GEO DataSets

(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) 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) 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) 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) 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) see Vodkin et al., BMC Genomics 5:73 (2004) for details of cDNAs represented on the arrays and Thibaud-Nissen et al., Plant Physiol 132:118-136 (2003); Zou et al. Mol Plant Microbe Interat 18:1161-1174 (2005); Zabala and Vodkin, Plant Cell 17: 2619-2632 (2005) for use of cDNA arrays in soybean. Protocol: PCR amplified cDNA inserts printed with Genemachines Omnigrid

Organism:

Glycine max

6 Series

82 Samples

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(Submitter supplied) see Vodkin et al., BMC Genomics 5:73 (2004) for details of cDNAs represented and Thibaud-Nissan, et al., Plant Physiol 132: 118-136 (2003); and Zabala and Vodkin, Plant Cell 17: 2619-2632 (2005) for use of cDNA arrays in soybean Protocol: amplified cDNAs printed with Genemachines Omnigrid

Organism:

Glycine max

12 Series

191 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) 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) Transcriptome expression analysis in peanut to date has been limited to a relatively small set of genes and only recently have moderately significant number of ESTs has been released into the public domain. Utilization of these ESTs for the oligonucleotide microarrays provides a means to investigate large-scale transcript responses to a variety of developmental and environmental signals, ultimately improving our understanding of plant biology. more...

Organism:

Arachis hypogaea

Type:

Expression profiling by array

Platform:

GPL6661

12 Samples

Download data: TXT

(Submitter supplied) From a set of 15 standard, normalized or full-length cDNA libraries, we generated 139 007 3'- or 5'-end sequenced ESTs, representing more than one-third of the c. 385 000 publicly available Populus ESTs. Clustering and assembly of 107 519 3'-end ESTs resulted in 14 451 contigs and 20 560 singletons, altogether representing 35 011 putative unique transcripts, or potentially more than three-quarters of the predicted c. more...

Organism:

Populus trichocarpa x Populus deltoides; Populus

Type:

Expression profiling by array

Platform:

GPL5921

10 Samples

Download data: TIFF

(Submitter supplied) Corning UltraGaps Protocol: The 15,496 clones from 14 poplar cDNA libraries (Ralph et al., 2006) were selected based on a CAP3 assembly (Huang and Madan, 1999; 95% identity and 40 bp overlap) of ca. 37,000 high-quality 3’ ESTs (i.e. longest available EST sequence from each putative unique transcript). Following in silico selection of candidates, clones were robotically rearrayed from daughter glycerol stock 384-well plates into 96-well plates prefilled with 7% glycerol in LB + ampicillin, incubated overnight at 37°C, and checked for uniform optical density. more...

Organism:

Populus

8 Series

158 Samples

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(Submitter supplied) Global gene expression was compared between root RNA samples from three-week-old Arabidopsis Col-0 plants subjected to 0.1% oxygen (balance nitrogen) or ambient atmospheric conditions.

Organism:

Arabidopsis thaliana

Type:

Expression profiling by array

Platform:

GPL198

4 Samples

Download data: CEL

(Submitter supplied) Several custom made Agilent arrays were hybridized to select the best 60-mers for the transcriptional profiling of C. acetobutylicum strains. Keywords: Test of 60-mer performance

Organism:

Clostridium acetobutylicum ATCC 824; Clostridium acetobutylicum

Type:

Expression profiling by array

Platforms:

GPL4030 GPL4029 GPL3820

12 Samples

Download data: TXT

(Submitter supplied) Set up and modification of Agilent standard protocols for a new custom 60-mer array for C. acetobutylicum. Keywords: Test of platform and protocols

Organism:

Clostridium acetobutylicum; Clostridium acetobutylicum ATCC 824

Type:

Expression profiling by array

Platform:

GPL4029

10 Samples

Download data: TXT

(Submitter supplied) In the present study, we were interested in gene expression changes in the pectoralis muscle of juvenile king penguins during the transition from terrestrial to marine life. Strictly terrestrial during their first year after hatching, king penguin chicks must then depart to sea to reach nutritional emancipation and pectoralis muscle is largely involved in penguin adaptation to the marine environment. more...

Organism:

Gallus gallus; Aptenodytes patagonicus

Type:

Expression profiling by array

Platform:

GPL3213

7 Samples

Download data: CEL