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accession-icon GSE10016
Expression data of Arabidopsis thaliana rosettes in an extended night
  • organism-icon Arabidopsis thaliana
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Usually starch is nearly depleted at the end of the night. To induce a gradual depletion of carbon, we have analysed the global response of transcripts during an extension of the night, where carbon becomes severely limiting from about four hours onwards.

Publication Title

Global transcript levels respond to small changes of the carbon status during progressive exhaustion of carbohydrates in Arabidopsis rosettes.

Sample Metadata Fields

Specimen part

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accession-icon SRP007896
Non-coding small RNA profiling by high throughput sequencing of bovine primary retinal microvascular endothelial cells
  • organism-icon Bos taurus
  • sample-icon 1 Downloadable Sample
  • Technology Badge IconIllumina Genome Analyzer II

Description

The aim of this study was to identify and quantify microRNAs and other small regulatory RNAs expressed in primary retinal microvascular endothelial cells (RMECs) using deep sequencing. RMECs were isolated, RNA extracted, a small RNA library prepared and deep sequencing performed. A total of 6.8 million reads were mapped to 250 known microRNAs in miRBase (release 16). Several novel microRNAs and multiple new members of the miR-2284/2285 family were detected. Several ~30 nucleotide sno-miRNAs were identified, with the most highly expressed being derived from snoRNA U78. Highly expressed microRNAs previously associated with endothelial cells included miR-126 and miR-378, but the most highly expressed was miR-21, comprising more than one third of all mapped reads. The independence from prior sequence knowledge provided by deep sequencing facilitates analysis of novel microRNAs and other small RNAs. This approach also enables quantitative evaluation of microRNA expression, which has highlighted the predominance of a small number of microRNAs in RMECs. Further characterisation of the functions of the highly expressed microRNAs will provide insights into endothelial biology. Overall design: Single sample of primary cell culture

Publication Title

Deep sequencing reveals predominant expression of miR-21 amongst the small non-coding RNAs in retinal microvascular endothelial cells.

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE10522
Expression data of Arabidopsis thaliana rosettes during chilling
  • organism-icon Arabidopsis thaliana
  • sample-icon 21 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

To investigate the response of Arabidopsis thaliana plants to non-freezing, cool temperatures, we subjected four week old plants to various chilling temperatures at defined times during the diurnal cycle to control for diurnal effects on transcription. From the same plants, metabolites and enzyme activities were measured as well. Interestingly a gradual change could be observed over a wide range of temperatures. Some of which could be attributed to the CBF program.

Publication Title

Multilevel genomic analysis of the response of transcripts, enzyme activities and metabolites in Arabidopsis rosettes to a progressive decrease of temperature in the non-freezing range.

Sample Metadata Fields

Specimen part

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accession-icon GSE3416
Diurnal gene expression in Arabidopsis thaliana Col-0 rosette leaves
  • organism-icon Arabidopsis thaliana
  • sample-icon 17 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

How do the transcript levels of leaf-expressed genes change in a normal day-night cycle? The interest is in genes that are regulated by the circadian clock and the diurnal component (i.e. light, metabolite changes). Plants were grown on soil in a 12/12 h light/dark rythm at 20C day and night. 5 weeks after germination the rosettes of the non-flowering plants were harvested, 15 plants per sample. Plants were harvested at 6 timepoints every 4 hours beginning with the end of the night (still in darkness).

Publication Title

Sugars and circadian regulation make major contributions to the global regulation of diurnal gene expression in Arabidopsis.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE85963
Carbon starvation along the maize leaf gradient
  • organism-icon Zea mays
  • sample-icon 43 Downloadable Samples
  • Technology Badge Icon Affymetrix Maize Genome Array (maize)

Description

gene expression profiling in different zones along the gradient of the growing maize leaf balde aover a time course of dirunal cycle and carbon starvation by extension of the night

Publication Title

The Interplay between Carbon Availability and Growth in Different Zones of the Growing Maize Leaf.

Sample Metadata Fields

Time

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accession-icon GSE83291
Transcriptome analysis of flower of Arabidopsis accessions
  • organism-icon Arabidopsis thaliana
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

This work purposed on screening candidates of key genes invovled in the production of phenylacylated flavonol-glycosides

Publication Title

Characterization of a recently evolved flavonol-phenylacyltransferase gene provides signatures of natural light selection in Brassicaceae.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE9365
Expression data from barley maturing and germinating grains
  • organism-icon Hordeum vulgare
  • sample-icon 32 Downloadable Samples
  • Technology Badge Icon Affymetrix Barley Genome Array (barley1)

Description

Plant seeds prepare for germination already during seed maturation. We performed a detailed transcriptome analysis of barley grain maturation, desiccation and germination in two tissue fractions (endosperm/aleurone = e/a and embryo = em) using the Affymetrix barley1 chip.

Publication Title

Barley grain maturation and germination: metabolic pathway and regulatory network commonalities and differences highlighted by new MapMan/PageMan profiling tools.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE1400
MCF-7 Fractionated RNA
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A Array (hgu133a)

Description

RNA from MCF-7 cells was fractionated by sucrose density gradient centrifugation to separate RNA associated with membrane-bound polysomes from RNA associated with free polysomes. These two populations were hybridized in triplicate to U133A microarrays.

Publication Title

Membrane-associated and secreted genes in breast cancer.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE20458
Increased leaf size: different means to an end
  • organism-icon Arabidopsis thaliana
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

The final size of plant organs such as leaves is tightly controlled by environmental and genetic factors that must spatially and temporally coordinate cell expansion and cell cycle activity. However this regulation of organ growth is still poorly understood. The aim of this study is to gain more insight in the genetic control of leaf size in Arabidopsis by performing a comparative analysis of transgenic lines that produce larger leaves under standardized environmental conditions. To this end, we selected five genes, belonging to different functional classes, that all positively affect leaf size when over-expressed: AVP1, GRF5, JAW, BRI1 and GA20OX1. We show that the increase in leaf area in these lines depends on leaf position and growth conditions and that all five lines affect leaf size differently. However, in all cases an increase in cell number is, entirely or predominantly, responsible for the leaf size enlargement. By means of analyses of hormone levels, transcriptome and metabolome we provide deeper insight in the molecular basis of the growth phenotype for the individual lines. A comparative analysis between them indicates that enhanced organ growth is governed by different, seemingly independent pathways. The analysis of transgenic lines simultaneously over-expressing two growth-enhancing genes further supports the concept that multiple pathways independently converge on organ size control in Arabidopsis.

Publication Title

Increased leaf size: different means to an end.

Sample Metadata Fields

Specimen part

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accession-icon GSE20455
Increased leaf size: different means to an end (experiment 1)
  • organism-icon Arabidopsis thaliana
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

The final size of plant organs such as leaves is tightly controlled by environmental and genetic factors that must spatially and temporally coordinate cell expansion and cell cycle activity. However this regulation of organ growth is still poorly understood. The aim of this study is to gain more insight in the genetic control of leaf size in Arabidopsis by performing a comparative analysis of transgenic lines that produce larger leaves under standardized environmental conditions. To this end, we selected five genes, belonging to different functional classes, that all positively affect leaf size when over-expressed: AVP1, GRF5, JAW, BRI1 and GA20OX1. We show that the increase in leaf area in these lines depends on leaf position and growth conditions and that all five lines affect leaf size differently. However, in all cases an increase in cell number is, entirely or predominantly, responsible for the leaf size enlargement. By means of analyses of hormone levels, transcriptome and metabolome we provide deeper insight in the molecular basis of the growth phenotype for the individual lines. A comparative analysis between them indicates that enhanced organ growth is governed by different, seemingly independent pathways. The analysis of transgenic lines simultaneously over-expressing two growth-enhancing genes further supports the concept that multiple pathways independently converge on organ size control in Arabidopsis.

Publication Title

Increased leaf size: different means to an end.

Sample Metadata Fields

Specimen part

View Samples
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refine.bio is a repository of uniformly processed and normalized, ready-to-use transcriptome data from publicly available sources. refine.bio is a project of the Childhood Cancer Data Lab (CCDL)

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Cite refine.bio

Casey S. Greene, Dongbo Hu, Richard W. W. Jones, Stephanie Liu, David S. Mejia, Rob Patro, Stephen R. Piccolo, Ariel Rodriguez Romero, Hirak Sarkar, Candace L. Savonen, Jaclyn N. Taroni, William E. Vauclain, Deepashree Venkatesh Prasad, Kurt G. Wheeler. refine.bio: a resource of uniformly processed publicly available gene expression datasets.
URL: https://www.refine.bio

Note that the contributor list is in alphabetical order as we prepare a manuscript for submission.

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