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    Results: 20

    1.

    RNA-Seq effectively monitors gene expression in Eutrema salsuginuem plants growing in an extreme natural habitat and in controlled growth cabinet conditions

    (Submitter supplied) Background: The investigation of extremophile plant species growing in their natural environment offers certain advantages, chiefly that plants adapted to severe habitats have a repertoire of stress tolerance genes that are regulated to maximize plant performance under physiologically challenging conditions. Accordingly, transcriptome sequencing offers a powerful approach to address questions concerning the influence of natural habitat on the physiology of an organism. more...
    Organism:
    Eutrema salsugineum
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL17514
    10 Samples
    Download data:
    GEO (TXT), SRA SRP028337
    Series
    Accession:
    GSE49378
    ID:
    200049378
    2.

    Transcriptomic and metabolomic analysis of Yukon Thellungiella plants grown in cabinets and their natural habitat

    (Submitter supplied) Background: Thellungiella salsuginea is an important model plant due to its natural tolerance to abiotic stresses including salt, cold, and water deficits. Microarray and metabolite profiling have shown that Thellungiella undergoes stress-responsive changes in transcript and organic solute abundance when grown under controlled environmental conditions. However, few reports assess the capacity of plants to display stress-responsive traits in natural habitats where concurrent stresses are the norm. more...
    Organism:
    Thellungiella
    Type:
    Expression profiling by array
    Platform:
    GPL2627
    12 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE41182
    ID:
    200041182
    3.

    Transcriptome sequencing and microarray design for functional genomics in the extremophile Arabidopsis relative Thellungiella salsuginea

    (Submitter supplied) Arabidopsis thaliana is not particularly stress tolerant and may lack protective mechanisms required to survive extreme environmental conditions. Thellungiella salsuginea has therefore attracted increasing interest as an alternative plant model species that possesses high tolerance of various abiotic stresses. While the T. salsuginea genome has recently been sequenced, its annotation is still far from complete and, due to the low number of ESTs available, evidence for actual transcriptional activity is lacking for most genes. more...
    Organism:
    Eutrema salsugineum; Arabidopsis thaliana
    Type:
    Expression profiling by array
    Platforms:
    GPL16263 GPL9020
    24 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE42156
    ID:
    200042156
    4.

    High-throughput sequencing of small RNA transcriptome reveals salt stressed regulated microRNAs in sugarcane

    (Submitter supplied) Salt stress is a primary cause of crop losses worldwide, and it has been the subject of intense investigation to unravel the complex mechanisms responsible for salinity tolerance. MicroRNA is implicated in many developmental processes and in responses to various abiotic stresses, playing pivotal roles in plant adaptation. Deep sequencing technology was chosen to determine the small RNA transcriptome of Saccharum sp cultivars grown on saline conditions. more...
    Organism:
    Saccharum hybrid cultivar SP70-1143
    Type:
    Non-coding RNA profiling by high throughput sequencing
    Platform:
    GPL16317
    4 Samples
    Download data:
    GEO (TXT), SRA SRP017293
    Series
    Accession:
    GSE42484
    ID:
    200042484
    5.

    RNA-Seq of Sorghum bicolor 9d seedlings in response to osmotic stress and abscisic acid

    (Submitter supplied) This study utilized next generation sequencing technology (RNA-Seq) to examine the transcriptome of sorghum plants challenged with osmotic stress and exogenous abscisic acid (ABA) to elucidate those genes and gene networks that contribute to sorghum's tolerance to water-limiting environments with a long-term aim of developing strategies to improve plant productivity under drought.
    Organism:
    Sorghum bicolor
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL13779
    24 Samples
    Download data:
    GEO (CSV), SRA SRP007361
    Series
    Accession:
    GSE30249
    ID:
    200030249
    6.

    Small RNA Solexa sequencing of 4 Plant Species in the Cucurbitaceae family

    (Submitter supplied) Total RNA was isolated from different tissues (leaf, stem and flesh, rind and placenta of the fruits) using TRIzol reagent and small RNA libraries were generated from four cucurbit species: bottle gourd (Lagenaria siceraria (accession Grif 1617 collection from India)), Cucurbita moschata (accession Grif 14244 Early Butternut) Cucurbita pepo (accession NSL98075 Table King), and watermelon (Citrullus lanatus var. more...
    Organism:
    Cucurbita pepo; Lagenaria siceraria; Cucurbita moschata; Citrullus lanatus subsp. vulgaris
    Type:
    Non-coding RNA profiling by high throughput sequencing
    4 related Platforms
    4 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE38176
    ID:
    200038176
    7.

    Gene expression biomarkers provide sensitive indicators of in planta nitrogen status in Maize

    (Submitter supplied) We have characterized the transcriptional response in Maize under limiting and sufficient nitrogen conditions, and have identified a set of genes whose expression profiles can quantitatively assess the response of plants to those conditions.
    Organism:
    Zea mays
    Type:
    Expression profiling by array
    Platform:
    GPL14616
    90 Samples
    Download data:
    GEO (CEL)
    Series
    Accession:
    GSE32361
    ID:
    200032361
    8.

    Analysis of the nitrate-responsive transcriptome of the Arabidopsis root

    (Submitter supplied) Nitrate and other nitrogen metabolites can act as signals that regulate global gene expression in plants. Adaptive changes in plant morphology and physiology triggered by changes in nitrate availability are partly explained by these changes in gene expression. Despite several genome-wide efforts to identify nitrate-regulated genes, no comprehensive study of the Arabidopsis root transcriptome under contrasting nitrate conditions has been carried out. more...
    Organism:
    Arabidopsis thaliana
    Type:
    Expression profiling by high throughput sequencing; Non-coding RNA profiling by high throughput sequencing
    Platform:
    GPL9062
    8 Samples
    Download data:
    GEO (TXT), SRA SRP018404
    Series
    Accession:
    GSE44062
    ID:
    200044062
    9.

    cDNA Microarray Analysis of Soybean NILs under Fe Sufficient Hydroponic Conditions

    (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:
    GEO (TXT)
    Series
    Accession:
    GSE7325
    ID:
    200007325
    10.

    cDNA Microarray Analysis of NILs under Fe Deficient Hydroponic Conditions

    (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:
    GEO (GPR)
    Series
    Accession:
    GSE7290
    ID:
    200007290
    11.

    The grapevine expression atlas reveals a deep transcriptome shift driving the entire plant into a maturation program

    (Submitter supplied) The first genome-wide transcriptomic atlas of grapevine (Vitis vinifera) is based on 54 diverse samples expressing ~93% of predicted grapevine genes. Pollen and senescent leaves have unique transcriptomes but microarray analysis grouped all other samples into vegetative/green or mature/woody categories based on maturity rather than organ identity. This fundamental transcriptome reprograming during maturation was highlighted by three distinct statistical approaches supported by gene coexpression analysis. more...
    Organism:
    Vitis vinifera
    Type:
    Expression profiling by array
    Platform:
    GPL13936
    162 Samples
    Download data:
    GEO (PAIR)
    Series
    Accession:
    GSE36128
    ID:
    200036128
    12.

    Genomic DNA hybridizations of Col-0, Tsu-1, and Kas-1 accessions of Arabidopsis thaliana

    (Submitter supplied) These data provide a basis for the detection of sequence based polymorphisms between the Col-1, Tsu-1, and Kas-1 accessions of Arabidopsis thaliana. The experimental data provides an initial characterization of differences among the accessions, as well as a means for improving gene expression studies with the filtering of SFP from arrays studies. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. more...
    Organism:
    Arabidopsis thaliana
    Type:
    Genome variation profiling by array
    Platform:
    GPL10050
    18 Samples
    Download data:
    GEO (CEL, TXT)
    Series
    Accession:
    GSE20340
    ID:
    200020340
    13.

    cRNA hybridizations of Tsu-1 and Kas-1 accessions of Arabidopsis thaliana under well-watered and mild soil drying

    (Submitter supplied) These data provide a basis for exploration of gene expression differences between physiologically extreme accessions of Arabidopsis thaliana. Recent studies have documented remarkable genetic variation among Arabidopsis thaliana accessions collected from diverse habitats and across its geographical range. Of particular interest are accessions with putatively locally adapted phenotypes – i.e., accessions with attributes that are likely adaptive under the climatic or habitat conditions of their sites of origin. more...
    Organism:
    Arabidopsis thaliana
    Type:
    Expression profiling by array
    Platform:
    GPL10050
    24 Samples
    Download data:
    GEO (CEL)
    Series
    Accession:
    GSE20339
    ID:
    200020339
    14.

    Transcriptome profiling of low temperature-treated cassava apical shoots reveals dynamic responses of a tropical plant to cold stress

    (Submitter supplied) Background: Cassava is an important tropical root crop adapted to a wide range of environmental stimuli such as drought and acid soils. Nevertheless, it is an extremely cold-sensitive tropical species. Thus far, there is limited information about gene regulation and signaling pathways related to the cold stress response in cassava. The development of microarray technology has accelerated the study of global transcription profiling under certain conditions. more...
    Organism:
    Manihot esculenta
    Type:
    Expression profiling by array
    Platform:
    GPL11271
    9 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE31073
    ID:
    200031073
    15.

    Effects of drought on gene expression in Maize reproductive and leaf meristem tissue revealed by RNA-seq

    (Submitter supplied) Purpose: To study the effects of drought at the transcriptomic level on two different actively dividing maize tissue: the ovaries, and the leaf meristem Methods: The Illumina reads were mapped to the maize B73 reference genome using Tophat followed by transcriptome reconstruction using Cufflinks. The FPKM valuse were extracted from cufflinks output and an R package called Limma was used to identify differentially expressed genes under drought under both tissues Results and Conclusions: Different processes which were differentially expressed under drought in both tissues were identified and analyzed in detail. more...
    Organism:
    Zea mays
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL13977
    8 Samples
    Download data:
    GEO (TXT), SRA SRP014792
    Series
    Accession:
    GSE40070
    ID:
    200040070
    16.

    Expression data of Arabidopsis thaliana wild-type plants and quadruple nas T-DNA insertion mutants grown under different Fe supply conditions

    (Submitter supplied) Essential metals such as iron are required for healthy plant growth. Fe is an important cofactor and catalytic element in many biological processes. Fe and other metals can also be toxic when present in excess. Therefore plants have mechanisms of metal homeostasis which involve coordination of metal ion transporters for uptake, translocation and compartmentalisation. The NAS genes are supposed to play an important role in Fe homeostasis. more...
    Organism:
    Arabidopsis thaliana
    Type:
    Expression profiling by array
    Platform:
    GPL198
    24 Samples
    Download data:
    GEO (CEL, CHP)
    Series
    Accession:
    GSE24348
    ID:
    200024348
    17.

    Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and Nrl-/- Retinal Transcriptomes

    (Submitter supplied) Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goals of this study are to compare NGS-derived retinal transcriptome profiling (RNA-seq) to microarray and quantitative reverse transcription polymerase chain reaction (qRT–PCR) methods and to evaluate protocols for optimal high-throughput data analysis. Methods: Retinal mRNA profiles of 21-day-old wild-type (WT) and neural retina leucine zipper knockout (Nrl−/−) mice were generated by deep sequencing, in triplicate, using Illumina GAIIx. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL11002
    6 Samples
    Download data:
    GEO (BAM, TXT, XLS), SRA SRP009096
    Series
    Accession:
    GSE33141
    ID:
    200033141
    18.

    Transcriptional Profiling Implicates Novel Interactions between Abiotic Stress and Hormonal Responses in Thellungiella

    (Submitter supplied) Thellungiella, an Arabidopsis-related halophyte, is an emerging model species for studies designed to elucidate molecular mechanisms of abiotic stress tolerance. Using a cDNA microarray containing 3628 unique sequences derived from previously reported libraries of stress-induced cDNAs of the Yukon ecotype of Thellungiella, we obtained transcript profiles of its response to drought, cold, high salinity and re-watering after drought. more...
    Organism:
    Thellungiella
    Type:
    Expression profiling by array
    Platform:
    GPL2627
    24 Samples
    Download data:
    GEO
    Series
    Accession:
    GSE2981
    ID:
    200002981
    19.

    Massive analysis of rice small RNAs: Mechanistic implications of regulated miRNAs and variants for differential target RNA cleavage

    (Submitter supplied) Small RNAs have variety of important roles in plant development, stress responses, and other processes. They exert their influence by guiding mRNA cleavage, translational repression, and chromatin modification. To identify novel and regulated rice miRNAs, 62 small RNA libraries were constructed from rice plants and deeply sequenced with Illumina technology. The libraries represent several tissues from control plants and plants subjected to different environmental stress treatments. more...
    Organism:
    Oryza sativa
    Type:
    Non-coding RNA profiling by high throughput sequencing
    Platforms:
    GPL9147 GPL9316
    62 Samples
    Download data:
    GEO
    Series
    Accession:
    GSE32973
    ID:
    200032973
    20.

    Transcriptome Profiling of Roots and leaves Under High Osmotic Stress in Arabidopsis

    (Submitter supplied) The functions of miRNAs and their target mRNAs in Arabidopsis development have been widely documented, however, roles of stress responsive miRNAs and their targets are not as well understood. Using small RNA deep sequencing and ATH1 microarrays to profile mRNAs, we identified IAR3 (IAA-Ala Resistant 3) as a novel target of miR167a.
    Organism:
    Arabidopsis thaliana
    Type:
    Expression profiling by array
    Platform:
    GPL198
    18 Samples
    Download data:
    GEO (CEL)
    Series
    Accession:
    GSE36789
    ID:
    200036789

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