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accession-icon GSE57440
Expression analysis of neurospheres generated in vitro
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Neurospheres generated in vitro were treated with non-epinephrine or potassium chloride. Gene expression analysis was then carried out to identify genes that are up or down regulated due to chemical treatement.

Publication Title

A comparative study of techniques for differential expression analysis on RNA-Seq data.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE27127
Exon-array profiling of Heat-shock stress response in HeLa cell line
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [probe set (exon) version (huex10st)

Description

The heat-shock stress response was studied at the level of exons using Affymetrix Exon-array profiling for both sense and anti-sense transcripts. Sense transcript profiling was done as per the protocol of Affymetrix Exon 1.0 ST array and anti-sense transcript array profiling was done using a modified protocol (Xijin Ge et al., BMC Genomics. 2008 Jan 22;9:27).

Publication Title

Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism.

Sample Metadata Fields

Sex, Specimen part, Cell line

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accession-icon GSE26776
Transcriptome-wide changes in HeLa cell line investigated in response to Heat-shock stress
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina human-6 v2.0 expression beadchip

Description

The repertoire of transcripts that are differentially regulated in response to Heat-shock were studied using Illumina WG-6 v2.0 BeadChip.

Publication Title

Heat shock factor binding in Alu repeats expands its involvement in stress through an antisense mechanism.

Sample Metadata Fields

Sex, Specimen part, Cell line

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accession-icon GSE12378
Integration of ERG gene mapping and gene expression profiling identifies distinct categories of human prostate cancer
  • organism-icon Homo sapiens
  • sample-icon 39 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Exon 1.0 ST Array [transcript (gene) version (huex10st)

Description

OBJECTIVE: Previous expression microarray analyses have failed to take into consideration the genetic heterogeneity and complex patterns of ERG gene alteration frequently found in cancerous prostates. The objective of this study is for the first time, to integrate the mapping of ERG gene alterations with the collection of expression microarray data.

Publication Title

Integration of ERG gene mapping and gene-expression profiling identifies distinct categories of human prostate cancer.

Sample Metadata Fields

Sex, Specimen part

View Samples
accession-icon GSE24170
Stable Set8 effect on gene expression in U2OS cells
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Ubiquitin-mediated proteolysis play a significant role in various biological processes including transcription, DNA repair and cell cycle progression. The identification of Set8 and Set8b (a splice isoform) histone H4K20 methyl transferase as a substrate for the cullin-based ubiquitin ligase (CRL4-Cdt2) demonstrate that this pathway plays a significant role in promoting cell cycle progression, specifically promoting G2 progression. This study investigate the effect of failure to degrade Set8 in S-phase of the cell cycle via CRL4-Cdt2 on gene expression.

Publication Title

CRL4(Cdt2) regulates cell proliferation and histone gene expression by targeting PR-Set7/Set8 for degradation.

Sample Metadata Fields

Cell line

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accession-icon SRP135821
RUNX1 mutations lead to a myeloid differentiation block by altering the RUNX1 transcriptional program (RNA-Seq)
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

Mutations in the RUNX1 gene (RUNX1mut) have been established in myelodysplasia (MDS), de novo and secondary acute myeloid leukaemia (AML), and are in general associated with an unfavourable clinical outcome. Familial RUNX1 mutations are associated with familial thrombocytopenia and these patients have a predisposition to AML development. However, a number of studies have been performed so far in mice which might be distinct from the human hematopoietic system. Therefore we studied the cellular phenotypes, the RUNX1 binding pattern and expression profile induced by RUNX1mut in cord blood (CB) CD34+ cells and induced pluripotent stem cell (iPSC) and compared these findings to primary RUNX1mut AML's. Overall design: A total of nine samples were subject to RNA-Seq including RUNX1mut-transduced cord blood CD34 cells and time-course iPSCs.

Publication Title

RUNX1 mutations enhance self-renewal and block granulocytic differentiation in human in vitro models and primary AMLs.

Sample Metadata Fields

Specimen part, Subject

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accession-icon SRP182844
Gene expression profile in response to HIF-1a inhibition together with PPARa activation and the postnatal factors (T3, IGF-1 and dexamethasone) in hiPSC-CMs
  • organism-icon Homo sapiens
  • sample-icon 36 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Methods: RNA-seq libraries were prepared using the Illumina TruSeq technology. The libraries were quantified and samples were multiplexed in each lane of the flowcell. Cluster generation was performed and then sequenced on the Illumina HiSeq2500 system. Reads were mapped on the Human Genome Reference (GRCh38) and normalized expression table was generated. Results: Among differentially expressed genes, compared with DMSO-treated hiPSC-CMs, 505 genes were upregulated in FM+WY+TID-treated hiPSC-CMs, with 72 genes commonly upregulated in both FM+WY+TID-treated hiPSC-CMs and LV groups and 949 genes were downregulated in FM+WY+TID-treated hiPSC-CMs and 2137 genes were downregulated in LV, with 437 genes downregulated in both FM+WY+TID-treated hiPSC-CMs and LV compared with DMSO-treated hiPSC-CMs . Conclusions: Data demonstrate increased expression of genes associated with many metabolic processes which are also highly enriched in human pediatric heart samples including many interconnected metabolic processes that are upstream of lipid metabolism and FAO, agreeing with the shift to FAO for energy utilization in more mature CMs, and decreased expression of genes involved in developmental processes, adhesion and signaling in both FM+WY+TID-treated hiPSC-CMs and LV. The overlap in both upregulated and downregulated genes in both groups confirmed an advanced degree of cardiomyocyte maturation in response to FM+WY+TID. Overall design: RNA-sequencing analysis was performed to compare global gene expression profiles of hiPSC-CMs at differentiation day 28 with maturation factors (FM+WY+TID) treatment (Treat) vs. DMSO treatment (DMSO) vs. left ventricle tissue sample (LV).

Publication Title

Targeting HIF-1α in combination with PPARα activation and postnatal factors promotes the metabolic maturation of human induced pluripotent stem cell-derived cardiomyocytes.

Sample Metadata Fields

Specimen part, Subject

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accession-icon SRP078938
Global gene expression profiles of cardiac progenitors differentiated from human pluripotent stem cells in 3D culture under simulated microgravity
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 1000

Description

Methods: RNA-seq libraries were prepared using the Illumina TruSeq RNA kit and the TrueSeq method was employed for mRNA enrichment. The libraries were quantified and samples were multiplexed in each lane of the flowcell. Cluster generation was performed and then sequenced on the Illumina HiSeq1000 system. Reads were mapped on the Human Genome Reference and normalized expression table was generated. Results: Among differentially expressed genes, 53 of them were up-regulated and 75 were down-regulated. Conclusions: Data demonstrate increased expression of genes associated with growth, development, and pro-survival in cardiac progenitors cultured under simulated microgravity compared with those cultured under standard gravity. Overall design: RNA-sequencing analysis was performed to compare global gene expression profiles of cells at differentiation day 8 under simulated microgravity vs. standard gravity.

Publication Title

Simulated Microgravity and 3D Culture Enhance Induction, Viability, Proliferation and Differentiation of Cardiac Progenitors from Human Pluripotent Stem Cells.

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon SRP068092
BBBomics - Human Blood Brain Barrier Transcriptomics Hub [RNA-seq]
  • organism-icon Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2000

Description

Functional and structural dysfunction of the blood brain barrier (BBB) leads to severe alterations in brain physiology and is believed to trigger neurodegeneration. To investigate the molecular mechanisms driving the BBB dysfunction, very few human BBB cell culture models are available; of which, the human microvascular endothelial cell line (hCMEC/D3) is the most widely used. Thus far, array-based approaches or targeted seqeuncing based approaches have been employed to characterize the gene expression of the hCMEC/D3 model. However,The goal of this study is to perform deep transcriptomic sequencing of the BBB cell line and obtain features like gene expression, expressed single nucleotide variants, alternate splice forms, circular RNAs, long non-coding RNAs and micro RNAs. Overall design: We have developed blood brain barriers transcriptomics landscape using RNA sequencing and micro RNA seqeuncing data obtained from replicates of hCMEC/D3 BBB cell line.

Publication Title

BBBomics-Human Blood Brain Barrier Transcriptomics Hub.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE60489
Global heart transcript data from fasted male BXD strains on chow or high fat diet
  • organism-icon Mus musculus
  • sample-icon 79 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 2.0 ST Array (mogene20st)

Description

Transcript data from heart tissue from fasted-state male BXD strains on chow or high fat diet

Publication Title

Quantifying and Localizing the Mitochondrial Proteome Across Five Tissues in A Mouse Population.

Sample Metadata Fields

Specimen part, 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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