title: Expression data of Soybean root apical meristem and leaf

status: Public on May 31 2011

city: Melbourne

first: farzad

last: haerizadeh

state: VIC.

address: University of Melbourne

department: land & food

country: Australia

institute: Melbourne University

summary:
we used soybean genome chips to investigate the expression pattern of about 37,500 unique ESTs locating on soybean Affymetrix chips (Affymetrix Inc.).
KEYWORDS: Tissue comparison

overall_design: we compared soybean root meristem samples with non-meristematic tissues in 10 days old vegetative stage seedlings to define a unique set of root meristem enriched genes.

first: Farzad

last: Haerizadeh

first: Prem

last: Bhalla


title: Impact of adcR delation on the transcriptome of Streptococcus pneumoniae D39 in the presence of Zinc

status: Public on May 13 2011

city: STOCKHOLM

first: Sulman

last: Shafeeq

address: nobel vag 16

department: MTC

country: Sweden

institute: Karolinska Institutet

summary: Transcriptome comparison of the Streptococcus pneumoniae D39 ΔadcR to D39 wild-type grown in CDM plus 0.2mM Zn2+.

overall_design: One condition design comparison of two strains including a dye swap

first: Tomas

middle: G

last: Kloosterman

first: Oscar

middle: P

last: Kuipers


status: Public on Oct 04 2010

city: Birmingham

first: Dongquan

last: Chen

state: AL

address: 1717 11th Ave South

department: Medicine

country: USA

institute: Univ of Alabama at Birmingham

summary:
Gene expression profiling in soybean under aluminum stress: mechanisms of magnesium amelioration of aluminum toxicity at gene expression level.
Micro-molar concentrations of magnesium in culture solution has been shown to ameliorate Al toxicity in soybean and other leguminous species. Different theories have been proposed to explain the chemical mechanisms of how the two ions interact to neutralize the toxic effect of aluminum in the plant root system. To understand the molecular mechanisms of the phenomenon at the gene expression level in soybean, we undertook a comparative transcriptome analysis in Al-tolerant and Al-sensitive genotypes treated with aluminum alone or aluminum plus magnesium using DNA microarrays. The results revealed magnesium enhances Al-tolerance level in the Al-tolerant genotype by down-regulating genes commonly induced in response to Al toxicity. We hypothesized that the magnesium-mediated alleviation of Al toxicity in the Al-tolerant genotype emanates from reduction in energy expenditure of gene expression induced in response to Al stress. Conversely, magnesium appears to ameliorate Al toxicity in the sensitive genotype by dual mechanisms of increasing the expression level of several genes involved in Al-tolerance and decreasing the expression level of most genes.
Keywords: Soybean, aluminum toxicity, magnesium, transcriptome

overall_design: Two genotypes: PI 416937 (p) and Young (y); two treatments: Aluminum (Al) or Al+magnesium (Mg); two time points: 12 and 72 hrs; 3 replicates.

first: K

middle: M

last: Soliman

first: D

last: Duressa


title: Genotyping human lymphoblastoid cell lines

status: Public on Aug 27 2010

city: Edinburgh

first: Nick

last: Gilbert

address: Crewe Rd South

department: Institute of Genetics and Molecular Medicine

country: United Kingdom

institute: The University of Edinburgh

summary: Genotyping FATO and SATO3 human lymphoblastoid cell lines

overall_design: Single samples prepared from SATO3 and FATO cells


title: Soybean root hair cell response to Bradyrhizobium japonicum inoculation

status: Public on Sep 16 2010

city: Columbia

first: Marc

last: Libault

state: MO

address: 1201 Rollins Street

department: Plant Sciences

institute: University of Missouri

summary: Soybean root hair transcriptional response to their inoculation by the symbiotic bacteria B. japonicum involved in soybean nodulation.  We used the first generation of an Affymetrix microarray to quantify the abundance of the transcripts from soybean root hair cells inoculated and mock-inoculated by B. japonicum. This experiment was performed on a time-course from 6 to 48 hours after inoculation.

overall_design: Soybean seeds were sowed on sterile agar medium and grown for 3 days in a growth chamber before being treated with H2O (mock-inoculated) or B. japonicum (inoculated). Soybean root hair cells were isolated at different time points (6hr, 12hr, 18hr, 24hr, 36hr, 48hr) after treatment. For each time point and condition, 3 or 4 independent biological replicates were produced.

first: M

first: L

last: Brechenmacher

first: J

last: Drnevich

middle: D

last: Bilgin

middle: J

last: Neece

first: S

last: Clough

first: G

last: Stacey


title: Expression of the Stress-Related Genes for Glutathione S-Transferase and Ascorbate Peroxidase in the Most-Glycinin-Deficient Soybean Cultivar Tousan205 during Seed Maturation.

status: Public on Jun 04 2010

city: Bunkyo-ku yayoi

first: Tomoyo

last: Narikawa

state: Tokyo

country: Japan

institute: University of Tokyo

summary:
Global analyses on gene expression profiles in two soybean species, Nanahomare and Tamahomare was performed using DNA microarray technique.  Nanahomare is glycinin deficient species, and is high in free amino acid content.  Tamahomare is parent species of Nanahomare.
In Nanahomare, stress related genes glutathione S-transferase and ascorbate peroxidase had higher expression than in Tamahomare, which suggests glycinin-deficiency caused stress in soy seeds, and that it lead Nanahomare to increase in free amino acid content.
Keywords: storage protein deficiency

overall_design: Soybean seeds were selected at two stages of Bean 5mm and Full-size for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain difference in gene expression between two species and find out which gene's or gene group's expression changes.


title: Microarray Analysis of Phytophthora sojae Gene Expression During  Early Infection

status: Public on Jul 19 2010

city: Blacksburg

first: sucheta

last: Tripathy

state: VA

address: 1, Washington street

department: Virginia  Bioinformatics Institute

institute: Virginia Tech

summary: P.sojae isolate P6954 - that is nearly identical with strain P6947 with the only exception that P6954 expresses Avr1b during infection is used in this study. 2 days post culture, P.sojae mycelia are inoculated onto 9 day old soybean hypocotyls of highly susceptible cultivar Sloan that were grown under natural sunlight inside a green house. Infected samples were harvested after 0, 3, 6 and 12 hours.

overall_design: We analyzed 12 soybean arrays.

first: Adriana

last: Ferrera

first: Sucheta

first: Brett

last: Tyler


title: Characterization of gene expression profile in developing soybean seeds by DNA microarray

status: Public on Jan 05 2011

summary:
Gene expression profiles in soybean seeds at 4 developmental stages, pod, bean 2 mm, bean 5 mm, and full-sized bean, were examined by DNA microarray analysis. Total genes of each samples were classified into 4 clusters according to developmental stages. Differentially expressed genes (DEGs) were extracted by comparing their expression in two adjacent stages, by using the rank product method.
To characterize the gene expression during seed development, DEGs were sorted into 8 clusters by the hclust function, according to gene expression patterns.
Keywords: time course

overall_design: Soybean seeds were selected at successive stages of early development for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain transitional changes in gene expression during seed develpment.


title: Comparative physiology and transcriptional networks underlying the heat shock response in Populus trichocarpa, Arabidopsis thaliana and Glycine max [Soy]

status: Public on Apr 01 2011

city: Oak Ridge

first: David

last: Weston

state: TN

department: Environmental Sciences Division

institute: David Weston

summary: The heat shock response continues to be layered with additional complexity as interactions and cross-talk among heat shock proteins, the reactive oxygen network and hormonal signaling are discovered. However, comparative analyses exploring variation in each of these processes among species remains relatively unexplored. In controlled environment experiments, photosynthetic response curves were conducted from 22 °C to 42 °C and indicated that temperature optimum of light saturated photosynthesis was greater for Glycine max relative to Arabidopsis thaliana or Populus trichocarpa. Transcript profiles were taken at defined states along the temperature response curves and inferred pathway analysis revealed species-specific variation in the abiotic stress and the minor carbohydrate raffinose/galactinol pathways. A weighted gene co-expression network approach was used to group individual genes into network modules linking biochemical measures of the antioxidant system to leaf-level photosynthesis among P. trichocarpa, G. max and A. thaliana. Network enabled results revealed an expansion in the G. max HSP17 protein family and divergence in the regulation of the antioxidant and heat shock module relative to P. trichocarpa and A. thaliana. These results indicate that although the heat shock response is highly conserved, there is considerable species-specific variation in its regulation.

overall_design: fully expanded leaf samples from 4 randomly collected plants per species were harvested at 4 physiological states as determined from prior gas exchange measurements (growth temperature - baseline, photosynthetic optimum, 20% inhibition of optimum and 30% inhibition of optimum).This resulted in 16 separate samples hybridized to independent microarrays totaling 4 – replicates x 4 physiological states).


title: Circadian clock controlled gene expression in soybean seeds

status: Public on Jun 21 2010

city: West Lafayette

first: Karen

middle: A

last: Hudson

state: IN

address: 915 West State Street

department: Crop Production and Pest Control

institute: USDA-ARS

summary: Microarray expression profiling was used to identify genes expressed in developing soybean (Glycine max) seeds that are controlled by the circadian clock. Plants with developing seeds were entrained to 12hour light: 12 hour dark cycles and sampled in constant light conditions.

overall_design: Soybean seeds entrained to 12 hour-light:12 hour dark photocycles were harvested after 24 hours of constant light and temperature conditions. Timepoint 24h represents subjective dawn. To minimize developmental variation, flowers were marked as they opened and seeds were harvested from marked pods after 5 weeks. There are two replicate samples at each time point, and each sample consists of 8 seeds collected from three diffferent plants.


title: Global transcriptome profiling of wild soybean (Glycine soja) roots under NaHCO3 treatment

status: Public on Aug 14 2010

city: Harbin

first: Yanming

last: Zhu

state: Heilongjiang

address: Wood Street 59

department: Life sciences

country: China

institute: Northeast Agriculture University

summary:
Plant roots are the primary site of perception and injury for saline-alkaline stress. The current knowledge of the saline-alkaline stress transcriptome is most focused on salt (NaCl) stress. Only a little alkaline (NaHCO3) stress transcriptome is limited to one time point after stress. Time-course analysis and comparative investigation on roots in the alkaline stress condition are needed to understand the gene response networks that are subject to alkaline tolerance.
We used microarrays to detail the global programme of gene expression underlying NaHCO3 treatment and identified distinct classes of regulated genes during this process.

overall_design: Three week old Glycine soja seedling roots from 3cm root apex were harvested in two independent biological replicates after 0, 0.5, 1, 3, 6, 12 and 24h treatment with 50mmol/L NaHCO3 stress for RNA extraction and hybridization on Affymetrix microarrays. To minimize biological variance, roots from three plants originating from the same experiment, condition and cultivar was pooled.

first: Ying

last: Ge

first: Yong

last: Li

first: De-Kang

last: Lv

first: Yan-Ming


title: Alterations in soybean gene expression profile after foliar application of lipo-chitooligosaccharide (LCO) from Bradyrhizobium japonicum under sub-optimal temperature

status: Public on Mar 20 2010

city: Ste-Anne-de-Bellevue

last: Wang

state: Quebec

address: 21111 Lakeshore Road

department: Dept. of Plant Science

country: Canada

institute: McGill University/MacDonald Campus

summary: Lipo-chitooligosaccharides (LCOs) produced by N2-fixing rhizobacteria initiate host nodule formation.  Foliar application of LCOs has been shown to induce stress-related genes under optimal growth conditions.  To study the effects of LCO foliar spray under stressed conditions, soybean seedlings grown at optimal temperature were exposed to sub-optimal temperature.  After a 5-day acclimation period, the first trifoliolate leaves were sprayed with 10-7 M LCO (NodBj-V (C18:1, MeFuc)) produced by Bradyrhizobium japonicum, and harvested at 0 and 48 h following treatment.  Microarray analysis was performed using Affymetrix GeneChip® Soybean Genome Arrays.  A total of 147 genes were differentially expressed 48 h after LCO treatment, including a number of stress-related genes and transcription factors.  In addition, during the 48 h following treatment, hundreds of genes were differentially expressed in LCO-treated plants, indicating that the dynamic soybean foliar transcriptome was highly responsive to LCO treatment.  The microarray data was supported by quantitative real-time PCR data.

overall_design: Soybean seedlings grown at optimal temperature (25 °C) were exposed to sub-optimal temperature (15 °C).  After a 5-day acclimation period, the first trifoliolate leaves were sprayed with 10-7 M LCO (NodBj-V (C18:1, MeFuc)) produced by Bradyrhizobium japonicum, and harvested at 0 and 48 h following treatment.  Total RNA was extracted and microarray analysis was performed using Affymetrix GeneChip® Soybean Genome Arrays.

first: Donald

middle: L

last: Smith


title: Dynamic transcriptomic profiles of zebrafish gills in response to zinc depletion

status: Public on May 20 2010

city: Cardiff

first: Peter

last: Kille

address: Park Place

department: Cardiff School of Biosciences

institute: Cardiff University

summary: Zinc deficiency is detrimental to organisms highlighting its role as an essential micronutrient contributing to numerous biological processes. To investigate the underlying molecular events invoked by zinc depletion we performed a temporal analysis of transcriptome changes observed within zebrafish gill. This tissue represents a model system for studying ion absorption across polarised cells as it provides a major pathway for fish to acquire zinc directly from water whilst sharing a conserved zinc transporting system with mammals. Zebrafish were treated with either zinc-depleted (water = 2.61 μg L-1; diet = 26 mg kg-1) or zinc-adequate (water = 16.3 μg L-1; diet = 233 mg kg-1) conditions for two weeks. Gill samples were collected at five time points and transcriptome changes analysed in quintuplicate using a 16K oligonucleotide array.

overall_design: Global transcript levels were measured in zebrafish gills using a oligonucleotide array either zinc-depleted or zinc-adequate diet. Gill samples were collected at five time points and transcriptome changes analysed in quintuplicate using a 16K oligonucleotide array

first: Dongling

last: Zheng

first: Graham

last: Feeney

first: Phil

last: Cunningham

first: Richard

last: Handy

first: Christer

last: Hogstrand


title: Expression data of Soybean (Glycine max) roots from different iron treatments.

status: Public on Sep 06 2010

city: St. Paul

first: Carroll

last: Vance

state: MN

address: 1991 Upper Buford Circle, 411 Borlaug Hall

department: Agronomy and Plant Genetics

institute: USDA-ARS, University of Minnesota

summary:
Two Near Isogenic soybean (Glycine max) lines were grown in hydroponic conditions with either 50uM ferric nitrate or 100uM ferric nitrate.  After 10 days, half the plants were harvested (total root tissue).  At 12 days after planting, iron was added to plants grown in low iron conditions bringing them up to sufficient iron growth conditions.  Root tissue was harvested for the remaining plants at 14 days after planting.
Gene expression analysis from root tissue of two Near Isogenic Lines (NILs), Clark (PI548553) and IsoClark (PI547430), grown in iron stress or iron stress recovered conditions.

overall_design: A total of 24 samples from four growth conditions, three biological replicates per treatment

first: Randy

middle: C

last: Shoemaker

first: Robert

last: Stupar

first: Jamie

last: O'Rourke

first: Bruna

last: Bucciarelli


title: Gene expression in Phytophthora sojae mycelia, germinating zoospores, and during infection of soybean hypocotyls

status: Public on Jun 22 2009

city: London

first: Mark

last: Gijzen

state: Ontario

address: 1391 Sandford Street

institute: Agriculture and Agri-Food Canada

summary:
Total RNA extracted from Phytophthora sojae (strain P6497) and infected soybean hypocotyls (cultivar Harosoy) provided template for synthesis of cDNA probes used in the microarray hybridizations. Infected plant hypocotyls were sampled 6 h, 12 h, 24 h, and 48 h after inoculation. Mycelia were grown on synthetic media (H&S) or vegetable juice media (V8). Zoospores were sampled at 0 h, 2 h and 6 h after inducing encystment and germination by agitation.
We used microarrays to characterize gene expression patterns in the root rot pathogen Phytophthora sojae and its host Glycine max.

Keywords: infection time course, zoospore germination time course, media formulation response

sample_organism:
Glycine max
Phytophthora sojae

overall_design: 28 samples from 9 treatments; 2 to 5 biological replicates per treatment.

first: Dinah

last: Qutob


title: Transcriptional profiling of root-knot nematode induced feeding sites in cowpea (Vigna unguiculata L. Walp)

status: Public on Feb 01 2009

city: RIVERSIDE

first: Sayan

last: Das

state: CA

address: 900 University Avenue

department: Botany and Plant Sc.

institute: University of California-Riverside

summary: In this study we have looked at the transcriptome profile of both incompatible and compatible cowpea-RKN interaction for two different time points using the Affymetrix soybean GeneChip. This is the first study of this kind in cowpea-RKN interaction. This study provides a broad insight into the Rk-mediated resistance in cowpea and creates an excellent dataset of potential candidate genes involved in both nematode resistance and parasitism, which can be further tested for their role in this biological process using functional genomics approaches. our results have shown that the root-knot nematode resistant pathway is still partially suppressed at 9 days post inoculation in resistant cowpea root. There is indication that subtle variation of ROS concentration, induction of toxins and other defense related genes play a role in this unique resistance mechanism. Further functional analysis of these differentially expressed genes will help us to understand this intriguing plant-nematode interaction in a more precise manner.

overall_design: Seeds of CB46 (resistant) and null-Rk (susceptible) cowpea genotypes were surface sterilized using 10% (v/v) bleach solution and were planted in growth pouches. Plants were grown under controlled environmental conditions of 26.7°C ± 0.5°C constant temperature and daily light/dark cycles of 16/8 hours. This temperature was used because it lies within the optimum temperature range of 26 – 28 °C for development and reproduction of M. incognita on cowpea in growth pouches. Each pouch was inoculated with 3000 J2 in 5 ml of deionized water, 12 days after planting (dap). Equal number of pouches was mock inoculated with 5 ml of deionized water to use as control. Nematode infected root tissue was excised using a sterile scalpel at 3 days post inoculation (dpi) and 9 dpi respectively under a magnifying glass and flash frozen immediately in liquid nitrogen. Approximately equal amount of root tissue was also excised and flash frozen from the control plants. The harvested tissue was stored in -80°C until RNA isolation. For 9 dpi samples 3 biological replicates were used for each treatment. So total number of soybean GeneChips used for 9dpi samples was 12. For 3 dpi samples two biological replicates were used for each treatment and a total of 8 GeneChips were used. Expression signals were first analyzed in Microarray Suite 5.0 software (MAS 5, Affymetrix Inc.) to determine the “present” probe set list. The detection algorithm uses probe pair intensities to generate a detection p-value and assign a “present”, “marginal”, or “absent” call. Each probe pair in a probe set has a potential vote in determining whether the measured transcript is or is not “present”.  The vote is described by the discrimination score (R). R is calculated for each probe pair and compared to a predefined threshold, Tau. Probe pairs with R higher than Tau vote “present” and the voting result is summarized as a p-value. The greater the number of discrimination scores (R) that are above Tau, the smaller the p-value and the more likely the given transcript is truly present in the sample. Only probe sets with a “present” call in all three replicates of at least one treatment was considered to be “expressed”.

first: Jeffrey

last: Ehlers

first: Timothy

last: Close

first: Philip

last: Roberts


title: Genome-wide analysis of gene expression in the soybean shoot apical meristem

status: Public on Feb 20 2009

city: Parkville

first: Chui

middle: E

last: WONG

state: Victoria

department: Land and Food

institute: University of Melbourne

summary:
The shoot apical meristem (SAM) contains undifferentiated stem cells that are responsible for the initiation of above-ground organs, and eventually the general architecture of the plant. To gain insight into the nature of genetic programs and the regulatory networks underlying SAM function in soybean, we have used Affymetrix soybean GeneChip® to investigate the transcript profiles associated with micro-dissected SAMs or axillary meristems (AMs). While the microarray data disclosed the conservation of transcriptional signature between the two types of meristems, subsequent comparison of SAM transcript profile with that of non-meristem (NM) tissue revealed a total of 1090 and 1523 transcripts that are significantly up- or down-regulated in the SAM. Further in situ hybridization analysis on selected transcripts has implicated their roles in SAM maintenance and the establishment of organ polarity. We also identified a gene that could potentially serve as a novel marker that distinguishes the differentiating cells in the meristem from the pluripotent stem cells. Along with many unknowns, transcripts with putative annotation have also been identified that has allowed us to infer SAM regulatory roles for various families of transcription factors as well as products associated with auxin-mediated responses, cell division and proliferation, epigenetic regulation, miRNA regulation and protein turnover. Computational analysis on the promoter regions of Arabidopsis orthologs of genes with high expression in the soybean SAM revealed a conserved over-representation of three cis-acting regulatory motifs. Our microarray data thus represents a rich source of target genes for further study into the meristem function and maintenance.
Keywords: meristem transcript profile

overall_design: A total of six microarray hybridization experiments were performed to obtain transcript profiles of the three tissues with the incorporation of two independent biological replicates.

first: Farzad

last: Haerizadeh

last: Wong

first: Mohan

middle: B

last: Singh

first: Prem

last: Bhalla


title: Storage Protein Suppression in Transgenic Soybean Cotyledons

status: Public on Nov 01 2008

first: monica

last: schmidt

address: 975 n. warson

institute: danforth center

summary: Suppression of both endogenous storage proteins in soybean cotyledons was accomplished by RNAi.  Microarray analysis was used to compare 3 samples, 1 nontransgenic control, 2 transgenic biological replicates.

overall_design:
3 samples.  Each sample had 2 technical replicates.
1. Control, nontransgenic
2. RNAi transgenic for storage protein suppression
3. Second RNAi transgenic for storage protein suppression, independent line from the first sample

first: Monica

last: Schmidt

first: Eliot

last: Herman


title: Transcript profiling of common bean using the Soybean Genome Array: optimizing analysis by masking biased probes

status: Public on Mar 01 2010

city: St Paul

first: Sam

last: Yang

address: 411 Upper Buford Circle

department: ARS

institute: USDA

summary: 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. We employed a method that masked putative probes targeting inter-species variable (ISV) regions between common bean and soybean. A masking signal intensity threshold was selected that optimized both sensitivity and specificity. After masking for ISV regions, the number of differentially-expressed genes identified in common bean was increased by about 2.8-fold reflecting increased sensitivity. Quantitative RT-PCR analysis of a total of 20 randomly selected genes and purine-ureides pathway genes demonstrated an increased specificity after masking for ISV regions. We also evaluated masked probe frequency per probe set to gain insight into the sequence divergence pattern between common bean and soybean. The results from this study suggested that transcript profiling in common bean can be done using the soybean GeneChip. However, a significant decrease in sensitivity and specificity can be expected. Problems associated with CSH GeneChip data can be mitigated by masking probes targeting ISV regions. In addition to transcript profiling CSH of the GeneChip in combination with masking probes in the ISV regions can be used for comparative ecological and/or evolutionary genomics studies.

sample_organism:
Glycine max
Phaseolus vulgaris

overall_design: We hybridized cRNA purified from nodule, leaf, and root of common bean and soybean in, triplicate, to the soybean GeneChip (18 GeneChip hybridizations = 2 species x 3 organs x 3 replicates).

first: S

middle: S

first: Oswaldo

last: Valdés-López

first: Wayne

last: Xu

first: John

middle: W

last: Gronwald

first: Georgina

last: Hernández

first: Carroll

last: Vance


title: Genomic Expression Profiling of Mature Soybean (Glycine max) Pollen

status: Public on Mar 26 2009

summary:
Background: Pollen, the male partner in the reproduction of flowering plants, comprises either two or three cells at maturity. The current knowledge of the pollen transcriptome is limited to the model plant Arabidopsis thaliana, which has tri-cellular pollen grains at maturity.
Comparative studies on pollen of other genera, particularly crop plants, are needed to understand the pollen gene networks that are subject to functional and evolutionary conservation. In this study, we used the Affymetrix Soybean GeneChip® to perform transcriptional profiling on mature bi-cellular soybean pollen.

Results: Compared to the sporophyte transcriptome, the soybean pollen transcriptome revealed a restricted and unique repertoire of genes, with a significantly greater proportion of specifically expressed genes than is found in the sporophyte tissue. Comparative analysis shows that, among the 37,500 soybean unique transcripts addressed in this study, 10,299 genes
(27.46%) are expressed in pollen. Of the pollen-expressed genes, about 9,489
(92.13%) are also expressed in sporophytic tissues, and 810 (7.87%) are selectively expressed in pollen. Overall, the soybean pollen transcriptome shows an enrichment of transcription factors (mostly zinc finger family proteins), cell cycle-related transcripts, signal recognition receptors, ethylene responsive factors, chromatin remodeling factors, and members of the ubiquitin proteasome proteolytic pathway. Moreover, we identify several new pollen-specific candidate genes that might play a significant role in pollen biology.

Conclusion: This is the first report of a soybean pollen transcriptional profile. These data extend our current knowledge regarding regulatory pathways that govern the gene regulation and development of pollen. We also demonstrate that pollen is a rich store of regulatory proteins that are essential and sufficient for de novo gene expression. A comparison between transcription factors up-regulated in soybean and those upregulated in Arabidopsis revealed some divergence in the numbers and kinds of regulatory proteins expressed in both species.

overall_design: GeneChip Soybean Genome array (Affymetrix, Inc.) containing 37,500 unique transcript (probe) was used in this study. Three biological replicates for pollen and two biological replicates for sporophytic tissues (GSM236910 and GSM237070) were used

first: Peter

last: Gresshoff


title: Analysis of Iron Deficiency in Soybean Leaf Tissue

status: Public on Sep 01 2009

city: Ames

first: Randy

last: Shoemaker

state: IA

address: 100 Osbourne Dr. G401

department: Agronomy

institute: Iowa State University

summary:
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.
Keywords: Stress Response

overall_design: This experiment was designed to compare expression profiles of Clark grown in iron sufficient and deficient iron conditions and of IsoClark grown in the same conditions.  Plants grown in iron sufficient conditions were used as controls and plants grown in iron deficient conditions were considered experimental.  For the Clark genotype, There were two biological replicates of iron deficient plants, and three biological replicates of iron sufficient plants.  The IsoClark genotype had three biological replicates for both iron sufficient and deficient conditions.

first: Jamie

last: O'Rourke

first: Michelle

last: Graham


title: Gene expression profiling implicates novel hormonal regulation of the floral initiation process in soybeans

status: Public on Jan 17 2009

first: Chui

last: WONG

summary:
The transition to flowering is characterized by a shift of the shoot apical meristem (SAM) from leaf production to the initiation of a floral meristem.  In this study, we addressed the nature of SAM gene networks involved in the early floral initiation process in the crop legume soybean. Unique aspects (such as pod development and nitrogen fixation) of legume development make them appealing for plant development studies. Soybean, a major oilseed crop, possesses varied maturity groups; hence, understanding and unravelling initial transition control has implications in manipulating crop yield. To this end, we performed global gene expression analysis using Affymetrix® soybean GeneChip® with RNA isolated from micro-dissected soybean SAMs at various time points after plants were shifted from long-day to short-day growth conditions. Analysis of the resulting microarray data revealed a total of 331 transcripts that have differential expression profiles. Intriguingly, about 20% of the transcripts affected by the switch in the development program have orthologs reported to be responsive to abscisic acid (ABA), suggesting an increase in ABA levels in the SAM during this developmental change. A subsequent immunoassay verified this, thereby implicating its possible function as an endogenous signal during the floral evocation process. The striking occurrence of abiotic stress-related transcripts, including trehalose metabolism genes, in SAMs during the early transition to floral meristems points to an overlap of abiotic stress and floral signalling pathways in soybean.  In addition, other hormones - auxin, jasmonic acid and brassinosteroids - and a number of candidate protein kinases may also act in the signalling process prior to or concurrently with the induction of the putative floral homeiotic transcripts. This indicates that molecular events mediated by multiple hormonal pathways are part of the mechanism employed by soybean to regulate the floral transition process.
Keywords: transcript profiling floral transition soybean shoot apical meristem

overall_design: SAMs were micro-dissected from soybean plants under the dissecting microscope at 40x magnification. Any leaf primordia were excluded in order to create a meristem-enriched tissue collection. Approximately 70 SAMs were dissected for each time point (0 SD, 1 SD, 2 SD, 4 SD and 6 SD). Two independent biological replicates were incorporated.


title: Detection and Validation of Single Feature Polymorphisms in Cowpea  using a Soybean Genome Array

status: Public on Feb 21 2008

first: Sayan

last: Das

summary:
Background:
Cowpea (Vigna unguiculata L. Walp) is an important food and fodder legume of the semiarid tropics and subtropics worldwide, especially in sub-Saharan Africa. High density genetic linkage maps are needed for marker assisted breeding but are not available for cowpea. A single feature polymorphism (SFP) is a microarray-based marker which can be used for high throughput genotyping and high density mapping.
Results:
Here we report detection and validation of SFPs in cowpea using a readily available soybean (Glycine max) genome array. Robustified projection pursuit (RPP) was used for statistical analysis using RNA as a surrogate for DNA. Using a 15% outlying score cut-off, 1058 potential SFPs were enumerated between two parents of a recombinant inbred line (RIL) population segregating for several important traits including drought tolerance, Fusarium and brown blotch resistance, grain size and photoperiod sensitivity. Sequencing of 25 putative polymorphism-containing amplicons yielded a SFP probe set validation rate of 68%.
Conclusions:
We conclude that the Affymetrix soybean genome array is a satisfactory platform for identification of some 1000's of SFPs for cowpea. This study provides an example of extension of genomic resources from a well supported species to an orphan crop. Presumably, other legume systems are similarly tractable to SFP marker development using existing legume array resources.

Keywords: Polymorphism discovery, array based genotyping

overall_design:
Expression data were generated by hybridizing cowpea cRNA to the soybean genome array. A statistical method called robustified projection pursuit (RPP) was used for Single Feature Polymorphism(SFP) analysis. Only the values from the PM probes were utilized. The use of RNA as a surrogate for genomic DNA eliminated interference from highly repetitive DNA as a technical impediment to SFP detection. An important aspect of the RPP method is that it first utilizes a probe set level analysis to identify SFP-containing probe sets and then chooses individual probes from within each SFP-containing probe set. The net result is the identification of probes that directly overlay polymorphic sequences.

Separate comparisons were made between two genotypes (with two replicates each) for unstressed and drought stressed treatments, resulting in two SFP lists. In the context of SFPs, there is no necessity to have separate stress and control lists; in fact it would be simpler and less costly to have only one SFP list from highly complex RNA made by blending stressed and unstressed RNA.  In our case, two separate lists were available as a consequence of another study not described here which compared gene expression patterns in stressed and control plants (data not shown). At 15% outlying score cut-off, we detected 488 SFP probes in stressed and 661 SFP probes in unstressed treatments. The union of these two lists contained 1058 SFP probes and the intersection contained 91. A total of 37 primer pairs targeting 37 putative SFP probe sets were initially tested, of which 25 yielded single amplicons of the expected sizes from both parents. These 25 amplicons targeted 14 probe sets selected from the intersection of the two SFP probe set lists and 11 from the remaining SFP probe sets. 9 of the 14 SFP probe sets (64%) from the intersection list were validated at the DNA sequence level and 8 of the other 11 (73%) were validated.

first: Prasanna

middle: R

last: Bhat

first: Xinping

last: Cui

first: Chinta

last: Sudhakar

first: Jeffrey

last: Ehlers

first: Steve

last: Wanamaker

first: Philip

last: Roberts

first: Timothy

last: Close


title: Expression survey of Rpp1 soybean line PI200492 resistant to P. pachyrhizi

status: Public on Jan 31 2008

city: Ft. Detrick

first: katherine

last: schneider

state: MD

address: 1301 Ditto Ave

department: FDWSRU

summary:
Affymetrix soybean genome arrays were used to identify genes differentially expressed in the immune resistance response at 6, 12, 24, and 48 hours after inoculation with Phakopsora pachyrhizi isolates TW72-1 or HW94-1
soybean + HW94-1 = resistant;  soybean + TW72-1 = susceptible
Keywords: time course

overall_design: For each of 4 time points (6, 12, 24 and 48 hours post inoculation) a soybean PI200492 plant was inoculated with 2 treatments: HW94-1, or TW72-1.  A mock inoculation was performed and sampled at time 0.    There were three biological replicates of the entire experiment, for a total of 27 samples.  During data analysis two samples failed the quality control metrics and were removed from the analysis, leaving 25 samples in the final data set.

first: Katherine

middle: T

last: Schneider

first: Jane

last: Choi

first: Nadim

last: Alkharouf

first: Nicole

last: Lum

first: David

last: Munroe

first: Benjamin

middle: F

last: Matthews

first: Reid

last: Frederick


title: Expression data from soybean seed compartments with embryos at the early maturation stage

status: Public on Jun 19 2007

city: Los Angeles

first: Bob

last: Goldberg

address: 610 Charles E Young Drive East

department: Molecular, Cell and Developmental Biology

institute: University of California, Los Angeles

summary:
We microdissected each compartment from 8-micron paraffin sections using the Leica LMD6000 system to identify all genes active in different compartments of a soybean seed containing a early maturation-stage embryo.
Keywords: cell type comparison

overall_design: early maturation-stage seed compartments were isolated using the Leica LMD6000 system. Total RNA was amplified and hybridized with Affymetrix Soybean Genome Arrays.

first: Shundai

last: Li

first: Chen

last: Cheng

first: Javier

last: Wagmaister

first: Anhthu

middle: Q

last: Bui

first: Brandon

middle: H

last: Le

first: Robert

first: John

last: Harada


title: Exploration of microarrays as tools to assess substantial equivalence of genetically modified soybeans

status: Public on Apr 15 2008

first: Martina

last: Stromvik

address: 21,111 Lakeshore Rd

department: Department of Plant Science

institute: McGill University

summary:
According to the Canadian Food Inspection Agency and Health Canada, genetically modified crops are considered safe if they are substantially equivalent to a conventional crop in regards to agronomic, physiological and compositional characteristics.  A recurring issue in safety assessment of genetically modified crops is the paucity of analytical methods to detect unintended or unexpected outcomes of genetic modification.  Traditional targeted compound comparative analyses are limited in scope and capacity to detect unintended changes in chemical composition.  This study explored the potential of using microarray technology to assess the substantial equivalence of gene expression profiles between genetically modified and conventional soybean cultivars.  Different pre processing methods were applied to the raw expression data from the arrays, and clustering methods were used to try and differentiate the genetically modified cultivars from the conventional cultivars.  Results showed that more variation existed between different strains of conventional cultivars than between conventional and genetically modified cultivars.

For more information, please see:  Cheng, K.C., Beaulieu, J., Iquira, E., Belzile, F.J., Fortin, M.G. and Strömvik, M.V. (2008). Effect of transgenes on global gene expression in soybean is within the natural range of variation of their conventional counterparts. Journal of Agricultural and Food Chemistry.
Keywords: Expression comparison between genetically modified cultivars

overall_design: Five samples (biological replicates) of total RNA from each of the five different soybean varieties were selected for hybridization to Affymetrix Soybean GeneChips, for a total of 25 chips (following total RNA integrity assessment).  Spike controls B2, bio-B, bio-C, bio-D and Cre-x were added to each hybridization cocktail.  Arrays were washed and stained in an Affymetrix Fluidics Station prior to scanning on the Affymetrix GeneChip Scanner 3000.  Image acquisition and processing was done with the Affymetrix Microarray Analysis Suite 5.0.

first: Keichin

first: Julie

last: Beaulieu

first: Marc

last: Fortin


title: Suppression of oleosin in soybean cotyledon

status: Public on Aug 15 2008

first: monica

last: schmidt

summary:
3 samples, 2 reps each. comparison of wildtype cotyledon to RNAioleosin transgenic
Using RNAi, the seed oil body protein 24-kDa oleosin has been suppressed in transgenic soybeans. The endoplasmic reticulum (ER) forms micro-oil bodies about 50 nm in diameter that coalesce with adjacent oil bodies forming a hierarchy of oil body sizes. The oil bodies in the oleosin knockdown form large oil body-ER complexes with the interior dominated by micro-oil bodies and intermediate-sized oil bodies, while the peripheral areas of the complex are dominated by large oil bodies. The complex merges to form giant oil bodies with onset of seed dormancy that disrupts cell structure. The transcriptome of the oleosin knockdown shows few changes compared to wild-type. Proteomic analysis of the isolated oil bodies of the 24-kDa oleosin knockdown shows the absence of the 24-kDa oleosin and the presence of abundant caleosin and lipoxygenase. The formation of the micro-oil bodies in the oleosin knockdown is interpreted to indicate a function of the oleosin as a surfactant.

overall_design: 2 biological replicates of transgenics, 2 technical replicates each

first: Monica

last: Schmidt

first: Eliot

last: Herman


title: Effect of foliar spray of lipo-chitooligosaccharide (Nod factor) on soybean leaf gene expression.

status: Public on Apr 03 2008

middle: K

last: Lindsay

address: 21111 Lakeshore Rd

department: Plant Science

summary:
Currently unpublished data suggested that the foliar application of the Bradyrhizobium japonicum Nod factor induced changes in hormone level and enzyme activity in soybean cv. OAC Bayfield. This study was designed to examine any possible differences in gene expression that occur as a result of the foliar treatment of Nod factor. The data herein are gene expression data of that experiment, from the sprayed, first trifoliolate leaf of each plant, 48 h after treatment.
Keywords: stress response

overall_design: This experimental design was a Completely Randomized Design (CRD), comparing 1 treatment (first trifoliolate leaf sprayed with 10^-7M LCO/Nod factor and 0.02% Tween 20) against a mock-treated control (first trifoliolate leaf sprayed with dH2O and 0.02% Tween 20). There are 3 replicates per treatment type, with a total of 6 samples for this experiment.

first: Donald

last: Smith


title: Expression data from soybean seed compartments with embryos at the cotyledon stage

status: Public on May 25 2007

summary:
We microdissected each compartment from 8-micron paraffin sections using the Leica LMD6000 system to identify all genes active in different compartments of a soybean seed containing a cotyledon-stage embryo.
Keywords: cell type comparison

overall_design: cotyledon-stage seed compartments were isolated using the Leica LMD6000 system. Total RNA was amplified and hybridized with Affymetrix Soybean Genome Arrays.


title: Expression data from soybean seed compartments with embryos at the globular stage

status: Public on Apr 26 2007

summary:
We microdissected each compartment from 6-micron paraffin sections using the Leica AS LMD system to identify all genes active in different compartments of a soybean seed containing globular-stage embryos.
Keywords: cell type comparison

overall_design: Globular-stage seed compartments were isolated using the Leica AS LMD system. Total RNA was amplified and hybridized with Affymetrix Soybean Genome Arrays.

first: Xingjun

last: Wang


title: Plant and pathogen gene expression during infection by P.sojae of 8 soybean cultivars varying in quantitative resistance

status: Public on Nov 09 2007

first: sucheta

last: Tripathy

summary:
Identify plant and pathogen genes differentially expressed during P. sojae infection of soybean cultivars differing in quantitative resistance, by using Affymetrix Soybean Genome Array analysis.
Keywords: genotypic variation on quantitative resistance

overall_design:
RNA samples from mock-inoculated soybean tissue contain 2%-16% spike-in RNA from Phytophthora sojae mycelium grown in liquid sucrose-salts medium.

4 Experimental Replicates x 8 cultivars x  2 Treatments (inoculated or mock) x 2 Timepoints (72hr or 120hr)  = 128 samples in total

first: Brett

last: Tyler

first: Saghai

last: Maroof

first: Ann

last: Dorrance

first: Ina

last: Hoeschele

first: Steve

last: Martin


title: Expression data from SRB embryo regions at the globular stage

status: Public on Apr 27 2007

first: Bob

last: Goldberg

summary:
We microdissected each embryo region from 6-micron paraffin sections using the Leica AS LMD system to identify all genes active in different embryo region of an SRB seed containing globular-stage embryos.
Keywords: cell type comparison

overall_design: Globular-stage embryo regions were isolated using the Leica AS LMD system. Total RNA was amplified and hybridized with Affymetrix Soybean Genome GeneChip Arrays.

first: Anhthu

last: Bui

first: Brandon

last: Le

first: Robert


title: Expression data from soybean seed compartments with embryos at the heart stage

status: Public on Apr 20 2007

summary:
We microdissected each compartment from 8-micron paraffin sections using the Leica AS LMD system to identify all genes active in different compartments of a soybean seed containing a heart-stage embryo.
Keywords: cell type comparison

overall_design: heart-stage seed compartments were isolated using the Leica AS LMD system. Total RNA was amplified and hybridized with Affymetrix Soybean Genome Arrays.

first: Javier

last: Wagmaister

first: Shundai

last: Li

first: Chen

last: Cheng

first: John

last: Harada


title: Expression patterns in time and space during P.sojae infection of soybean cultivars differing in quantitative resistance

status: Public on Nov 26 2007

summary:
Four selected soybean genotypes with varying degrees of quantitative resistance that were well-characterized were selected for this study. These included two resistant genotypes (V71-370, Conrad), and two susceptible genotypes (Sloan, and VP-RIL9). A P. sojae isolate, PT2004C2.S1 , which is virulent to the soybean genotypes carrying Rps1a, Rps1b, Rps1k, Rps2, Rps3a, Rps3c, Rps4, Rps5, Rps6, or Rps7, was used in this study.
Keywords: Genotypic variation on quantitative resistance

overall_design:
The experiment was repeated four times.
Factors assayed included:

Genotype: 4 genotypes (V71-370, Conrad, Sloan, and VP-RIL9)
Treatment: pathogen-inoculated vs. mock-inoculated
Sampling time: 1, 2, 3 and 5dpi
Sampling sites: Upper section and Lower section (for 3dpi and 5dpi pathogen-inoculated samples only) vs whole section (for all the mock-inoculated samples at all time points, and the inoculated samples at 1and 2dpi).

first: B

first: S

first: A

first: I


title: Gene expression analysis in soybean with respect to Pahakopsora pachyrhizii at V2 growth stage

status: Public on Feb 22 2007

city: Knoxville

first: Dilip

middle: Raj

last: Panthee

address: 2431 Joe Johnson Dr.

institute: University of Tennessee

summary:
A small number of genes (25) expressed differentially with respect to Phakopsora pachyrhizii at V2 growth stage.
We used Affymetrix soybean microarrays to detail the global gene expression underlying host reaction to Phakopsora pachyrhizii and identified differentially expressed genes during this process.
Keywords: Infection by pathogen

overall_design: Soybean cv. 5601T plants were grown in greenhouse in six 4-liter pots. Three weeks old plants at V2 growth stage in three out of six pots were inoculated with Phakopsora pachyrhizi and remaining three pots were used as control. Leaf samples from all pots were collected 72 hours after inoculation and RNA was extracted using Tri-Regent. Microarray analysis was performed using Affymetrix platform.


title: B cell response to ELC and lipopolysaccharide treatment

status: Public on Feb 13 2004

city: Pasadena

first: Sangdun

last: Choi

address: 1200 E. California Blvd

department: Biology

institute: California Institute of Technology

summary:
Temporal analysis (60, 180, 360 min) of B cells treated with ELC alone, lipopolysaccharide alone or ELC and lipopolysaccharide (all in triplicates).
Keywords: other

first: Yun Anna

last: Cao

first: Mi Sook

last: Chang

first: Sun Young

last: Lee

first: Meghdad

last: Rahdar

last: Hsueh


title: Combined gene expression and QTL analysis of soybean quantitative resistance to Phytophthora sojae

status: Public on May 30 2008

first: sucheta

last: Tripathy

address: 1, Washington street

institute: Virginia Tech

summary: To identify soybean genes and QTLs associated with quantitative resistance to infection by the oomycete pathogen Phytophthora sojae, we conducted a very large-scale microarray experiment using 2522 Affymetrix GeneChips. The experiment involved assaying a total of 298 soybean recombinant inbred lines together with internal checks.

overall_design: A total of 298 soybean recombinant inbred lines (F12 RILs, labeled from R001 to R317) derived from a G. max (V71-370) and G. soja (PI407162) cross were assayed with two experimental replicates. 295 out of the 298 RILs were assayed in experimental replicate I, with the plants organized into 16 blocks, while in experimental replicate II 288 RILs were assayed in 13 blocks. Three soybean genotypes (V71-370, Sloan and VPRIL9) were included within each block as internal controls. Replicates of each set of the three controls, incubated in the same growth chamber, were harvested at three different times (approximately 9 am, 10:30 am, and 12 pm). A P. sojae isolate, PT2004C2.S1, which is virulent to the soybean lines carrying Rps1a, Rps1b, Rps1k, Rps2, Rps3a, Rps3c, Rps4, Rps5, Rps6, or Rps7, was used in this study. For each soybean line, approximately 30 seedlings were inoculated on the roots with P. sojae and after 5 days, 7.5 mm root segments were collected from immediately above and below the upper margin of the visible lesion (referred to as the "Upper" and "Lower" infection courts). From approximately 20 mock-inoculated plants, 15 mm root segments ("Mock") were collected from positions on the roots matching the lesions on the pathogen-inoculated plants.


title: Genotype, haplotype and copy number variation in worldwide human populations.

status: Public on Feb 05 2008

city: Bethesda

first: J Raphael

last: Gibbs

address: 35 Convent Drive, Bldg 35/1A1015, MSC3707

department: Computational Biology Core

institute: National Institutue on Aging, NIH

type:
Genome variation profiling by SNP array
SNP genotyping by SNP array

summary:
Genome-wide patterns of variation across individuals provide a powerful source of data for uncovering the history of migration, range expansion, and adaptation of the human species. However, high-resolution surveys of variation in genotype, haplotype and copy number have generally focused on a small number of population groups. Here we report the analysis and public release of high-quality genotypes at 525,910 single-nucleotide polymorphisms (SNPs) and 396 copy-number-variable loci in a worldwide sample of 29 populations. Analysis of SNP genotypes yields strongly supported fine-scale inferences about population structure. Increasing linkage disequilibrium is observed with geographic distance from Africa, as expected under a serial founder effect for an out-of-Africa spread of human populations. New approaches for haplotype analysis produce inferences about population structure that complement results based on unphased SNPs. Despite a difference from SNPs in the frequency spectrum of the copy-number variants (CNVs) detected—including a comparatively large number of CNVs in previously unexamined populations from Oceania and the Americas—the global distribution of CNVs largely accords with population structure analyses for SNP data sets of similar size. Our results produce new inferences about inter-population variation, support the utility of CNVs in human population-genetic research, and serve as a genomic resource for human-genetic studies in diverse worldwide populations.
Keywords: High Density SNP array

overall_design: We genotyped 513 individuals drawn from 29 populations of the Human Genome Diversity Panel (HGDP; http://www.cephb.fr/HGDP-CEPH-Panel/) using Illumina Infinium HumanHap550 Genotyping BeadChips (Illumina Inc., San Diego, CA, www.illumina.com).

first: Noah

last: Rosenberg

first: Andrew

last: Singleton