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accession-icon GSE19467
Characterization of Populus Class III HDZIPs
  • organism-icon Populus tremula x populus alba
  • sample-icon 11 Downloadable Samples
  • Technology Badge Icon Affymetrix Poplar Genome Array (poplar)

Description

Comparison of wild type Populus to transgenics expressing either a miRNA-resistant Populus ortholog of ATHB15/CORONA or miRNA-resistant Populus ortholog of REVOLUTA

Publication Title

The Populus class III HD ZIP, popREVOLUTA, influences cambium initiation and patterning of woody stems.

Sample Metadata Fields

Specimen part

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accession-icon SRP155332
RNAseq data of two week-old soybean leaves response to cold stress
  • organism-icon Glycine max
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Transcriptome analysis of cold-treated leaves (unifoliates) of soybean seedlings were performed. RNAseq analysis was performed using two lanes on a Illumina HiSeq2000 and sequenced on a 100bp, paired-end run. Overall design: Two-weeks old soybean (c.v. 'Williams 82') seedlings were cold-treated (4 °C) starting at 4 h after the lights turned on (Zeitgeber Time, ZT4 h, 18 hours light/6 hours dark) and maintaining 4 °C continuously with the light cycle till harvest time (0, 1, and 24 hours). All treatment samples were performed in triplicate (with n=6 plants per replication).

Publication Title

The Ethylene Signaling Pathway Negatively Impacts CBF/DREB-Regulated Cold Response in Soybean (<i>Glycine max</i>).

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE44623
Transcriptional responses of the zebrafish (Danio rerio) brain to acute sodium selenite supplementation.
  • organism-icon Danio rerio
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Zebrafish Genome Array (zebrafish)

Description

The possible benefits of selenium (Se) supplementation are currently under investigation for prevention of certain cancers and treatment of neurological disorders. Little is known concerning the response of the brain to increased dietary Se under conditions of Se sufficiency, despite the majority of Se supplementation trials occurring in healthy subjects considered Se sufficient. We evaluated the transcriptional response of the zebrafish (Danio rerio) brain to supplementation with nutritionally relevant levels of dietary Se (sodium selenite) during conditions of assumed Se sufficiency.

Publication Title

Sex-specific transcriptional responses of the zebrafish (Danio rerio) brain selenoproteome to acute sodium selenite supplementation.

Sample Metadata Fields

Sex, Age, Specimen part, Treatment

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accession-icon GSE38729
Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio)
  • organism-icon Danio rerio
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Zebrafish Genome Array (zebrafish)

Description

Domesticated animal populations often show profound reductions in predator avoidance and fear-related behavior compared to wild populations. These reductions are remarkably consistent and have been observed in a diverse array of taxa including fish, birds, and mammals. Experiments conducted in common environments indicate that these behavioral differences have a genetic basis. In this study, we quantified differences in fear-related behavior between wild and domesticated zebrafish strains and used microarray analysis to identify genes that may be associated with this variation.

Publication Title

Brain transcriptome variation among behaviorally distinct strains of zebrafish (Danio rerio).

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE28815
Expression comparison between SMC4 and conventional cultures
  • organism-icon Homo sapiens
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

The undifferentiated state of pluripotent stem cells depends heavily on the culture conditions. We show that a unique combination of small molecules, SMC4, added to culture conditions converts primed pluripotent stem cells to a more nave state. By conducting Affymetix analysis we show of majority of lineage markers are repressed in SMC4 culture.

Publication Title

A novel platform to enable the high-throughput derivation and characterization of feeder-free human iPSCs.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon SRP125980
Mutant IDH1 promotes glioma formation in vivo [RNA-seq]
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

RNA was isolated from FFPE samples of IDH1 mutant, WT tumors and normal brains Overall design: Determination of the glioma subtype in IDH1 mutant and WT tumors

Publication Title

Mutant IDH1 Promotes Glioma Formation In Vivo.

Sample Metadata Fields

Specimen part, Subject

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accession-icon GSE46633
Inducible expression of MyoD directly mediates myogenic conversion of human induced pluripotent stem cells (iPSCs) derived from Duchenne muscular dystrophy (DMD).
  • organism-icon Homo sapiens
  • sample-icon 7 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Genome-wide gene expression analysis of MyoD-infected DMD-specific iPSCs (GM05112-M5.1) on days 0 (untreated), day 3 and day 8 post Dox treatment, human primary myoblasts (undifferentiated and as differentiated myotubes), and undifferentiated iPSCs from healthy donors (iPSCs-1 and iPSCs-2).

Publication Title

Myogenic differentiation of muscular dystrophy-specific induced pluripotent stem cells for use in drug discovery.

Sample Metadata Fields

Specimen part

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accession-icon GSE66260
Distinct gene expression programs during erythropoiesis from adult and cord blood progenitor cells compared to hiPSCs
  • organism-icon Homo sapiens
  • sample-icon 73 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Transcriptome Array 2.0 (hta20)

Description

Erythropoiesis in mammals replenishes the circulating red blood cell (RBC) pool from hematopoietic stem/progenitor cells (HSPCs). Two distinct erythropoietic programs have been described. In the first trimester, hematopoietic precursors in the fetal yolk sac follow a primitive pattern of erythropoiesis. However, in the second trimester, hematopoietic stem cells (HSCs) from the fetal liver and later from the bone marrow differentiate by a definitive program of erythropoiesis to yield enucleated erythrocytes. RBCs can also be derived from human induced pluripotent stem cells (hiPSCs) and can express many of the red cell proteins required for normal erythrocyte function, presaging in vitro RBC production for clinical use. However, expansion and enucleation from hiPSCs is less efficient than with erythroblasts (EBs) derived from adult or cord blood progenitors. We hypothesized that substantial differential gene expression during erythroid development from hiPSCs compared to that from adult blood or cord blood precursors could account for these hitherto unexplained differences in proliferation and enucleation. We have therefore grown EBs from human adult and cord blood progenitors and from hiPSCs. Gene expression during erythroid culture from each erythroblast source was analyzed using algorithms designed to cluster co-expressed genes in an unsupervised manner and the function of differentially expressed genes explored by gene ontology. Using these methods we identify specific patterns of gene regulation for adult- and cord- derived EBs, regardless of the medium used, that are substantially distinct from those observed during the differentiation of EBs from hiPSC progenitors which largely follows a pattern of primitive erythropoiesis.

Publication Title

Distinct gene expression program dynamics during erythropoiesis from human induced pluripotent stem cells compared with adult and cord blood progenitors.

Sample Metadata Fields

Specimen part

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accession-icon GSE11107
Effect of starvation on the transcriptomes of the brain and liver in adult female zebrafish (Danio rerio)
  • organism-icon Danio rerio
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Zebrafish Genome Array (zebrafish)

Description

We used microarray analyses in adult female zebrafish (Danio rerio) to identify metabolic pathways regulated by starvation in two key organs that 1) serve biosynthetic and energy mobilizing functions (liver) and 2) consume energy and direct behavioral responses (brain). Starvation affected the expression of 574 transcripts in the liver, indicating an overall decrease in metabolic activity, reduced lipid metabolism, protein biosynthesis and proteolysis, and cellular respiration, and increased gluconeogenesis. Starvation also regulated expression of many components of the Unfolded Protein Response, the first such report in a species other than yeast (Saccharomyces cerevisiae) and mice (Mus musculus). The response of the zebrafish hepatic transcriptome to starvation was strikingly similar to that of rainbow trout (Oncorhynchus mykiss), but very different from common carp (Cyprinus carpio) and mouse. The transcriptome of zebrafish whole brain was much less affected than the liver, with only two differentially expressed genes, both down-regulated. Down-regulation of one of these genes, matrix metalloproteinase 9 (mmp9), suggests increased inhibition of apoptosis (neuroprotection) and decreased restructuring of the extracellular matrix in the brain of starved zebrafish. The low level of response in the transcriptome of whole zebrafish brain agrees with observations that the brain is metabolically protected compared to the rest of the body.

Publication Title

Effect of starvation on transcriptomes of brain and liver in adult female zebrafish (Danio rerio).

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE50868
Induction of Ground-State Pluripotency by Minimal Factor Episomal-Expression in Single Cell Format
  • organism-icon Homo sapiens
  • sample-icon 17 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Human pluripotent stem cells in culture are often associated with the prime state which represents a more developed state relative to the nave state which is often associated with the inner cell mass and thought to have the potential to give rise to all cell types. We have developed a small molecule-driven cocktail FMM that maintains human pluripotent stem cells in a state similar to the naive state as defined by several properties including gene expression profile.

Publication Title

Platform for induction and maintenance of transgene-free hiPSCs resembling ground state pluripotent stem cells.

Sample Metadata Fields

Specimen part

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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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