GEO DataSets

(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) 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 barbadense; Gossypium hirsutum; Gossypium arboreum; Gossypium raimondii

Type:

Expression profiling by array

Platform:

GPL8672

89 Samples

Download data: CEL, CHP

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

Organism:

Gossypium hirsutum; Gossypium arboreum; Gossypium raimondii; Gossypium barbadense

Type:

Expression profiling by array

Platform:

GPL8672

30 Samples

Download data: CEL, CHP

(Submitter supplied) Transcriptome analysis in cotton during fibre development stages. To study the molecular response of drought stress in cotton under field condition global gene expression analysis was carried out at fibre development stages (0, 5, 10 and 20 dpa/Days post anthesis). Gossypium hirsutum cv. Bikaneri Nerma was used for the gene expression analysis. Cotton plants were subjected to drought stress at peak flowering stage. more...

Organism:

Gossypium barbadense; Gossypium raimondii; Gossypium hirsutum; Gossypium arboreum

Type:

Expression profiling by array

Platform:

GPL8672

24 Samples

Download data: CEL, CHP

(Submitter supplied) Transcriptome analysis in cotton under drought stress. To study the molecular response of drought stress in cotton under field condition global gene expression analysis was carried out in leaf tissue. Gossypium hirsutum cv. Bikaneri Nerma was used for the gene expression analysis. Cotton plants were subjected to drought stress at peak flowering stage. Leaf samples were collected when the soil moisture content was 19.5% which is 50% of the normal control plots. more...

Organism:

Gossypium barbadense; Gossypium raimondii; Gossypium hirsutum; Gossypium arboreum

Type:

Expression profiling by array

Platform:

GPL8672

6 Samples

Download data: CEL, CHP

(Submitter supplied) Purpose: found out the regulated genes of nulliplex-branch and its forming molecular mechanism Methods: shoot apical mRNA and miRNA in two nulliplex branch and two normal branch cotton of three development stages were generated by deep sequencing, in triplicate, using Illumina HiSeq 2000. Results: we found 3 825 and 353 specific stage differnent expressed genes in pre-budding stage of island cotton and upland cotton, respectively. more...

Organism:

Gossypium barbadense; Gossypium hirsutum

Type:

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

Platforms:

GPL16485 GPL19651

72 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) Cotton fiber ESTs were generated from 7-10 dpa fibers from the diploid species, Gossypium arboreum L. cv. AKA8401, at the Cotton Functional Genomic Center (CFGC) at the University of California-Davis (UCD) (cfgc.ucdavis.edu). A Unigene (UG)/Non-redundant (NR) set of 13,947 quality-controlled consensus sequences that define the cotton fiber transcriptome during rapid fiber elongation was assembled by Arpat et al 2004. more...

Organism:

Gossypium arboreum

2 Series

12 Samples

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(Submitter supplied) Website: http://cottongenomecenter.ucdavis.edu/production.asp

Organism:

Gossypium hirsutum

Download data

(Submitter supplied) We used a next-generation sequencing approach, Illumina Digital Gene Expression II (DGEII) technology, to Genome-wide profiling of gene expression during somatic (SE) and zygotic embryo (ZE) development. As a result, 4242 differentially expressed genes (DEGs) were identified between SE and ZE. Expression pattern cluster and functional classification analysis of the differentially expressed genes revealed that large number of genes indicative of response to stress highly expressed in somatic embryos. more...

Organism:

Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platform:

GPL16485

6 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:

Gossypium hirsutum; Arabidopsis thaliana

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) We explored the transcriptomic alterations associated with domestication by interrogating a developmental time course of cotton fibers from the wild G. hirsutum var. yucatanense and a representative of an elite domesticated line.

Organism:

Gossypium; Gossypium hirsutum

Type:

Expression profiling by array

Platform:

GPL6989

30 Samples

Download data: TXT

(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 raimondii; Gossypium hirsutum; Gossypium arboreum

Type:

Expression profiling by array

Platform:

GPL8062

40 Samples

Download data: GPR

(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) 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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(Submitter supplied) 10584 spot Cotton Ovule cDNA MicroArray Protocol: The cotton ovule cDNA microarray comprised a total of 10,410 PCR amplified inserts from cDNA clones. The PCR amplified inserts were purified using ethanol, sodium acetate precipitation. The PCR amplicons were re-suspended in 10 micro liters of 50% DMSO. Quality control of the amplified products was done by separation on agarose gels containing EtBr. Spotting was performed using a VersArray ChipWriter Pro (BioRad) arrayer equipped with 24 Stealth Micro Spotting Pins SMP 3 (Telechem International Inc.). Samples were spotted onto CMT-GAPS II™ coated microarray slides (Corning). Post-printing slide processing was performed by baking the slides at 80 oC for 3 hours.

Organism:

Gossypium hirsutum

4 Series

65 Samples

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(Submitter supplied) The in-house print of the Cotton Array Version 2 was supplied by Dr. Z. Jeffrey Chen, The University of Texas at Austin, Institute for Cellular and Molecular Biology

Organism:

Gossypium hirsutum; Gossypium arboreum; Gossypium raimondii

2 Series

120 Samples

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