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accession-icon GSE95609
Comparative transcriptional profiling of Arabidopsis yda11 mutant and wild-type plants after infection with Plectosphaerella cucumerina
  • organism-icon Arabidopsis thaliana
  • sample-icon 30 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Comparative transcriptomic analysis of Arabidopsis thaliana yda11 plants (in Col-0 background), and wild-type plants (Col-0) non-infected or infected with the necrotrophic fungal pathogen Plectosphaerella cucumerina BMM (PcBMM)

Publication Title

YODA MAP3K kinase regulates plant immune responses conferring broad-spectrum disease resistance.

Sample Metadata Fields

Specimen part, Treatment, Time

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accession-icon SRP133496
Arabidopsis SCW4 RNAi line transcriptome
  • organism-icon Arabidopsis thaliana
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Plants with decreased SWC4 expression levels displayed several pleiotropic phenotypic alterations, suggesting that this gene participates in the regulation of different developmental processes. To evaluate genes whose expression was misregulated in SCW4 RNAi line, we performed RNA-seq differential expression analysis.

Publication Title

Arabidopsis SWC4 Binds DNA and Recruits the SWR1 Complex to Modulate Histone H2A.Z Deposition at Key Regulatory Genes.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE18603
Expression data from esd7-1 mutant vs wt (Ler)
  • organism-icon Arabidopsis thaliana
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We have characterized a mutation affecting the Arabidopsis EARLY IN SHORT DAYS 7 (ESD7) gene encoding the catalytic subunit of the DNA polymerase epsilon (e), AtPOL2A. esd7-1 mutations causes early flowering independently of photoperiod, shortened inflorescence internodes and altered leaf and root development. esd7-1 was a hypomorphic allele whereas KO alleles displayed an embryo-lethal phenotype. The SAM and the RAM in the esd7-1 seedlings were found to exhibit an altered disposition that might correlate with the abnormal expression pattern of SAM and RAM marker genes. esd7-1 showed higher sensitivity to DNA damaging reagents than wild type plants and altered expression of genes involved in DNA repair mechanisms by homologous recombination. Moreover, esd7 early flowering phenotype requires functional FT and SOC1 proteins and might be also related to the mis-regulation of AG and AG-like gene expression found in esd7. Loci involved in the modulation of the chromatin structural dynamics, such as TFL2 and EBS, which negatively regulate FT expression, were found to interact genetically with ESD7, and the carboxy terminus of ESD7 interacted with TFL2 in vitro. Besides, fasciata2 (fas2) mutations suppressed esd7 early flowering phenotype and INCURVATA 2 (ICU2) was found to be epistatic to ESD7. Discrete regions of the chromatin of FT and AG loci were enriched in activating epigenetic marks in the esd7-1 mutant. We concluded that ESD7 might be participating in processes involved in chromatin-mediated cellular memory.

Publication Title

EARLY IN SHORT DAYS 7 (ESD7) encodes the catalytic subunit of DNA polymerase epsilon and is required for flowering repression through a mechanism involving epigenetic gene silencing.

Sample Metadata Fields

Specimen part

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accession-icon GSE85029
Dido as a switchboard that regulates self-renewal and differentiation in embryonic stem cells
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

DIDO as a Switchboard that Regulates Self-Renewal and Differentiation in Embryonic Stem Cells.

Sample Metadata Fields

Specimen part

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accession-icon GSE85006
Dido as a switchboard that regulates self-renewal and differentiation in embryonic stem cells (Affy)
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Transition from symmetric to asymmetric cell division requires precise coordination of differential gene expression. Embryonic stem cells (ESC) strongly express Dido3, whose C-terminal truncation impedes ESC differentiation while retaining self-renewal. We show that Dido3 binds to its gene locus via H3K4me3 and RNA pol II and, at differentiation onset, induces expression of its splice variant Dido1, which then leads to Dido3 degradation and downregulation of stemness genes. We propose that Dido isoforms act as a switchboard to regulate genetic programs for ESC transition from pluripotency maintenance to promotion of differentiation.

Publication Title

DIDO as a Switchboard that Regulates Self-Renewal and Differentiation in Embryonic Stem Cells.

Sample Metadata Fields

Specimen part

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accession-icon GSE52046
Expression data from Col-0 and sp1,spx2 under phosphate starvation stress and recovery after resupplying phosphate
  • organism-icon Arabidopsis thaliana
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We performed a transcriptomic analysis of Pi-starvation and recovery after resupplying Pi in Arabidopsis thaliana (Columbia-0) wild type plants and double mutant spx1,spx2. Results show that SPX1 is a Pi-dependent inhibitor of the transcription factor PHR1, a central regulatory protein in the control of transcriptional responses to Pi starvation.

Publication Title

SPX1 is a phosphate-dependent inhibitor of Phosphate Starvation Response 1 in Arabidopsis.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE106322
Arabidopsis degradome analysis from Tobacco rattle virus (TRV) infected plants
  • organism-icon Arabidopsis thaliana
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We aimed to identify targets of miRNAs/small RNAs in Arabidopsis inflorescences after infection with Tobacco rattle virus (TRV).

Publication Title

No associated publication

Sample Metadata Fields

Age, Specimen part

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accession-icon E-MEXP-3283
Transcription profiling by array of Arabidopsis mutant for axr3 after treatment with naphthalene-1-acetic acid
  • organism-icon Arabidopsis thaliana
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Differentially expressed genes in response to the phytohormone auxin in wild type and a conditional auxin signalling mutant

Publication Title

No associated publication

Sample Metadata Fields

Age, Specimen part, Compound, Time

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accession-icon GSE69828
Expression data of Arabidopsis seedlings in response to ARR1 or cytokinins, in the presence and absence of DELLA proteins
  • organism-icon Arabidopsis thaliana
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

DELLA proteins interact with ARR1 and modulate its activity.

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

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accession-icon GSE63774
Longissimus Thoracis and subcutaneous fat transcriptome study in lambs
  • organism-icon Ovis aries
  • sample-icon 40 Downloadable Samples
  • Technology Badge Icon Ovine Gene 1.1 ST Array (ovigene11st)

Description

Feeding animals with either concentrates supplemented with vitamin E or alfalfa grazing has been proven to reduce the oxidative process that occurs in meat products. Indoor-kept lambs were fed a standard concentrate (n=7, C) or concentrate supplemented with vitamin E (n=7, VE) for 30 days before slaughtering all animals at 2224 kg of live weight. Simultaneously, 7 unweaned lambs grazed in alfalfa paddocks (ALF) with their dams. Global transcriptomic data of longissimus thoracis (LT) muscle and subcutaneous fat (SF) with the Affymetrix Ovine Gene 1.1 microarray was used. In LT muscle when ALF group was compared with C group, were identified 41 genes differentially expressed. Among these genes 32 were down- regulated and 9 were up- regulated. Meanwhile when VE treatment was compared with C group were identified a total of 29 genes, 26 were down- regulated and 3 genes were up- regulated. In SF when ALF treatment was compared with C, were identified only 4 genes differentially expressed, all of them up-regulated in ALF group. Meanwhile when VE treatment was compared with C group, were identified a total of 330 genes. Among them, 295 genes were up- regulated and 35 were down- regulated. In LT muscle the clusters corresponding to gene expression profiles from treatments ALF, C and VE were clearly separated from each other. In SF, ALF group, overlap with VE and C treatments, however, VE and C clearly were separate in different clusters. These differentially expressed genes were selected for a functional analysis by using DAVID. In LT muscle some of the identified significant biological processes were catabolic and lipid process (down-regulated, except CPT1B) (CPT1B, PLA2G16, SPSB1, LRTOMT, PLCD4, FBXO9, CNBP and CYP27A1) and muscle organ differentiation (down-regulated) (CPT1B, MYOD1, MYLK2 and MSTN) in ALF; whereas intracellular signaling cascade (IGF1R, DEF8, AKAP7 and CISH) was down-regulated. In SF, vitamin E supplementation had an important effect; most of the genes were up-regulated. DAVID analysis showed that biosynthesis lipid pathway was the most represented with 20 genes, such as EBP, MVD, CYP51A1, DHCR7, HMGCS1, LSS and FDFT1 implicated in cholesterol synthesis. Further exploration of the links between these genes and vitamin E will lead to a better understanding of how vitamin E affects the oxidative process that occurs in meat products.

Publication Title

Genome-wide expression profiling in muscle and subcutaneous fat of lambs in response to the intake of concentrate supplemented with vitamin E.

Sample Metadata Fields

Sex, Treatment

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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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