GEO DataSets

(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) 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) 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) MicroRNAs (miRNAs) are endogenous non-coding ~21 nucleotide (nt) RNAs that regulate gene expression at transcriptional and post-transcriptional levels in plants and animals. They play an important role in development, abiotic stress responses or pathogen responses. miRNAs with their related target genes have been widely studied in model plants，and increasing studies have been performed on some crops，however, the number of identified miRNAs in cotton was limited, and global identification of related targets through degradome sequencing has not been developed previously. more...

Organism:

Gossypium hirsutum

Type:

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

Platform:

GPL16101

4 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

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(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

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

Organism:

Gossypium hirsutum

Type:

Expression profiling by array

Platform:

GPL4739

6 Samples

Download data: XLS

(Submitter supplied) A method was developed to isolate RNA from 1 dpa fiber. ESTs derived from this and other cotton mRNAs were sequenced and assembled into contigs. Contigs composed of EST unique to libraries of interest and unique singletons were represented on a microarray. Microarrays were hybridized with labed nucleic acids derived from 10 dpa fiber and 1 dpa fiber to identify genes differentially regulated during fiber initiation and fiber elongation. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by array

Platform:

GPL4739

3 Samples

Download data: XLS

(Submitter supplied) A method was developed to isolate RNA from 1 dpa fiber. ESTs derived from this and other cotton mRNAs were sequenced and assembled into contigs. Contigs composed of EST unique to libraries of interest and unique singletons were represented on a microarray. Microarrays were hybridized with labed nucleic acids derived from whole 1 dpa ovules and 1 dpa fiber to identify genes differentially regulated during fiber initiation. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by array

Platform:

GPL4739

3 Samples

Download data: XLS

(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:Identification of genes and miRNAs responsible for salt tolerance in upland cotton (Gossypium hirsutum L.) would help reveal the molecular mechanisms of salt tolerance. We performed physiological experiments and transcriptome sequencing (mRNA-seq and small RNA-seq) of cotton leaves under salt stress using Illumina sequencing technology. And quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis Methods:We investigated two distinct salt stress phases—dehydration (4 h) and ionic stress (osmotic restoration; 24 h)—that were identified by physiological changes of 14-day-old seedlings of two cotton genotypes, one salt tolerant and the other salt sensitive, during a 72-h NaCl exposure. more...

Organism:

Gossypium hirsutum

Type:

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

Platform:

GPL16485

12 Samples

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(Submitter supplied) In this study, it is noticeable that 32 tea-specific miRNAs were confirmed on the base of genome survey, using deep sequencing and microarray hybridization, and many miRNAs might associate with secondary metabolites synthesis.

Organism:

Camellia sinensis

Type:

Non-coding RNA profiling by high throughput sequencing

Platform:

GPL20107

1 Sample

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 barbadense; Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL25504 GPL19231

16 Samples

Download data: TXT

(Submitter supplied) Cycloheximide treatment of cotton ovules Keywords: Antibiotic Treatment

Organism:

Gossypium hirsutum

Type:

Expression profiling by array

Platform:

GPL3035

6 Samples

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(Submitter supplied) Transcriptional profiling of cotton fiber cells from two cotton germplasm lines, MD 52ne and MD 90ne. Comparison of fiber cell transcription profiles is between the two germplasm lines and over a developmental time-course from 8 to 24 days post anthesis in four day intervals.

Organism:

Gossypium hirsutum; Gossypium raimondii; Gossypium arboreum

Type:

Expression profiling by array

Platform:

GPL8062

80 Samples

Download data: GPR

(Submitter supplied) Transcriptional profiling of cotton ovule cells. Comparison of expression of genes in cultured ovules (-1 DPA) treated with or without phytohormones (5um IAA and 1um GA) and over a time-course from 0 to 12 hours.

Organism:

Gossypium hirsutum; Gossypium arboreum; Gossypium raimondii

Type:

Expression profiling by array

Platform:

GPL8062

40 Samples

Download data: GPR

(Submitter supplied) Cotton ovule development, mutant vs wild type, Comparisons of DP16 0 dpa ovule Keywords: WildType vs Mutant

Organism:

Gossypium hirsutum

Type:

Expression profiling by array

Platform:

GPL3035

41 Samples

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(Submitter supplied) DP16 ovules of -4, -2, 2 dpa compared to 0 dpa Keywords: Time Course

Organism:

Gossypium hirsutum

Type:

Expression profiling by array

Platform:

GPL3035

15 Samples

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