GEO DataSets

(Submitter supplied) Two fiber tissues harvested 10 days post anthesis from upland cotton trees grown under the same green house conditions except for different seasons of the year were used for RNA extraction. Small RNA molecules under 30 bases were amplified and isolated from an agarose gel. The purified DNA was used directly for cluster generation and sequencing analysis using the Illumina Genome Analyzer according to the manufacturer's instructions. more...

Organism:

Gossypium hirsutum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9362

2 Samples

Download data: FASTA

(Submitter supplied) To examine expression of miRNAs in cotton fiber development, we employed miRNA microarrays and compared miRNA accumulation level in cotton fibers, cotton leaves and mutant fibers.

Organism:

Arabidopsis thaliana; Gossypium hirsutum

Type:

Non-coding RNA profiling by array

Platform:

GPL8814

36 Samples

Download data: TXT

(Submitter supplied) Cotton fibers are seed trichomes, and their development undergoes a series of rapid and dynamic changes from fiber cell initiation, elongation to primary and secondary wall biosynthesis and fiber maturation. Previous studies showed that cotton homologues encoding putative MYB transcription factors and phytohormone responsive factors were induced during early stages of ovule and fiber development. Many of these factors are targets of microRNAs (miRNAs). more...

Organism:

Gossypium hirsutum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL9362

4 Samples

Download data: TXT

(Submitter supplied) A gene expression profiling study on two major cotton species that are cultivated for fibre, Gossypium hirsutum (L.) and Gossypium barbadense (L.), at different stages during fibre development using a printed cDNA microarray was undertaken to identify potential candidate genes for manipulation to improve fibre quality. Keywords: Species comparison, development

Organism:

Gossypium barbadense; Gossypium hirsutum

Type:

Expression profiling by array

Platform:

GPL4043

18 Samples

Download data: GPR

(Submitter supplied) We have designed and implemented a novel NimbleGen microarray platform capable of measuring global gene expression in Gossypium species. This custom designed microarray features ~60mer generic probes those were created by first assembling EST contigs from G.arboreum, G.raimondii, and G. hirsutum libraries and has the ability to measure total gene expression. Protocol: Oligonucleotide arrays were synthesized by NimbleGen Systems, Inc by maskless array synthesis using a digital micromirror array-mediated,parallel synthesis process incorporating 5'-photoprotected phosphoramidites. more...

Organism:

Gossypium

4 Series

93 Samples

Download data: NDF, NGD

(Submitter supplied) Cotton is the most important economic crop that provides natural fibre and by-products such as oil and protein. The global gene expression could provide insight into the biological processes underlying growth and development, which involving suites of genes expressed with temporal and spatial controls by regulatory networks. Improvement of cotton fiber in yield and quality is the main goal for molecular breeding, but many previous research have been largely focused on identifying genes only in fibres, so that we ignore seed which may play an important role in the development of fibers. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19231

21 Samples

Download data: BW

(Submitter supplied) Background: Dwarf cottons are more resistant to damage from wind and rain and associated with stable, increased yields, and also desirable source for breeding the machine harvest varieties. In an effort to uncover the transcripts and miRNA networks involved in plant height, the transcriptome and small RNA sequencing were performed based on dwarf mutant Ari1327 (A1), tall-culm mutant Ari3697 (A3) and wild type Ari971 (A9) in Gossypium hirsutum. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL16485

6 Samples

Download data: FA, TXT

(Submitter supplied) Purpose: The goal of this experiment was to use RNA-seq to compare the two commercial cotton species Gossypium hirsutum and Gossypium barbadense and determine what transcripts may account for the better fiber quality in the latter. Methods: RNA was extracted from Gossypium barbadense or Gossypium hirsutum fibers at 10, 15, 18, 21, and 28 days post anthesis. Paired-end, 100-bp RNA-seq was performed on an Illumina HiSeq2000 and the reads were mapped to the Gossypium raimondii genome at www.phytozome.net and non-homologous contig assemblies from Gossypium arboreum. more...

Organism:

Gossypium hirsutum; Gossypium barbadense

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL19651 GPL16485

30 Samples

Download data: FA, XLSX

(Submitter supplied) Cotton fiber were used for the expression analysis at different developmental stages Affymetrix Cotton Genome array were used for the global profiling of gene expression of cotton fiber at different developmental stages

Organism:

Gossypium raimondii; Gossypium hirsutum; Gossypium arboreum; Gossypium barbadense

Type:

Expression profiling by array

Platform:

GPL8672

89 Samples

Download data: CEL, CHP

(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) DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites via distinct pathways. Cotton is an allotetraploid consisting of two progenitor genomes. Each cotton fiber is a rapidly-elongating cell derived from the ovule epidermis, but the molecular basis for this developmental transition is unknown. Here we analyzed methylome, transcriptome, and small RNAome and revealed distinct changes in CHH methylation during ovule and fiber development. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing; Methylation profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19231

21 Samples

Download data

(Submitter supplied) DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites. CHH methylation is established by the small RNA-directed DNA methylation (RdDM) pathway. Cotton is an allotetraploid consisting of two progenitor genomes, and each cotton fiber is a rapidly-elongating cell from the ovule epidermis. Here we show that inhibiting DNA methylation impairs fiber development. more...

Organism:

Gossypium hirsutum

Type:

Methylation profiling by high throughput sequencing

Platform:

GPL19231

6 Samples

Download data: TXT

(Submitter supplied) DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites. CHH methylation is established by the small RNA-directed DNA methylation (RdDM) pathway. Cotton is an allotetraploid consisting of two progenitor genomes, and each cotton fiber is a rapidly-elongating cell from the ovule epidermis. Here we show that inhibiting DNA methylation impairs fiber development. more...

Organism:

Gossypium hirsutum

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL19231

9 Samples

Download data: TXT

(Submitter supplied) DNA methylation is essential for plant and animal development. In plants, methylation occurs at CG, CHG, and CHH (H = A, C or T) sites. CHH methylation is established by the small RNA-directed DNA methylation (RdDM) pathway. Cotton is an allotetraploid consisting of two progenitor genomes, and each cotton fiber is a rapidly-elongating cell from the ovule epidermis. Here we show that inhibiting DNA methylation impairs fiber development. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL19231

6 Samples

Download data: TXT