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GSE55835
Arabidopsis thaliana
33 Downloadable Samples
Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
During cold acclimation plants increase their freezing tolerance in response to low non-freezing temperatures. This is accompanied by many physiological, biochemical and molecular changes that have been extensively investigated. In addition, many cold acclimated plants become more freezing tolerant during exposure to mild, non-damaging sub-zero temperatures. There is hardly any information available about the molecular basis of this adaptation. However, Arabidopsis thaliana is among the species that acclimate to sub-zero temperatures. This makes it possible to use the molecular and genetic tools available in this species to identify components of sub-zero signal transduction and acclimation. Here, we have used microarrays and a qRT-PCR primer platform covering 1880 genes encoding transcription factors to monitor changes in gene expression in the accessions Columbia-0, Rschew and Tenela during the first three days of sub-zero acclimation at -3C. The results indicate that gene expression during sub-zero acclimation follows a tighly controlled time-course. Especially AP2/EREBP and WRKY transcription factors may be important regulators of sub-zero acclimation, although the CBF signal transduction pathway seems to be less important during sub-zero than during cold acclimation. Globally, we estimate that approximately 5% of all Arabidopsis genes are regulated during sub-zero acclimation. Particularly photosynthesis-related genes were down-regulated and genes belonging to the functional classes of cell wall biosynthesis, hormone metabolism and RNA regulation of transcription were up-regulated. Collectively, these data provide the first global analysis of gene expression during sub-zero acclimation and allow the identification of candidate genes for forward and reverse genetic studies into the molecular mechanisms of sub-zero acclimation.
Publication Title
Global changes in gene expression, assayed by microarray hybridization and quantitative RT-PCR, during acclimation of three Arabidopsis thaliana accessions to sub-zero temperatures after cold acclimation.
Sample Metadata Fields
Specimen part, Time
View Samples- Arabidopsis thaliana
- 52 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Nine accessions of Arabidopsis were sampled before and after 14d of cold acclimation at 4°C. Transcript data were combined with metabolite data and related to quantitative measurement of plant freezing tolerance as determined by leaf electrolyte leakage assays.
Publication Title
Natural genetic variation of freezing tolerance in Arabidopsis.
Sample Metadata Fields
Specimen part
View Samples- Arabidopsis thaliana
- 21 Downloadable Samples
- Arabidopsis Gene 1.0 ST Array (aragene10st)
Description
During low temperature exposure, temperate plant species increase their freezing tolerance in a process termed cold acclimation. During deacclimation in response to warm temperatures cold acclimated plants lose freezing tolerance and resume growth and development. While considerable effort has been directed toward understanding the molecular and metabolic basis of cold acclimation, much less information is available about the regulation of deacclimation. Here, we report metabolic (GC-MS) and transcriptional (microarrays, qRT-PCR) responses underlying deacclimation during the first 24 h after a shift of cold acclimated Arabidopsis thaliana (Columbia-0) plants to warm temperature. The data revealed a faster response of the transcriptome than of the metabolome and provided evidence for tightly regulated temporal responses at both levels. Metabolically deacclimation is associated with decreasing contents of sugars, amino acids and glycolytic and TCA cycle intermediates, indicating an increased need for carbon sources and respiratory energy production associated with growth resumption under warm temperature conditions. Deacclimation also involves extensive down-regulation of protein synthesis and changes in the metabolism of lipids and cell wall components. Altered hormonal regulation appears particularly important during deacclimation, with changes in the expression of genes related to auxin, gibberellin, brassinosteroid, jasmonate and ethylene metabolisms. Several transcription factor families controlling fundamental aspects of plant development are significantly regulated during deacclimation, emphasizing that loss of freezing tolerance and growth resumption are interrelated processes that are transcriptionally highly interrelated. Expression patterns of some clock oscillator components during deacclimation resembled those under warm conditions, indicating at least partial re-activation of the circadian clock. This study provide the first comprehensive analysis of the regulation of deacclimation in cold acclimated plants. The data indicate cascades of rapidly regulated genes and metabolites that underly the developmental switch resulting in reduced freezing tolerance and the resumption of growth. They constitute a reference dataset of genes, metabolites and pathways that are crucial during the first rapid phase of deacclimation and will be useful for the further analysis of this important but under-researched plant process.
Publication Title
Rapid transcriptional and metabolic regulation of the deacclimation process in cold acclimated Arabidopsis thaliana.
Sample Metadata Fields
Specimen part, Treatment
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
Arabidopsis plants growing under diurnal conditions were transferred to cold of approximately one day duration, starting at different times of the day. All comparisons are of unreplicated pairs and are thus not designed to identify cold-responsive gens in isolation but are rather to supplement existing publicly available data. The overall aim was to use a diverse set of experiments to see which factors have the greatest influence on the identity of cold-responsive genes.
Publication Title
Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome.
Sample Metadata Fields
Age, Specimen part, Time
View Samples- Arabidopsis thaliana
- 6 Downloadable Samples
- Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)
Description
To address the neglected possibility for global mRNA changes in microarray experiments we developed a simple method to generate external controls for Affymetrix microarrays to allow these platforms to measure absolute mRNA expression at the global level. We used publicly available data to select probesets that never detect endogenous transcripts, and used PCR and IVT to generate synthetic mRNAs corresponding to them. After quality control and testing, these control transcripts were spiked into total RNA samples from plants before and after 24 h of cold treatment. Due to changes in the proportion of mRNA, these data reveal intensity-dependent bias in expression estimates based on standard all-gene normalizations. When not accounted for, this leads to false classification of the differential expression for thousands of genes.
Publication Title
Disruption of the Arabidopsis circadian clock is responsible for extensive variation in the cold-responsive transcriptome.
Sample Metadata Fields
Age, Specimen part
View Samples- Homo sapiens
- 56 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
A novel multi-network approach reveals tissue-specific cellular modulators of fibrosis in systemic sclerosis.
Sample Metadata Fields
Sex, Specimen part, Disease, Disease stage, Treatment, Subject
View Samples- Mus musculus
- 3 Downloadable Samples
Illumina HiSeq 2500
Description
Purpose: Majority of pancreatic cancer (PDAC) patient deaths are associated to the metastatic progression of disease. To identify novel targeted-therapies, a complete understanding of transformation in genetic landscape in tumors during disease progression is needed. Widely in use, the artificially immortalized PDAC cell lines do not rightly represent the progression because of multiple donors and disparate genetic characteristics. To identify key genes underlying the progression of PDAC from localized disease to a metastatic form, we performed whole transcriptome RNA-Sequencing analysis of cell models representing localised to metaststic stage through paired-end deep sequencing Method: Mouse expressing a Cre-activated KrasG12D allele inserted into the endogenous Kras locus, and these mice were crossed with mice expressing Cre recombinase in pancreatic tissue by virtue of a PDX-1 promoter-driven transgene. Next a cross between K-rasG12D Pdx-Cre and p16-/- mice, transgenic K-rasG12D Pdx-Cre p16-/- mice were generated harboring tissue specific mutant Kras and p16 deletion resulting in an earlier appearance of PanIN lesions followed by rapid progression into highly invasive and metastatic pancreatic cancers. Results: Transgenic K-rasG12D Pdx-Cre p16-/- mice developed spontaneous- localized, invasive and metastatic pancreatic tumors and transcriptome of these cell models representing localized, invasive and metastatic pancreatic tumors were sequenced. Conclusions: Based on genetic analysis of a same-lineage genetic background cell models, this study identifies a novel molecular pathway underlying the progression of pancreatic cancer disease. This study shows that Intestine Specific Homeobox (ISX) gene is a novel biomarker unique to pancreatic cancer progression. Overall design: By using tumors from K-rasG12D/p16-/- transgenic mice, we generated a spectrum of spontaneous (without immortalization) murine cell models representing localized (HI-Panc-L), invaise (HI-Panc-I) and metastatic (HI-Panc-M) stages. HI-Panc progression model is a valuable tool and by studying gene expression during progression of pancaretic cancer from localised to metaststic stage in a genetically same linaege wll be beneificail for pancartic cancer reaserch.
Publication Title
Characterization of Novel Murine and Human PDAC Cell Models: Identifying the Role of Intestine Specific Homeobox Gene ISX in Hypoxia and Disease Progression.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 12 Downloadable Samples
- Affymetrix Human Genome U133A 2.0 Array (hgu133a2)
Description
Alveolar rhabdomyosarcoma (aRMS) is a soft tissue sarcoma associated with the skeletal muscle lineage. The majority of aRMS tumors express the fusion protein PAX3-FOXO1 (PF), which has proven chemically intractable. As such, we identified proteins downstream from or cooperate with PF to support tumorigenesis, including SFRP3 (FRZB). Suppression of SFRP3 using lentivirally transduced shRNAs inhibits cell growth in vitro and tumor growth in vivo. This study aims to identify the genetic changes that underlie the SFRP3 suppression-mediated decreased cell growth. We analyzed changes using Gene Ontology (GO) enrichment and found the induced genes were enriched in striated muscle development/differentiation. In contrast, the repressed genes were enriched in response to stimulus and cell cycle/mitosis genes. We also observed as expected downregulation of SFRP3 (FRZB) but also downregulation of Wnt pathway-repressing genes such as CTBP2 (a transcriptional repressor of TCF, similar to CTBP1 ) and NAV2 (which is downstream from APC). Conversely, we noted upregulation of genes including CCND1 (cyclin D1) and SNAI2 (SLUG), both Wnt signaling target genes and WNT6, which is known to inhibit myoblast proliferation but induce myoblast elongation.
Publication Title
Secreted Frizzled-Related Protein 3 (SFRP3) Is Required for Tumorigenesis of PAX3-FOXO1-Positive Alveolar Rhabdomyosarcoma.
Sample Metadata Fields
Disease, Cell line, Treatment
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
To investigate transcriptional differences between HCM and WT cells Overall design: Examination of HCM vs WT Cells, with 3 replicates of each sample
Publication Title
A Contraction Stress Model of Hypertrophic Cardiomyopathy due to Sarcomere Mutations.
Sample Metadata Fields
Specimen part, Disease, Disease stage, Subject
View Samples- Mus musculus
- 14 Downloadable Samples
- Illumina HiSeq 2500, Illumina HiSeq 2000
Description
We investigated microRNA expression in motoneurons by performing small RNA sequencing of fluorescence-activated cell sorting (FACS)-isolated motoneurons labelled with the Hb9:gfp transgenic reporter and Hb9:gfp negative non-motoneurons including spinal interneurons. We find that one microRNA, microRNA-218, is highly enriched and abundantly expressed in motoneurons. Furthermore, we find that miR-218 is transcribed from alternative, motoneuron-specific alternative promoters embedded within the Slit2 and Slit3 genes by performing RNA sequencing of FACS-isolated motoneurons and a dissected embryonic floor plate cells which served as a control. Next, we performed RNA sequencing of FACS-isolated wild type (WT) motoneurons and motoneurons lacking miR-218 expression (218DKO motoneurons), and find that a large set of genes (named ''TARGET218'' genes) with predicted miR-218 binding sites are de-repressed in the absence of miR-218 expression. Finally, we examine the expression of TARGET218 genes in other neuronal subpopulations by FACS-isolating V1, V2a, and V3 interneurons expressing Cre-inducible fluorescent reporters and performing RNA sequencing. We find that the TARGET218 network of genes is depleted in wild-type motoneurons versus these interneuron types. Additionally, these genes are expressed at similar levels in 218DKO motoneurons compared with interneuron subtypes, suggesting that this genetic network. Overall design: Examination of mRNA expression in spinal progenitor, glial, and neuronal subpopulations.
Publication Title
Loss of motoneuron-specific microRNA-218 causes systemic neuromuscular failure.
Sample Metadata Fields
Specimen part, Subject
View Samples