GEO DataSets

(Submitter supplied) To gain novel insights into the molecular mechanisms underlying Pima cotton fiber quality, expression profiling of the Pima fiber transcriptome was performed as a function of development. The profiling was performed at 6 developmental time points: 8, 11, 14, 17, 21, and 24dpa. The expression profiling using long oligonucleotide microarray showed dynamic changes to the fiber transcriptome that correlate to morphogenesis, and biological cellular processes. more...

Organism:

Gossypium barbadense; Gossypium arboreum

Type:

Expression profiling by array

Platform:

GPL6917

6 Samples

Download data: TXT

(Submitter supplied) In order to study gene expression at the genomic level during elongation and secondary cell wall synthesis of upland cotton fiber, oligonucleotide microarrays were employed. RNA was isolated from fibers in 7 different time points beginning prior to peak fiber expansion, continuing through termination of fiber expansion and ending at peak cellulose synthesis (5, 8, 10, 14, 17, 21, and 24dpa). The arrays contained ~25,000 oligonucleotides representing ~12,200 genes designed from a fiber EST database during peak cell expansion. more...

Organism:

Gossypium hirsutum; Gossypium arboreum

Type:

Expression profiling by array

Platform:

GPL6917

6 Samples

Download data: TXT

(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 arboreum; Gossypium hirsutum; Gossypium raimondii

Type:

Expression profiling by array

Platform:

GPL8062

80 Samples

Download data: GPR

(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

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(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 barbadense; Gossypium hirsutum

Type:

Expression profiling by high throughput sequencing

Platforms:

GPL16485 GPL19651

30 Samples

Download data: FA, XLSX

(Submitter supplied) affy_cotton_2011_12 - affy_cotton_2011_12 - In this study we characterized the fiber transcriptomes of the two species, Gossypium hirsutum and Gossypium barbadense that were parental genotypes of a RIL mapping population used previously for phenotypic QTL and expression QTL mapping., We used 454 deep pyrosequencing to characterize cDNAs from developing fibers at two key developmental time-points; 10 and 22 days post anthesis. more...

Organism:

Gossypium barbadense; Gossypium raimondii; Gossypium hirsutum; Gossypium arboreum

Type:

Expression profiling by array

Platform:

GPL8672

4 Samples

Download data: CEL

(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 hirsutum; Gossypium barbadense

Type:

Expression profiling by array

Platform:

GPL4043

18 Samples

Download data: GPR

(Submitter supplied) Cotton is one of the most commercially important Fiber crops in the world and used as a source for natural textile Fiber and cottonseed oil. The fuzzless-lintless ovules of cotton mutants are ideal source for identifying genes involved in Fiber development by comparing with Fiber bearing ovules of wild-type. To decipher molecular mechanisms involved in Fiber cell development, transcriptome analysis has been carried out by comparing G. more...

Organism:

Gossypium hirsutum; Gossypium barbadense; Gossypium raimondii; Gossypium arboreum

Type:

Expression profiling by array

Platform:

GPL8672

30 Samples

Download data: CEL, CHP

(Submitter supplied) Sea-island cotton (Gossypium barbadense L.) has superior fiber quality properties such as length, fineness and strength, while Upland cotton (Gossypium hirsutum L.) is characterized by high yield. To reveal features of Upland cotton and Sea-island cotton fiber cells, differential genes expression profiles during fiber cell elongation and in secondary wall deposits were established using cDNA microarray technology. more...

Organism:

Gossypium barbadense; Gossypium hirsutum

Type:

Expression profiling by array

Platform:

GPL2610

15 Samples

Download data: TXT

(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) 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) Comparative analysis of transcriptome profiles of G. arboreum L. cv. and its fuzzy-lintless mutant (ANOI 1960) at 0 and 10 dpa. Cotton is one of the most commercially important fibre crops in the world and used as a source for natural textile fibre and cottonseed oil. The fuzzy-lintless ovules of cotton mutants are ideal source for identifying genes involved in fibre development by comparing with fibre bearing ovules of wild-type. more...

Organism:

Gossypium arboreum; Gossypium hirsutum; Gossypium raimondii; Gossypium barbadense

Type:

Expression profiling by array

Platform:

GPL8672

12 Samples

Download data: CEL, CHP

(Submitter supplied) exceptional example of evolutionary innovation is the single-celled seed trichome in Gossypium ("cotton fiber"). We have used fiber development in Gossypium as a system to understand how morphology can rapidly evolve. Fiber has undergone considerable morphological changes between the short, tightly adherent fibers of G. longicalyx and the derived long, spinable fibers of its closest relative, G. herbaceum, that facilitated cotton domestication. more...

Organism:

Gossypium hirsutum; Gossypium herbaceum; Gossypium barbadense; Gossypium raimondii; Gossypium arboreum; Gossypium longicalyx

Type:

Expression profiling by array

Platform:

GPL4808

48 Samples

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(Submitter supplied) Reactive oxygen species (ROS) play a prominent role in signal transduction and cellular homeostasis in plants. However, imbalances between generation and elimination of ROS can give rise to oxidative stress in growing cells. Because ROS are important to cell growth, ROS modulation could be responsive to natural or human-mediated selection pressure in plants. To study the evolution of oxidative stress related genes in a single plant cell, we conducted comparative expression profiling analyses of the elongated seed trichomes (‘‘fibers’’) of cotton (Gossypium), using a phylogenetic approach. more...

Organism:

Gossypium; Gossypium hirsutum; Gossypium arboreum; Gossypium raimondii; Gossypium tomentosum

Type:

Expression profiling by array

Platform:

GPL6989

18 Samples

Download data: CALLS, FTR, TXT

(Submitter supplied) The comparative analysis between 57-4 and Pima S-1 identified 284 genes in anthers and 1,864 genes in ovules as being differentially expressed in the semigametic genotype. Based on gene functions, 127 differentially expressed genes were common to both semigametic anthers and ovules, with 115 being consistently differentially expressed in both tissues. Nine of those genes were selected for qRT-PCR analysis, seven of which were confirmed. more...

Organism:

Gossypium hirsutum; Gossypium barbadense; Gossypium raimondii; Gossypium arboreum

Type:

Expression profiling by array

Platform:

GPL8672

4 Samples

Download data: CEL

(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

Download data

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

Organism:

Gossypium hirsutum

Type:

Expression profiling by array

Platform:

GPL4739

6 Samples

Download data: XLS