stages of development. more...

Organism:

Gossypium hirsutum; Gossypium barbadense

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25504 GPL19231

16 Samples

Download data: TXT

(Submitter supplied) Through genome-wide comparative transcriptome analysis of 63 samples, the current study identified nine key genes and pathways associated with biological process of yield heterosis in upland cotton. Our results and data resources provide novel insights and will be useful for dissecting the molecular mechanism of yield heterosis in cotton.

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL23158

63 Samples

Download data: XLSX