GEO DataSets

(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) 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) The purpose of this experiment was to identify any genes differentially expressed between the Soybean Near Isogenic Lines iron efficient Clark and iron inefficient IsoClark under iron sufficient hydroponic conditions. These genes would represent constituative genetic differences between the NILs. Keywords: Near Isogenic Line Comparison of Unstressed Soybean Plants

Organism:

Glycine max

Type:

Expression profiling by array

Platform:

GPL3015

6 Samples

Download data: TXT

(Submitter supplied) This experiment was designed to identify candidate genes related to iron deficiency chlorosis in soybeans that are differentially expressed between near isogenic lines developed for their differential tolerance to low iron conditons. Keywords: Stress Response Analysis

Organism:

Glycine max

Type:

Expression profiling by array

Platform:

GPL1013

6 Samples

Download data: GPR

(Submitter supplied) Background The soybean (Glycine max) cotyledon is a specialized tissue whose main function is to serve as a nutrient reserve that supplies the needs of the young plant throughout seedling development. During this process the cotyledons experience a functional transition to a mainly photosynthetic tissue. To identify at the genetic level the specific active elements that participate in the natural transition of the cotyledon from storage to photosynthetic activity, we studied the transcript abundance profile at different time points using a new soybean oligonucleotide chip containing 19,200 probes (70-mer long). more...

Organism:

Glycine max

Type:

Expression profiling by array

Platform:

GPL4635

48 Samples

Download data: GPR

(Submitter supplied) A maize array was fabricated with 5,376 unique expressed sequence tag (EST) clones sequenced from 4-day-old roots, immature ears and adult organ cDNA libraries. To elucidate organ relationships, relative mRNA levels were quantified by hybridization with embryos, three maize vegetative organs (leaf blades, leaf sheaths and roots) from multiple developmental stages, husk leaves and two types of floral organs (immature ears and silks). more...

Organism:

Zea mays

Type:

Expression profiling by array

Platform:

GPL12

24 Samples

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(Submitter supplied) A maize array fabricated with 5,376 unique expressed sequence tag (EST) clones sequenced from 4-day-old roots, immature ears and adult organ cDNA libraries. mRNA source: Zea mays strain with genetic background K55 (75%), W23 (20%), Robertson's Mutator (5%).

Organism:

Zea mays

1 Series

24 Samples

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(Submitter supplied) 9,216 single-spotted cDNA clones from embryo, seed coat, flower and whole pod libraries Keywords = soybean

Organism:

Glycine max

5 Series

131 Samples

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(Submitter supplied) Background: To understand gene expression networks leading to functional properties of the soybean seed, we have undertaken a detailed examination of soybean seed development during the stages of major accumulation of oils, proteins, and starches, as well as the desiccating and mature stages, using microarrays consisting of up to 27,000 soybean cDNAs. Results: It was discovered that genes related to cell growth and maintenance processes, as well as energy processes like photosynthesis, decreased in expression levels as the cotyledons approached the mature, dry stage. more...

Organism:

Glycine max

Type:

Expression profiling by array

Platforms:

GPL229 GPL1012 GPL1013

48 Samples

Download data: GPR

(Submitter supplied) Isolation of genes from Aspergillus nidulans grown in different complex carbohydrates by NSH and the NSH method was evaluated by using single channel non competitive slide based hybridizations Keywords = NSH Keywords = subtraction Keywords = aspergillus Keywords = polysaccharide Keywords = exopolygalacturonase Keywords: repeat sample

Organism:

Aspergillus nidulans

Type:

Expression profiling by array

Platform:

GPL566

21 Samples

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(Submitter supplied) By sequencing 36 cDNA libraries with Illumina technology, we identified genes differentially expressed in soybean plants in response to water deficit and genes that were either up- or down-regulated in different periods of the day. Of 54,175 predicted soybean genes (Glyma v1.1), 35.52% exhibited expression oscillations in a 24 h period. This number increased to 39.23% when plants were submitted to water deficit. more...

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

36 Samples

Download data: TXT, XLS

(Submitter supplied) This study was designed to identify candidate genes associated with iron efficiency in soybeans. Two genotypes, Clark (PI548553) and IsoClark (PI547430), were grown in both iron sufficient (100uM Fe(NO3)3) and iron deficient (50uM Fe(NO3)3) hydroponics conditions. The second trifoliate was harvested for RNA extraction for the microarray experiment. Candidate genes were identified by comparing gene expression profiles within genotypes between the two iron growth conditions. more...

Organism:

Glycine max

Type:

Expression profiling by array

Platform:

GPL4592

11 Samples

Download data: CEL

(Submitter supplied) Examination of soybean hypocotyls, G. max cv. Harosoy (Rps7), at 3, 6, 12, 24 and 48 hours after inoculation with P. sojae, race 2, isolate P6497 Patterns of Gene Expression Upon Infection of Soybean Plants by Phytophthora sojae. P. Moy, D. Qutob, B. P. Chapman, I. Atkinson, and M. Gijzen. Pages 1051-1062. Publication no. M-2004-0728-01R. Molecular Plant-Microbe Interactions, October 2004, Volume 17, Number 10. more...

Organism:

Glycine max; Phytophthora sojae

Type:

Expression profiling by array

Platform:

GPL1206

50 Samples

Download data: TIFF

(Submitter supplied) Purpose: Comprehensive comparison of gene-expression profiles between 3mlpa (mutant with low phytic acid) and 3MWT (non-mutant with normal phyic acid) soybean lines (Glycine max) at five stages of seed development using RNA-Seq approaches. Methods: mRNA sequencing reads (101SE) were generated in triplicate from five seed developmental stages of 3mlpa and 3MWT soybean line using Illumina HiSeq 2000. Results: A total of 4235 differentially expressed genes, including 512-transcription factor genes were identified. Eighteen biological processes such as apoptosis, glucan metabolism, cellular transport, photosynthesis and 9 transcription factor families including WRKY, CAMTA3 and SNF2 were enriched during seed development. Genes associated with apoptosis, glucan metabolism, and cellular transport showed enhanced expression in early stages of lpa seed development, while those associated with photosynthesis showed decreased expression in late developmental stages. Conclusion: This study provides a global perspective of transcriptomal changes during soybean seed development in 3mlpa mutant. The results suggest that low phtic acid-causing mutations in 3mlpa play a role in inducing and suppressing plant defense responses during early and late stages of seed development, respectively.

Organism:

Glycine max

Type:

Expression profiling by high throughput sequencing

Platform:

GPL15008

30 Samples

Download data: TXT, XLSX

(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) This is a chicken multi-tissue cDNA microarray with 12752 elements. It comprises clones from chicken EST collections generated by BBSRC, University of Delaware and the Fred Hutchinson Cancer Research Center. Sequence information is available from GenBank for all features on the array. Protocol: The clone-set was amplified in 96 well plates and re-arrayed into a 384-well Montage (Millipore) filtration plate to isolate the amplified DNA products. more...

Organism:

Gallus gallus

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(Submitter supplied) Background The application of microarray technology to functional genomic analysis in the chicken has been limited by the lack of arrays containing large numbers of genes. Results We have produced cDNA arrays using chicken EST collections generated by BBSRC, University of Delaware and the Fred Hutchinson Cancer Research Center. From a total of 363,838 chicken ESTs representing 24 different adult or embryonic tissues, a set of 11,447 non-redundant ESTs were selected and added to an existing collection of clones (4,162) from immune tissues and a chicken bursal cell line (DT40). more...

Organism:

Gallus gallus

5 Series

60 Samples

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(Submitter supplied) Common bean (Phaseolus vulgaris) and soybean (Glycine max) both belong to the Phaseoleae tribe and share significant coding sequence homology. To evaluate the utility of the soybean GeneChip for transcript profiling of common bean, we hybridized cRNAs purified from nodule, leaf, and root of common bean and soybean in triplicate to the soybean GeneChip. Initial data analysis showed a decreased sensitivity and specificity in common bean cross-species hybridization (CSH) GeneChip data compared to that of soybean. more...

Organism:

Glycine max; Phaseolus vulgaris

Type:

Expression profiling by array

Platform:

GPL4592

18 Samples

Download data: CEL