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accession-icon GSE114108
Expression data from mouse monocyte- and common- dendritic progenitors (MDP and CDP) from Ikaros mutant in response to gamma-secretase inhibitor (GSI)
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Ikaros hypomorphic mice (IkL/L) show plasmacytoid dendritic cell (pDC) defects with an absence of pDCs in the peripheral organs and a reduction of pDCs in the bone marrow (BM). Moreover in vitro differentiation of pDC from IkL/L total BM cells is also defective.

Publication Title

Ikaros cooperates with Notch activation and antagonizes TGFβ signaling to promote pDC development.

Alternate Accession IDs

E-GEOD-114108

Sample Metadata Fields

Treatment

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accession-icon GSE48203
Expression data from tumoral thymocytes and DP thymocytes expressing an activated form of b-catenin in mouse T cells
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

To assess the importance of the Wnt pathway during T cell develoment, we generated a mouse line (R26-cat) in which high levels of active -catenin are maintained throughout T cell development. Young R26-cat mice (6-week-old) show a differentiation block at the CD4+CD8+ DP stage. All R26-cat mice develop T cell leukemias with a DP phenotype at 5-6 months of age.

Publication Title

β-Catenin activation synergizes with Pten loss and Myc overexpression in Notch-independent T-ALL.

Alternate Accession IDs

E-GEOD-48203

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE96849
SAGA Is a General Cofactor for RNA Polymerase II Transcription
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 66 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

The SAGA co-activator has been implicated in the regulation of a smal subset of genes in budding yeast in transcriptomic analyses performed in steady-state levels of RNA.

Publication Title

SAGA Is a General Cofactor for RNA Polymerase II Transcription.

Alternate Accession IDs

E-GEOD-96849

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE96830
Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factor TFIID
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome 2.0 Array (yeast2)

Description

RNA Pol II transcription has been implied to be either regulated by the general transcription factor TFIID or the co-activator SAGA. Also, this dominancy of either SAGA or TFIID might be according to the existance, or not, of a TATA consensus sequence.

Publication Title

Transcription of Nearly All Yeast RNA Polymerase II-Transcribed Genes Is Dependent on Transcription Factor TFIID.

Alternate Accession IDs

E-GEOD-96830

Sample Metadata Fields

Treatment

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accession-icon E-MTAB-3400
Response of two clavata 1 mutants to Ralstonia solanacearum
  • organism-icon Arabidopsis thaliana
  • sample-icon 23 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

In this experiment, we compared transcriptome of 2 homozygous knock out mutants in the CLV1 gene (clv1-12 and clv1-13) to their wild type Ws-2 when challenged with the virulent Rd15 strain of Ralstonia solanacearum. The two mutants show a significant delay of symptom appearance. The experiment was conducted on roots and leaves of 4 week old plants harvested at the time of inoculation and when the first symptoms appeared on the susceptible wild type (4 days after inoculation).

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part, Disease stage

View Samples
accession-icon E-MEXP-152
Transcription profiling of response of adult Drosophila to oxidative and ER stress
  • organism-icon Drosophila melanogaster
  • sample-icon 7 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome Array (drosgenome1)

Description

We used oligonucleotide microarrays to address the specificities of transcriptional responses of adult Drosophila to different stresses induced by paraquat and H2O2, two oxidative stressors, and by tunicamycin which induces an endoplasmic reticulum (ER) stress. Flies were tested 24 hours after exposure to continuous stresses induced by ingestion of paraquat, H2O2 or tunicamycin at concentrations leading to similar effects on viability. We used concentrations of 1% H2O2, 5mM paraquat and 12uM of tunicamycin which lead to negligeable mortality at 24 hours. A paraquat concentration of 15mM was also used for comparison with previous studies Both specific and common responses to the three stressors were observed and whole genome functional analysis identified several important classes of stress responsive genes. Within some functional classes, we observed large variabilities of transcriptional changes between isozymes, which may reflect unsuspected functional specificities.

Publication Title

Genome wide analysis of common and specific stress responses in adult drosophila melanogaster.

Alternate Accession IDs

None

Sample Metadata Fields

Sex, Age, Compound, Time

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accession-icon E-MTAB-2734
Transcription profiling during differentiation of the neural tube in HH stage 10 chick embryos
  • organism-icon Gallus gallus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Chicken Genome Array (chicken)

Description

The spinal cord is generated progressively as cells leave the caudal region of the elongating body axis such that the temporal steps of neural differentiation become spatially separated along the head to tail axis. At key stages, it is therefore possible to isolate near-adjacent cell populations from the same embryo in distinct differentiation states. Cells in the caudal lateral epiblast adjacent to the primitive streak (also known as the stem zone, SZ, in the chick) express both early neural and mesodermal genes. Other cells in the stem zone will gastrulate to form the paraxial mesoderm or remain in the epiblast cell sheet and become neural progenitors. These latter cells form a new region called the preneural tube (PNT), which is flanked by unsegmented presomitic mesoderm and represents an early neural progenitor state that can be induced by FGF signalling to revert back to a multi-potent SZ state. Rostral to this, the closed caudal neural tube (CNT) is flanked by somites and is an early site of co-expression of genes characteristic of neural progenitors, and of ventral patterning genes (Diez del Corral et al., 2003). The CNT contains the first few neurons and exposure to FGF cannot revert this tissue to a multi-potent SZ state (Diez del Corral et al., 2002). The transition from the PNT to the CNT thus involves commitment to a neural fate that this is regulated by a switch from FGF to retinoid signalling. More advanced neuroepithelium is then located in more rostral neural tube (RNT), in which neuronal differentiation is ongoing and dorsoventral pattern is refined. This experiment uses the Affymetrix GeneChip chicken genome microarray to compare the transcriptomes of microdissections of these spatially distinct cell populations from the elongating neural axis of HH stage 10 chick embryos. Dissections were carried out in L15 medium at 4°C and explants pooled in TRIzol reagent (Gibco) for RNA extraction. Notochord was removed by controlled trypsin digestion that aimed to keep the neural ventral midline. For the microarrays, at least five tissue samples for each region were pooled to make each of three biological replicates for each (n>15 for each region).

Publication Title

Major transcriptome re-organisation and abrupt changes in signalling, cell cycle and chromatin regulation during neural differentiation in vivo

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part

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accession-icon GSE61412
Expression data from advanced stage of murine pancreatic ductal adenocarcinoma (PDAC) and control pancreas
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

We used microarrays to detail the global gene expression signature of PDAC and to identify distinct up- and down-regulated transcripts in these tumors compared to control pancreas. We also established from this dataset the metabolic signature of PDAC in order to define new metabolic therapeutic target for pancreatic cancer.

Publication Title

Cholesterol uptake disruption, in association with chemotherapy, is a promising combined metabolic therapy for pancreatic adenocarcinoma.

Alternate Accession IDs

E-GEOD-61412

Sample Metadata Fields

Sex, Age, Specimen part

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accession-icon E-MTAB-3402
Response of clavata 2-7 mutant to Ralstonia solanacearum
  • organism-icon Arabidopsis thaliana
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

In this experiment, we compared transcriptome of one knock out mutants in the CLV2 gene (clv2-7) to his wild type Col-0 when challenged with the virulent GMI1000 strain of Ralstonia solanacearum. This mutant shows a significant delay of symptom appearance. The experiment was conducted on roots and leaves of 4 week old plants harvested at the time of inoculation and when the first symptoms appeared on the susceptible wild type (4 days after inoculation - 25% of wilted leaves: disease index 1, D1).

Publication Title

No associated publication

Alternate Accession IDs

None

Sample Metadata Fields

Specimen part, Disease stage

View Samples
accession-icon E-MTAB-542
Transcription profiling by array of Arabidopsis plants inccoculated with Ralstonia solanacearum hrpB strain (avirulent strain) and 5 days (25% of wilted leaves) after challenge inoculation with the GMI1000 virulent R. solanacearum strain
  • organism-icon Arabidopsis thaliana
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Microarray analysis was performed on the aerial parts of 5 plants collected 24 hours after water treatment or inoculation by the Ralstonia solanacearum hrpB strain (avirulent strain) and 5 days (25% of wilted leaves) after challenge inoculation with the GMI1000 virulent R. solanacearum strain. We compared trancriptome expression level of protected plants (hrpB prinoculation) versus non protected plants (water treatment), 24H after treatment and 5 days (25% of wilted leaves) after challenge inoculation with the GMI1000 virulent R. solanacearum strain

Publication Title

Molecular Mechanisms of Biological Control on Arabidopsis thaliana / Ralstonia solanacearum pathosystem

Alternate Accession IDs

None

Sample Metadata Fields

Age, Specimen part, Subject

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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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