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accession-icon GSE21611
Oscillating gene expression determines competence for periodic branching in the Arabidopsis root
  • organism-icon Arabidopsis thaliana
  • sample-icon 39 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

The Oscillation Zone (OZ) of unsynchronized roots was disected and divided into an upper (OZ2) and lower (OZ1) half .

Publication Title

Oscillating gene expression determines competence for periodic Arabidopsis root branching.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE60157
Bird Factors integrate positional signals to coordinate asymmetric cell division and cell fate
  • organism-icon Arabidopsis thaliana
  • sample-icon 38 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

We sorted for GFP+ cells using the enhancer trap J0571 with the UAS promoter driving the expression of different BIRD genes. Different genetic backgrounds are use and listed below.

Publication Title

Transcriptional control of tissue formation throughout root development.

Sample Metadata Fields

Specimen part

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accession-icon GSE15876
The SHR/SCR pathway directly activates genes involved in asymmetric cell division in the Arabidopsis root
  • organism-icon Arabidopsis thaliana
  • sample-icon 23 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Asymmetric division of cortex/endodermal initials (CEI) in the Arabidopsis root generates two layers of ground tissue and is controlled by a finely orchestrated interplay between the transcription factors, SHORT ROOT (SHR) and SCARECROW (SCR). To understand the dynamics of the SHR/SCR regulatory network we performed microarray time course experiments using inducible versions of SHR and SCR and examined their transcriptional effects specifically in the ground tissue.

Publication Title

Spatiotemporal regulation of cell-cycle genes by SHORTROOT links patterning and growth.

Sample Metadata Fields

Treatment

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accession-icon GSE16469
Cell signalling by microRNA165/6 directs gene dose dependent root cell fate
  • organism-icon Arabidopsis thaliana
  • sample-icon 3 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

A key question in developmental biology is how cells exchange positional information for proper patterning during organ development. In plant roots the radial tissue organization is highly conserved with a central vascular cylinder in which two water conducting cell types, protoxylem and metaxylem, are patterned centripetally. We show that this patterning occurs through crosstalk between the vascular cylinder and the surrounding endodermis mediated by cell-to-cell movement of a transcription factor in one direction and microRNAs in the other. SHORT ROOT, produced in the vascular cylinder, moves into the endodermis to activate SCARECROW. Together these transcription factors activate MIR165a and 166b. Endodermally produced miR165/6 then acts to degrade its target mRNAs encoding class III homeodomain-leucine zipper transcription factors in the endodermis and stele periphery. The resulting differential distribution of target mRNA in the vascular cylinder determines xylem cell types in a dosage dependent manner.

Publication Title

Cell signalling by microRNA165/6 directs gene dose-dependent root cell fate.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE53378
Adipose transcriptome and microRNA profiles after surgery-induced weight loss
  • organism-icon Homo sapiens
  • sample-icon 13 Downloadable Samples
  • Technology Badge Icon Affymetrix Multispecies miRNA-3 Array (mirna3), Affymetrix Human Gene 2.0 ST Array (hugene20st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Surgery-Induced Weight Loss Is Associated With the Downregulation of Genes Targeted by MicroRNAs in Adipose Tissue.

Sample Metadata Fields

Sex, Specimen part, Subject

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accession-icon GSE53376
Adipose transcriptome and microRNA profiles after surgery-induced weight loss [mRNA]
  • organism-icon Homo sapiens
  • sample-icon 13 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 2.0 ST Array (hugene20st), Affymetrix Multispecies miRNA-3 Array (mirna3)

Description

Molecular mechanisms associated with pathophysiological variations in adipose tissue (AT) are not fully recognized. The main aim of this study was to identify novel candidate genes and miRNAs that may contribute to the pathophysiology of hyperplastic AT. Therefore, wide gene and microRNA (miRNA) expression patterns were assessed in subcutaneous AT of 16 morbidly obese women before and after surgery-induced weight loss. Validation of microarray data was performed by quantitative real-time PCR both longitudinally (n=25 paired samples) and cross-sectionally (25 obese vs. 26 age-matched lean women). Analyses in macrophages and differentiated human adipocytes were also performed to try to comprehend the associations found in AT. 5,018 different probe sets identified significant variations in gene expression after treatment (adjusted p-value<0.05). A set of 16 miRNAs also showed significant modifications. Functional analysis revealed changes in genes and miRNAs associated with cell cycle, development and proliferation, lipid metabolism, and the inflammatory response. Canonical affected pathways included TREM1, PI3K, and EIF2 signaling, hepatic stellate cell activation, and mitochondrial function. Increased expression of SLC27A2, ELOVL6, FASN, GYS2, LGALS12, PKP2, ACLY, and miR-575, as well as decreased FOS, EGFL6, PRG4, AQP9, DUSP1, RGS1, EGR1, SPP1, LYZ, miR-130b, miR-221, and miR-155, were further validated. The clustering of similar expression patterns for gene products with related functions revealed molecular footprints, some of them described for the first time, which elucidate changes in biological processes after the surgery-induced weight loss.

Publication Title

Surgery-Induced Weight Loss Is Associated With the Downregulation of Genes Targeted by MicroRNAs in Adipose Tissue.

Sample Metadata Fields

Sex, Specimen part, Subject

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accession-icon SRP181957
Molecular basis of neuronal subtype bias introduced by proneural factors Ascl1 and Neurog2 (single-cell RNA-seq)
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

Basic helix-loop-helix (bHLH) proneural transcription factors (TFs) Ascl1 and Neurog2 are integral to the development of the nervous system. Here, we investigated the molecular mechanisms by which Ascl1 and Neurog2 control the acquisition of generic neuronal fate and impose neuronal subtype identity. Using direct neuronal programming of embryonic stem cells, we found that Ascl1 and Neurog2 regulate distinct targets by binding to largely different sets of sites. Their divergent binding pattern is not determined by the previous chromatin state but distinguished by specific E-box enrichments which reflect the DNA sequence preference of the bHLH domain. The divergent Ascl1 and Neurog2 binding patterns result in distinct chromatin accessibility and enhancer activity landscapes that shape the binding and activity of downstream TFs during neuronal specification. Our findings suggest that proneural factors contribute to neuronal diversity by differentially altering the chromatin landscapes that shape the binding of neuronally expressed TFs. Overall design: Single-cell RNA-seq was used to characterize gene expression in mixed populations of mES cells containing induced expression of either Ascl1 or Neurog2.

Publication Title

Proneural factors Ascl1 and Neurog2 contribute to neuronal subtype identities by establishing distinct chromatin landscapes.

Sample Metadata Fields

Specimen part, Treatment, Subject

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accession-icon GSE117013
Gene expression array of brain, mandible and maxilla tissues from P0 FoxO6-/- and wildtype mice
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

FoxO6 is expressed in the brain, craniofacial region and somite, but the precise role of FoxO6 in craniofacial development remain unknown. We found that FoxO6 is expressed specifically in craniofacial tissues and FoxO6-/- mice undergo expansion of the face, frontal cortex, olfactory component and skull.

Publication Title

FoxO6 regulates Hippo signaling and growth of the craniofacial complex.

Sample Metadata Fields

Specimen part

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accession-icon SRP161686
Epigenetic signatures associated with paternally-expressed imprinted genes in the endosperm
  • organism-icon Arabidopsis thaliana
  • sample-icon 5 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Genomic imprinting is an epigenetic phenomenon causing parental alleles to be active depending on their parent-of-origin. In plants, imprinted genes are mainly confined to the endosperm, an ephemeral tissue supporting embryo development. Differential methylation of histone H3 on lysine 27 (H3K27me3) established by the Polycomb Repressive Complex 2 (PRC2) is a major regulatory mechanism determining activity of paternally expressed imprinted genes (PEGs) in animals and plants.  Here, we show that the coding region of many PEGs is marked by an epigenetic signature of H3K27me3, H3K9me2 and CHG methylation and that the combination of these three modifications correlates with paternally-biased gene expression in the endosperm. The maternal alleles of PEGs are marked by CHG methylation in the central cell, indicating that the repressive epigenetic signature of PEGs is established before fertilization. We use the presence of the three modifications to predict novel PEGs and propose that genomic imprinting is substantially more common than previously estimated based on expression data.   Overall design: Col × Ler reciprocal crosses were performed using Arabidopsis lines expressing PHE1::NTF and PHE1::BirA. 4DAP siliques were collected and tissue homogenization and nuclei purification were performed from three biological replicates for LerxCol and two for ColxLer using INTACT. Total RNA was extracted from purified nuclei using the mirVana Isolation Kit Protocol (Ambion). mRNA extraction was performed using NEBNext Poly(A) mRNA Magnetic Isolation and the Libraries were prepared with the NEBNext Ultra II RNA Library Prep Kit from Illumina. Samples were sequenced at the National Genomic Infrastructure (NGI) from SciLife Laboratory (Uppsala, Sweden) on an Illumina HiSeq2500 in paired-end 125bp read length.

Publication Title

Epigenetic signatures associated with imprinted paternally expressed genes in the Arabidopsis endosperm.

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE29115
Microarray Expression Data from Haematopoietic Differentiated Human Embryonic Stem Cells
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

The underlying mechanisms which are responsible and govern early haematopoietic differentiation during development are poorly understood. Gene expression comparison between pluripotent human embryonic stem cells and earliest haematopoietic progenitors may reveal novel transcripts and pathways and provide crucial insight into early haematopoietic lineage specification and development.

Publication Title

Large-scale transcriptional profiling and functional assays reveal important roles for Rho-GTPase signalling and SCL during haematopoietic differentiation of human embryonic stem cells.

Sample Metadata Fields

Specimen part, Cell line

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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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