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accession-icon GSE97743
Host transcription profile in nasal epithelium and blood of hospitalized children under two years old with Respiratory Syncitial Virus infection
  • organism-icon Homo sapiens
  • sample-icon 332 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Host Transcription Profile in Nasal Epithelium and Whole Blood of Hospitalized Children Under 2 Years of Age With Respiratory Syncytial Virus Infection.

Sample Metadata Fields

Sex, Age, Specimen part, Disease, Disease stage

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accession-icon GSE28422
Effects of resistance exercise and resistance training on the skeletal muscle transcriptome in young and old adults
  • organism-icon Homo sapiens
  • sample-icon 109 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Global microarray (HG U133 Plus 2.0) was used to investigate the effects of resistance exercise and resistance training on the skeletal muscle transcriptome profile of 28 young and old adults. Vastus lateralis muscle biopsies were obtained pre and 4hrs post resistance exercise in the beginning (untrained state) and at the end (trained state) of a 12 wk progressive resistance training program.

Publication Title

Transcriptome signature of resistance exercise adaptations: mixed muscle and fiber type specific profiles in young and old adults.

Sample Metadata Fields

Sex, Specimen part, Time

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accession-icon GSE28392
Effects of resistance exercise on the transcriptome in MHC I and MHC IIa muscle fibers of young and old women
  • organism-icon Homo sapiens
  • sample-icon 70 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Global microarray (HG U133 Plus 2.0) was used for the first time to investigate the effects of resistance exercise on the transcriptome in slow-twitch myosin heavy chain (MHC) I and fast-twitch MHC IIa muscle fibers of young and old women. Vastus lateralis muscle biopsies were obtained pre and 4hrs post resistance exercise in the beginning (untrained state) and at the end (trained state) of a 12 wk progressive resistance training program.

Publication Title

Transcriptome signature of resistance exercise adaptations: mixed muscle and fiber type specific profiles in young and old adults.

Sample Metadata Fields

Sex, Specimen part, Subject, Time

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accession-icon GSE25941
Effects of age on the skeletal muscle transcriptome
  • organism-icon Homo sapiens
  • sample-icon 34 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Global microarray (HG U133 Plus 2.0) was used to investigate the basal level skeletal muscle transcriptome profile of young and old adults. One vastus lateralis muscle biopsy was obtained in the basal state from 36 different subjects.

Publication Title

Transcriptome signature of resistance exercise adaptations: mixed muscle and fiber type specific profiles in young and old adults.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE77861
African American esophageal squamous cell carcinoma expression profile reveals loss of detox networks
  • organism-icon Homo sapiens
  • sample-icon 14 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Esophageal carcinoma is the third most common gastrointestinal malignancy worldwide and is generally unresponsive to therapy. African Americans have an increased risk for esophageal squamous cell cancer (ESCC), the subtype that shows marked variation in geographic frequency. To identify key genes involved in ESC carcinogenesis in African Americans we conducted microarray expression profiling and found a significant dysregulation of genes encoding stress response and drug-metabolizing enzymes, mainly in NRF2 pathway. The involvement of NRF2 mediated oxidative damage represent a key step in the evolution of African American ESCC. Loss of activity of these enzymes would confer increased sensitivity of esophageal cells to xenobiotics, such as alcohol and tobacco smoke, and may account for the high incidence of ESCC in this ethnic group. The differential expression profile also indicates an inflammatory component and tissue regeneration in ESCC tumorigenesis. Together, these findings suggest a remarkable interplay of genetic and environmental factors in the pathogenesis of African American ESCC.

Publication Title

African-American esophageal squamous cell carcinoma expression profile reveals dysregulation of stress response and detox networks.

Sample Metadata Fields

Race

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accession-icon GSE52227
Discovery of genes involved in facial midline specification
  • organism-icon Gallus gallus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Chicken Genome Array (chicken)

Description

The patterning of the facial midline involves early specification of neural crest cells to form skeletal tissues that support the upper jaw . In order to understand the molecular mechanisms involved we have taken advantage of a beak duplication model developed in the chicken embryo. Here we can induce the transformation of the side of the beak into a second midline that is easily identifiable by the formation of a supernumerary egg tooth. The phenotype is induced by implanting two microscopic beads, one soaked in retinoic acid and the other soaked in Noggin into the side of the head of the chicken embryo. Here we use microarrays to profile expression of maxillary mesenchyme 16h after placing the beads. A subset of genes were validated using in situ hybridization and QPCR. The aims of the study are to test the function of these genes using retroviral transgenesis, knockdown with morpholinos or expression of secreted proteins and their application to the embryo.

Publication Title

Identification and functional analysis of novel facial patterning genes in the duplicated beak chicken embryo.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon SRP040327
Epigenetic Repogramming by an Environmental Carcinogen Through Chromatin Domain Disruption [RNA-Seq]
  • organism-icon Homo sapiens
  • sample-icon 2 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

Alterations in chromatin modifications, including DNA methylation and histone modification patterns, have been characterized under exposure of several environmental pollutants, including nickel. As with other carcinogenic metals, the mutagenic potential of nickel compounds is low and is not well correlated with its carcinogenic effects. Nickel exposure, however, is associated with alterations in chromatin modifications and related transcriptional programs, suggesting an alternative pathway whereby nickel exposure can lead to disease. To investigate the extent to which nickel exposure disrupts chromatin patterns, we profiled several histone modifications, including H3K4me3, H3K9ac, H3K27me3 and H3K9me2 as well as the insulator binding protein CTCF and the transcriptomes of control BEAS-2B cells and cells treated with nickel for 72 hours. Our results show significant alterations of the repressive histone modification H3K9me2 in nickel-exposed cells with spreading of H3K9me2 into new domains associated with gene silencing. We furthermore show that local regions of active chromatin can protect genes from nickel-induced H3K9me2 spreading. Interestingly, we show that nickel exposure selectively disrupts weaker CTCF sites, leading to spreading of H3K9me2 at these regions. These results have major implications in the understanding of how environmental carcinogens can affect chromatin dynamics and the consequences of chromatin domain disruption in disease progression. Overall design: Treat BEAS-2B cells with NiCl2 for 72 hours and compare histone modification, CTCF binding to control BEAS-2B cells to see how they regulated gene expression by RNA-seq

Publication Title

Epigenetic dysregulation by nickel through repressive chromatin domain disruption.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP000599
Genome-wide annotation of small RNAs expressed in HeLa and HepG2 cells
  • organism-icon Homo sapiens
  • sample-icon 40 Downloadable Samples
  • Technology Badge IconIlluminaGenomeAnalyzer

Description

We report an applicaton of small RNA sequencing using high throughput next generation sequencing to identify the small RNA content of cell lines. By sequencing over 30 million reads we could identify a new class of small RNAs previousy observed with tiling arrays and mapping to promoter regions of coding genes. We also identified a large number of small RNAs corresponding to internal exons of coding genes. By using different enzymatic treatments and immunoprecipitation experiments, we have determined that both the promoter associated small RNAs as well as ones within the body of the genes bear 5'' cap structures. Overall design: Examination of the expression of small RNAs (<200nt).

Publication Title

Post-transcriptional processing generates a diversity of 5'-modified long and short RNAs.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE35243
Expression data from embryonic mouse pleuroperitoneal folds and diaphragms
  • organism-icon Mus musculus
  • sample-icon 24 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Microarray data from this study represent the first global transcriptional survey of gene expression during early compared to late diaphragm formation.

Publication Title

Congenital diaphragmatic hernia candidate genes derived from embryonic transcriptomes.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE44943
HIF-1 dependent gene expression upon S. aureus infection
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

HIF-1 is an important transcription factor for immune responses to bacterial infection. We wanted to analyze the HIF-1 dependent gene expression upon S. aureus infection and analyzed the gene expression of HepG2 nt and HepG2 HIF-1-/- cells four hours upon infection using affymetrix human gene 1.0 st. gene arrays.

Publication Title

Hypoxia-inducible factor 1-regulated lysyl oxidase is involved in Staphylococcus aureus abscess formation.

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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