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accession-icon GSE67838
Identification of post-transcriptional regulatory networks during myeloblast-to-monocyte differentiation transition
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Identification of post-transcriptional regulatory networks during myeloblast-to-monocyte differentiation transition.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE67826
Identification of post-transcriptional regulatory networks during myeloblast-to-monocyte differentiation transition [mRNA]
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Treatment of leukemia cells with 1,25-dihydroxyvitamin D3 may overcome their differentiation block and lead to the transition from myeloblasts to monocytes. To identify microRNA-mRNA networks relevant for myeloid differentiation, we profiled the expression of mRNAs and microRNAs associated to the low- and high-density ribosomal fractions in leukemic cells and in their differentiated monocytic counterpart. Intersection between mRNAs shifted across the fractions after treatment with putative target genes of modulated microRNAs showed a series of molecular networks relevant for the monocyte cell fate determination

Publication Title

Identification of post-transcriptional regulatory networks during myeloblast-to-monocyte differentiation transition.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE22207
Identification of promoter sequence elements involved in specific recognition by the S subunit of bacterial RNA polymerase.
  • organism-icon Escherichia coli str. k-12 substr. mg1655
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix E. coli Genome 2.0 Array (ecoli2)

Description

Promoter recognition by bacterial RNA polymerase is mediated by subunits, which assemble transiently to RNA polymerase core enzyme (E) during transcription initiation. subunits drive transcription of specific sets of genes by allowing RNA polymerase to interact with different promoter sequences. However, 70, the housekeeping subunit, and S, an alternative subunit mainly active during slow growth and in response to cellular stresses, appear to recognize almost identical promoter sequences, raising the question of how promoter selectivity is achieved in the bacterial cell. To identify sequence determinants for selective promoter recognition, we performed a run-off/microarray experiment (ROMA): in vitro transcription experiments were carried out with RNA polymerase saturated either with 70 (E70) or with S (ES) using the whole Escherichia coli genome as DNA template, and transcript levels were determined by microarray analysis. We found that several genes associated with bacterial growth (e.g., ribosomal operons) were transcribed more efficiently by E70. In contrast, ES transcribed preferentially genes involved in stress responses, secondary metabolism, as well as regulatory RNAs and intergenic regions with yet unknown function. Genes preferentially recognized in vitro by ES showed reduced expression in ES -deficient mutant strain of E. coli. Sequence comparison of E70- versus ES dependent promoters confirms that the presence of a -35 sequence and the relative location of UP elements affect promoter interaction with either form of RNA polymerase, and suggests that a G/C bias in the -2/+1 nucleotides would favour efficient promoter recognition by E70.

Publication Title

In vitro transcription profiling of the σS subunit of bacterial RNA polymerase: re-definition of the σS regulon and identification of σS-specific promoter sequence elements.

Sample Metadata Fields

Disease

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accession-icon GSE139380
Aberrant expression of RSK1 characterizes high-grade gliomas with immune infiltration
  • organism-icon Homo sapiens
  • sample-icon 30 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

The p90 ribosomal S6 kinase (RSK) family, a downstream target of Ras/extracellular signal-regulated kinase (ERK) signaling, can mediate cross-talk with the mammalian target of rapamycin complex 1 (mTORC1) pathway. As RSK connects two oncogenic pathways in gliomas, we investigated the protein levels of the RSK isoforms RSK1-4 in non-tumoral brain (NB) and grade I-IV gliomas. RSK4 expression was not detected in any brain tissues, whereas RSK3 expression was very low, with GBMs demonstrating the lowest RSK3 protein levels. When compared to NB or low-grade gliomas (LGG), a group of glioblastomas (RSK1hi) that excluded long-survivor cases expressed higher levels of RSK1. No difference was observed in RSK2 median-expression levels among NB and gliomas; however, high levels of RSK2 in glioblastomas (GBM) were associated with worse survival. RSK1hi and, to a lesser extent, RSK2hi GBMs, showed higher levels of phosphorylated RSK, which indicates RSK activation. Transcriptome analysis indicated that most RSK1hi GBMs belonged to the mesenchymal subtype, and RSK1 expression strongly correlated with gene expression signature of immune infiltrates, in particular of activated-natural killer cells and M2 macrophages. In an independent cohort, we confirmed that RSK1hi GBMs exclude long-survivors, and RSK1 expression was associated with high protein levels of the mesenchymal subtype marker LAPTM5, as well as with high expression of CD68, which indicated the presence of infiltrating immune cells. An RSK1 signature was obtained based on differentially expressed mRNAs and validated in public glioma datasets. Enrichment of RSK1 signature followed glioma progression, recapitulating RSK1 protein expression, and was associated with worse survival not only in GBM but also in LGG. In conclusion, both RSK1 and RSK2 associate with glioma malignity, but displaying isoform-specific peculiarities. The progression-dependent expression and association with immune infiltration, suggests RSK1 as a potential progression marker and therapeutic target for gliomas.

Publication Title

Aberrant expression of RSK1 characterizes high-grade gliomas with immune infiltration.

Sample Metadata Fields

Specimen part

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accession-icon GSE31759
Drought stress in Wheat at grain filling stage
  • organism-icon Triticum turgidum subsp. durum, Triticum aestivum
  • sample-icon 17 Downloadable Samples
  • Technology Badge Icon Affymetrix Wheat Genome Array (wheat)

Description

To provide a global study of transcriptome changes under drought stress, the gene expression levels of a durum wheat genotype (Triticum durum Desf. cultivar Creso) and two bread wheat genotypes (Triticum aestivum L. cultivar Chinese Spring -CS- and its deletion line CS_5AL-10) were investigated. The 5A chromosome deletion line (5AL-10) lacks the distal part (43%) of the long arm of chromosome 5A. Each genotype was subjected to two different levels of water stress at the grain filling stage. After anthesis, three different levels of soil water content (SWC) were induced as described below: control (CTRL; SWC=28%), moderate stress (MS; SWC=18%), and severe stress (SS; SWC=12.5%). For each sample, three biological replicates were performed, for a total of 27 hybridizations. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Alessio Aprile. The equivalent experiment is TA23 at PLEXdb.]

Publication Title

Transcriptional profiling in response to terminal drought stress reveals differential responses along the wheat genome.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE64328
Transcriptional Regulationand Chromatin Dynamics inHuman Epithelial Cell Differentiation
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer IIx

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Dynamic Transcriptional and Epigenetic Regulation of Human Epidermal Keratinocyte Differentiation.

Sample Metadata Fields

Specimen part, Disease

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accession-icon SRP070902
Transcriptional Regulationand Chromatin Dynamics inHuman Epithelial Cell Differentiation (RNA-seq)
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconNextSeq500

Description

Transcriptional profiling of KP and DK through RNA-seq Overall design: RNA-sequencing of KP and DK

Publication Title

Dynamic Transcriptional and Epigenetic Regulation of Human Epidermal Keratinocyte Differentiation.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE64299
Transcriptional Regulationand Chromatin Dynamics inHuman Epithelial Cell Differentiation (expression)
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer IIx

Description

Gene expression profiling of progenitor and differentiated keratinocytes by Affymetrix microarray

Publication Title

Dynamic Transcriptional and Epigenetic Regulation of Human Epidermal Keratinocyte Differentiation.

Sample Metadata Fields

Specimen part

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accession-icon SRP051321
Transcriptional Regulationand Chromatin Dynamics inHuman Epithelial Cell Differentiation (CAGE)
  • organism-icon Homo sapiens
  • sample-icon 1 Downloadable Sample
  • Technology Badge IconIlluminaGenomeAnalyzerIIx

Description

Investigation of promoters usage in KP cells Overall design: KP cells promoter usage profiling by CAGE-seq

Publication Title

Dynamic Transcriptional and Epigenetic Regulation of Human Epidermal Keratinocyte Differentiation.

Sample Metadata Fields

No sample metadata fields

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accession-icon E-MEXP-232
Platform comparison and transcription profiling of MDA-MB-231 human metastatic breast cancer cells, cultured for 48 h in the absence (control) or presence (treated) of 32 ?M resveratrol to evaluate Amersham CodeLink UniSet Human 10K I BioArray and Affymetrix GeneChip HG-U133A)
  • organism-icon Homo sapiens
  • sample-icon 3 Downloadable Samples
  • Technology Badge IconUNKNOWN

Description

Evaluation of two commercial microarray platforms (Amersham CodeLink UniSet Human 10K I BioArray and Affymetrix GeneChip HG-U133A). Both platforms have been tested on gene expression profiling of MDA-MB-231 human metastatic breast cancer cells, cultured for 48 h in the absence (control) or presence (treated) of 32 µM resveratrol.

Publication Title

Strategies for comparing gene expression profiles from different microarray platforms: application to a case-control experiment.

Sample Metadata Fields

Sex, Specimen part, Disease, Disease stage, Cell line, Compound

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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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