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accession-icon GSE41890
Expression data from multiple sclerosis patients in remission and relapse
  • organism-icon Homo sapiens
  • sample-icon 67 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Whole-genome expression of peripheral blood leukocytes was measured in 22 patients and 24 controls using the Human Gene 1.0 ST array by Affymetrix

Publication Title

Transcriptomic profile reveals gender-specific molecular mechanisms driving multiple sclerosis progression.

Sample Metadata Fields

Sex, Age, Specimen part, Disease

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accession-icon GSE108998
Allopregnanolone alters the gene expression profile of human glioblastoma cells
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Glioblastomas (GBM) are one of the most frequent and aggressive brain tumors. In these malignancies, progesterone (P4) promotes proliferation, migration, and invasion. The P4 metabolite allopregnanolone (3-THP) similarly promotes cell proliferation in the U87 human GBM cell line.

Publication Title

Allopregnanolone Alters the Gene Expression Profile of Human Glioblastoma Cells.

Sample Metadata Fields

Specimen part, Cell line, Treatment

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accession-icon GSE58758
Expression data from PAO1 and its creBC derivative mutant (PAOcreBC)
  • organism-icon Pseudomonas aeruginosa
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Pseudomonas aeruginosa Array (paeg1a)

Description

We used microarrays to determine the expression profile of the P. aeruginosa creBC mutant regarding its parental wild type strain PAO1.

Publication Title

The Pseudomonas aeruginosa CreBC two-component system plays a major role in the response to β-lactams, fitness, biofilm growth, and global regulation.

Sample Metadata Fields

Treatment

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accession-icon SRP001536
Sorting of Drosophila small silencing RNAs partitions microRNA* strands into the RNA interference pathway
  • organism-icon Drosophila melanogaster
  • sample-icon 13 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer

Description

In flies, small silencing RNAs are sorted between Argonaute1 (Ago1), the central protein component of the microRNA (miRNA) pathway, and Argonaute2 (Ago2), which mediates RNA interference. Extensive double-stranded character—as is found in small interfering RNAs (siRNAs)—directs duplexes into Ago2, whereas central mismatches, like those found in miRNA/miRNA* duplexes, direct duplexes into Ago1. Central to this sorting decision is the affinity of the small RNA duplex for the Dcr-2/R2D2 heterodimer, which loads small RNAs into Ago2. Here, we show that while most Drosophila miRNAs are bound to Ago1, miRNA* strands accumulate bound to Ago2. Like siRNA loading, efficient loading of miRNA* strands in Ago2 favors duplexes with a paired central region and requires both Dcr-2 and R2D2. Those miRNA and miRNA* sequences bound to Ago2, like siRNAs diced in vivo from long double-stranded RNA, typically begin with cytidine, whereas Ago1-bound miRNA and miRNA* disproportionately begin with uridine. Consequently, some pre-miRNA generate two or more isoforms from the same side of the stem that differentially partition between Ago1 and Ago2. Our findings provide the first genome-wide test for the idea that Drosophila small RNAs are sorted between Ago1 and Ago2 according to their duplex structure and the identity of their first nucleotide. Overall design: Sequencing of small RNAs (either total small RNAs or Ago1-associated small RNAs) in wild-type, dcr-2 and r2d2 mutant flies. Small RNA sequencing, Small RNAs (18-29 nt long), Size selection (18 to 30 nt).

Publication Title

Target RNA-directed trimming and tailing of small silencing RNAs.

Sample Metadata Fields

Specimen part, Subject

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accession-icon SRP043482
Drosophila melanogaster Transcriptome or Gene expression
  • organism-icon Drosophila melanogaster
  • sample-icon 7 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer IIx, Illumina HiSeq 2000

Description

piRNA 1U does not cause the secondary piRNA 10A

Publication Title

The initial uridine of primary piRNAs does not create the tenth adenine that Is the hallmark of secondary piRNAs.

Sample Metadata Fields

Sex, Specimen part, Cell line, Treatment

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accession-icon SRP092592
Whole-transcriptome profiling of neovascularized corneas reveal miR-204 as a potent biotherapy deliverable by rAAVs [RNA-Seq]
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Current drugs that directly target pro-angiogenic factors to inhibit or reverse corneal neovascularization, the major sight-threatening pathology caused by angiogenic stimuli, require multiple rounds of administration and have limited efficacies. Here we report the profiling of anti-angiogenic corneal microRNAs (miRNAs), and a framework that employs discovered miRNAs as biotherapies deliverable by recombinant adeno-associated viruses (rAAVs). By querying differentially expressed miRNAs in neovascularized mouse corneas induced by alkali-burn, we have revealed 39 miRNAs that are predicted to target more than 5,500 differentially expressed corneal mRNAs. Among these corneal miRNAs, we selected miR-204 and assessed its efficacy as a therapeutic miRNA in injured corneas. Our results show that delivery of miR-204 by rAAV is efficacious and safe for mitigating corneal NV. Overall, our work demonstrates the discovery of therapeutic miRNAs in corneal disorders and their translation into viable clinical vectors. Overall design: Profiling of mRNAs in normal mouse corneas and corneas injured by alkali burn treatment.

Publication Title

Transcriptome Profiling of Neovascularized Corneas Reveals miR-204 as a Multi-target Biotherapy Deliverable by rAAVs.

Sample Metadata Fields

Sex, Specimen part, Cell line, Subject

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accession-icon SRP018855
An Ancient Transcription Factor Initiates the Burst of piRNA Production During Early Meiosis in Mouse Testes (RNA-Seq)
  • organism-icon Mus musculus
  • sample-icon 20 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Animal germ cells produce PIWI-interacting RNAs (piRNAs), small silencing RNAs that suppress transposons and enable gamete maturation. Mammalian transposon-silencing piRNAs accumulate early in spermatogenesis, whereas pachytene piRNAs are produced later during post-natal spermatogenesis and account for >95% of all piRNAs in the adult mouse testis. Mutants defective for pachytene piRNA pathway proteins fail to produce mature sperm, but neither the piRNA precursor transcripts nor the trigger for pachytene piRNA production is known. Here, we show that the transcription factor A-MYB initiates pachytene piRNA production. A-MYB drives transcription of both pachytene piRNA precursor RNAs and the mRNAs for core piRNA biogenesis factors, including MIWI, the protein through which pachytene piRNAs function. A-MYB regulation of piRNA pathway proteins and piRNA genes creates a coherent feed-forward loop that ensures the robust accumulation of pachytene piRNAs. This regulatory circuit, which can be detected in rooster testes, likely predates the divergence of birds and mammals. Overall design: Transcriptome and ChIP sequencing in mouse and rooster testes

Publication Title

An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE17629
Circadian analysis of miRNAs and their targets
  • organism-icon Drosophila melanogaster
  • sample-icon 27 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome 2.0 Array (drosophila2)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

A role for microRNAs in the Drosophila circadian clock.

Sample Metadata Fields

Specimen part, Time

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accession-icon GSE25899
Paternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammals
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals.

Sample Metadata Fields

Sex, Age

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accession-icon GSE25896
Paternally-induced transgenerational environmental reprogramming of metabolic gene expression in mammals (Affymetrix)
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Epigenetic information can be inherited through the mammalian germline, and represents a plausible transgenerational carrier of environmental information. To test whether transgenerational inheritance of environmental information occurs in mammals, we carried out an expression profiling screen for genes in mice that responded to paternal diet.

Publication Title

Paternally induced transgenerational environmental reprogramming of metabolic gene expression in mammals.

Sample Metadata Fields

No sample metadata fields

View Samples
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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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Developed by the Childhood Cancer Data Lab

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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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