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accession-icon GSE23301
Quantitative transcriptomic analysis of abscisic acid-induced and reactive oxygen species-dependent expression changes and proteomic profiling in Arabidopsis suspension cells
  • organism-icon Arabidopsis thaliana
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Early rapid changes in response to the phytohormone abscisic acid (ABA) have been observed at the transcript level, but little is known how these transcript changes translate to changes in protein abundance under the same conditions. Here we have performed a global quantitative analysis of transcript and protein changes in Arabidopsis suspension cells in response to ABA using microarrays and quantitative proteomics. In summary, 3494 transcripts and 50 proteins were significantly regulated by ABA over a treatment period of 2024 h. Abscisic acid also caused a rapid and strong increase in production of extracellular reactive oxygen species (ROS) with an average half-rise time of 33 sec. A subset of ABA-regulated transcripts were differentially regulated in the presence of the ROS scavenger dimethylthiourea (DMTU) as compared with ABA alone, suggesting a role for ROS in the regulation of these ABA-induced genes. Transcript changes showed an overall poor correlation to protein changes (r = 0.66). Only a subset of genes was regulated at the transcript and protein level, including known ABA marker genes. We furthermore identified ABA regulation of proteins that function in a branch of glucosinolate catabolism previously not associated with ABA signaling. The discovery of genes that were differentially regulated at the transcript and at the protein level emphasizes the strength of our combined approach. In summary, our dataset not only expands previous studies on gene and protein regulation in response to ABA, but rather uncovers unique aspects of the ABA regulon and gives rise to additional mechanisms regulated by ABA.

Publication Title

Quantitative transcriptomic analysis of abscisic acid-induced and reactive oxygen species-dependent expression changes and proteomic profiling in Arabidopsis suspension cells.

Sample Metadata Fields

Age, Specimen part, Cell line, Time

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accession-icon GSE7112
Abscisic acid effect on wild type and the abh1 mutant
  • organism-icon Arabidopsis thaliana
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Analysis of the abh1 mutant Arabidopsis plants following treatment with 50 uM abscisic acid (ABA). ABH1 encodes the large (80kDa) subunit of the nuclear mRNA cap binding complex and affects early ABA signal transduction events (Hugouvieux et al., 2001, Cell 106, 477).

Publication Title

mRNA cap binding proteins: effects on abscisic acid signal transduction, mRNA processing, and microarray analyses.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE9247
Effect of histone deacetylase inhibitors on osteoblast gene expression
  • organism-icon Mus musculus
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Background:

Publication Title

Gene profile analysis of osteoblast genes differentially regulated by histone deacetylase inhibitors.

Sample Metadata Fields

No sample metadata fields

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accession-icon E-MEXP-1443
Transcription profiling by array of Arabidopsis guard cells and mesophyll cells in response to ABA treatment
  • organism-icon Arabidopsis thaliana
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Transcriptional profiling of guard cells and mesophyll cells in response to ABA treatment

Publication Title

Isolation of a strong Arabidopsis guard cell promoter and its potential as a research tool.

Sample Metadata Fields

Specimen part, Disease, Disease stage, Compound

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accession-icon GSE2198
Comparison of transcripts from the anterior tibialis, gastrocnemius, and liver of glycogen synthase WT, GSL30 or KO mice
  • organism-icon Mus musculus
  • sample-icon 34 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Expression 430A Array (moe430a)

Description

Anterior tibialis removed from 3-month old muscle glycogen synthase WT or knockout mouse. RNA was extracted using GibcoBRL TRIzol Reagent and a Quiagen RNeasy kit. Targets were produced using standard Affymetrix procedures from about 5ug of total RNA. GSM40057-GSM40063 AND GSM40956.

Publication Title

Gene expression profiling of mice with genetically modified muscle glycogen content.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP062389
Human telomerase RNA processing and quality control
  • organism-icon Homo sapiens
  • sample-icon 33 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

RNA sequencing of HeLa cells treated with siRNA against the RNA exosome components hRRP40, hRRP6, hDIS3, and hRRP6/hDIS3 or the splicing inhibitors Isoginkgetin and spliceostatin A, respectively. Overall design: Stranded, ribo-depleted RNA seq profiles of HeLa cells treated with exosome targeting siRNAs or splicing inhibitors using Illumina HiSeq. All experiments were carried out in triplicate starting with independent cell cultures

Publication Title

Human Telomerase RNA Processing and Quality Control.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE51691
Expression data from glp-1(e2141) hermaphrodites maintained with or without males for 8 days
  • organism-icon Caenorhabditis elegans
  • sample-icon 11 Downloadable Samples
  • Technology Badge Icon Affymetrix C. elegans Genome Array (celegans)

Description

Males induce dramatic physiological changes to hermaphrodites, including a significant shortening of lifespan. We have termed this effect as male-induced demise (MID) of hermaphrodites. This experiment was performed to analyse changes in gene expression due to the presence of males. We have shown that Knock down of utx-1 ameliorates the MID. In this experiment we also examine male-induce gene expression that may be altered when knocking down expression of utx-1 via RNAi.

Publication Title

Males shorten the life span of C. elegans hermaphrodites via secreted compounds.

Sample Metadata Fields

Specimen part

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accession-icon GSE38856
Protein sets define disease states and predict in vivo effects of drug treatment
  • organism-icon Mus musculus
  • sample-icon 38 Downloadable Samples
  • Technology Badge IconIllumina MouseWG-6 v2.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Protein sets define disease states and predict in vivo effects of drug treatment.

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon GSE116309
Analysis of gene expression dynamics during iPS cell derivation from mouse embryonic fibroblasts using reprogramming systems with different Klf4 stoichiometry
  • organism-icon Mus musculus
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

The forced expression of Yamanaka factors (Oct3/4, Sox2, Klf4, and c-Myc) reprograms cells into induced pluripotent stem cells (iPSCs) through a series of sequential cell fate conversions. The order and robustness of gene expression changes are highly depended on the Yamanaka factor stoichiometry. We specifically focused on two different reprogramming paths induced by high- and low-Klf4 stoichiometry, which were accomplished by introducing OK+9MS or OKMS polycistronic cassettes, respectively, into mouse embryonic fibroblasts. By comparing these reprograming intermediates with embryonic stem cells (ESCs) and primary keratinocytes, we identified high-Klf4 specific, transiently up-regulated epithelial genes. We found that expression of these epithelial genes was enriched in a TROP2-positive cell population. Moreover, we identified a set of transcription factors which are candidates for the regulation of transiently expressed epithelial genes, and revealed their connection to high-Klf4-specific reprogramming hallmarks.

Publication Title

OVOL1 Influences the Determination and Expansion of iPSC Reprogramming Intermediates.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE38855
Protein sets define disease states and predict in vivo effects of drug treatment [WAT]
  • organism-icon Mus musculus
  • sample-icon 15 Downloadable Samples
  • Technology Badge IconIllumina MouseWG-6 v2.0 expression beadchip

Description

Gaining understanding of common complex diseases and their treatments are the main drivers for life sciences. As we show here, comprehensive protein set analyses offer new opportunities to decipher functional molecular networks of diseases and assess the efficacy and side-effects of treatments in vivo. Using mass spectrometry, we quantitatively detected several thousands of proteins and observed significant changes in protein pathways that were (dys-) regulated in diet-induced obesity mice. Analysis of the expression and post-translational modifications of proteins in various peripheral metabolic target tissues including adipose, heart, and liver tissue generated functional insights in the regulation of cell and tissue homeostasis during high-fat diet feeding and medication with two antidiabetic compounds. Protein set analyses singled out pathways for functional characterization, and indicated, for example, early-on potential cardiovascular complication of the diabetes drug rosiglitazone. In vivo protein set detection can provide new avenues for monitoring complex disease processes, and for evaluating preclinical drug candidates.

Publication Title

Protein sets define disease states and predict in vivo effects of drug treatment.

Sample Metadata Fields

Sex, Age, Specimen part

View Samples
...

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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