GEO DataSets

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

Type:

Expression profiling by array

Platform:

GPL8672

12 Samples

Download data: CEL, CHP

(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 arboreum; Gossypium hirsutum; Gossypium barbadense; Gossypium raimondii

Type:

Expression profiling by array

Platform:

GPL8672

4 Samples

Download data: CEL

(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) 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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(Submitter supplied) Comment: This is the second version of the cotton nucleotide platform. Three independently designed sets of IDT (Coralville, IA, USA) oligonucleotides are included on this microarray platform. The first set of 1,152 oligonulceotides were designed by the Chen lab formerly located at Texas A&M. A second set of 12,006 oligonucleotides was designed by the Wendel lab located at Iowa State University. The third set of oligonucleotides (9,629) was designed by The Institute for Genomic Research (TIGR) in collaboration with the Chen Lab at The University of Texas using the latest TIGR cotton EST assembly (CGI8). Version 1 (GEO# GPL4305) included dual spotted oligonucleotides from only the first two sets of oligonucleotides. We have not distinguished which features were specifically designed from each of the different Gossypium species because all probes were designed from an assembly of Gossypium ESTs. An effort to do so may have been misleading, since all probes are expected to hybridize equally well to homologs across the different species, due to their limited coding sequence divergence. The oligo probes have been annotated with GenBank accession identifiers based on any one of the following criteria. 1) GB_ACC: A probe was specifically designed to target a particular mRNA with associated GenBank accession identifier. 2) GB_LIST1: A high quality alignment (length >= 60 and percent identities >= 92%) to a member of either the ESTother or nt databases. 3) GB_LIST2: A high quality alignment (length >= 60 and percent identities >= 92%) to a contig member of the estinformatics (http://www.estinformatics.org/) assembly for Gossypium (assembly date: 12/31/2006). These annotations are based on EST membership in the aligned contig and not on direct high quality alignment to any member EST. Therefore, the number of associated accessions can be quite large. A number of probes failed to meet any of these criteria and, therefore, have not been annotated with GenBank accession identifiers. However, their available information can be accessed at http://cottonevolution.info/microarray. Protocol: An aliquot of 384-well plates from all three sets (see description) of oligonucleotides was hydrated in water and diluted to the printing concentration with 3X SSC. A single spot of each oligo from a single pin-dip was printed on each Corning epoxy slide at the Washington University Microarray Core facility using a locally constructed linear servo arrayer (after the DeRisi model, http://derisilabs.ucsf.edu/). After printing, slides were allowed to dry in 50-70% humidity for 12-16 hrs at room temperature and subsequently cross-linked at 150 mJoules in a Strata-linker (Stratagene, Inc., La Jolla, CA, USA). Two slides from each print batch are assessed for quality using SpotCheck (Genetix). Batches of printed cotton microarrays and associated quality data are publicly available at http://cottonevolution.info.

Organism:

Gossypium barbadense; Gossypium hirsutum; Gossypium arboreum; Gossypium raimondii

2 Series

84 Samples

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(Submitter supplied) Comment: On this platform, we have not distinguished which features were specifically designed from each of the three different Gossypium species because all probes were designed from a single assembly of Gossypium ESTs. An effort to do so, may have been misleading since all probes are expected to hybridize equally well to homologs in all three species due to their limited coding sequence divergence. more...

Organism:

Gossypium hirsutum; Gossypium arboreum; Gossypium raimondii

2 Series

19 Samples

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(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) 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