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accession-icon SRP162020
Antiviral and anti-inflammatory properties of novel anti-HIV candidate ABX464 promotes specifics RNA splicing while preserving cellular RNA integrity.
  • organism-icon Homo sapiens
  • sample-icon 18 Downloadable Samples
  • Technology Badge IconNextSeq 500

Description

Purpose: To ensure that ABX464 acted specifically on HIV splicing and did not significantly or globally affect the splicing events of human genes, we used an assembly approach of HIV (YU2 strain) putative transcripts and human long non-coding sequences from paired-reads (2x75bp) captured on a NimbleGen SeqCap® EZ Developer Library (Roche/NimbleGen). Methods: Cells were infected with 80 ng of p24/106 cells of the YU-2 strain for 4 to 6 hours and then rinsed with PBS before medium renewal, followed by high-throughput RNAseq from custom SeqCap EZ capture libraries. Each raw dataset of the samples contained between 5 and 30 million paired-end reads (75 bp), with an average of approximately 12 million raw reads per sample. Results: The raw reads were then cleaned and assembled per library to generate contigs, giving an average of 930 contigs per sample for further analyses. Conclusions: Our results show that high-throughput analyses coupled with bioinformatics-specific tools offers a comprehensive and more accurate view of mRNA splicing within a cell. Overall design: We used buffy coats from HIV-negative individuals were obtained from the local blood donation center, then human peripheral blood mononuclear cells (PBMCs) were isolated by Ficoll (Histopaque, Sigma) gradient centrifugation. Cells were infected with 80 ng of p24/106 cells of the YU-2 strain for 4 to 6 hours and then rinsed with PBS before medium renewal.

Publication Title

Both anti-inflammatory and antiviral properties of novel drug candidate ABX464 are mediated by modulation of RNA splicing.

Sample Metadata Fields

Specimen part, Treatment, Subject

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accession-icon GSE6024
eif3h/WT polysome loading
  • organism-icon Arabidopsis thaliana
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Microarray comparisons of polysome loading in wild-type Arabidopsis and eif3h mutant

Publication Title

On the functions of the h subunit of eukaryotic initiation factor 3 in late stages of translation initiation.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE6025
eif3h/WT transcript level
  • organism-icon Arabidopsis thaliana
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Microarray comparisons of transcript level in wild-type Arabidopsis and eif3h mutant plants.

Publication Title

On the functions of the h subunit of eukaryotic initiation factor 3 in late stages of translation initiation.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP018945
Interferon-mediated innate immune responses against malaria parasite liver stages
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer

Description

Identification of innate immune responses in the livers of mice infected with liver-stage arresting, transgenic, Plasmodium yoelii parasites. Overall design: Whole liver samples from mock and P. yoelli fabb/f- infected C57BL/6 and BALB/cJ mice. Samples were taken 1 and 3 days post infection

Publication Title

Interferon-mediated innate immune responses against malaria parasite liver stages.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE27296
Targeting genes of AP-2d in the mouse midbrain
  • organism-icon Mus musculus
  • sample-icon 2 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)

Description

Identification of AP-2d target genes in the midbrain of E15 mouse embryos

Publication Title

AP-2δ is a crucial transcriptional regulator of the posterior midbrain.

Sample Metadata Fields

Specimen part

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accession-icon GSE45423
Gene expression profile in the heart of wild type and Adenosine Receptor A2a over expressing mice
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Adenosine binds to 4 G protein-coupled receptors located on the cardiomyocyte (A1-R, A2a-R, A2b-R and A3-R) and modulates cardiac function during both ischemia and load-induced stress. While the role of adenosine receptor-subtypes has been well defined in the setting of ischemia-reperfusion, far less is known regarding their roles in protecting the heart during other forms of cardiac stress.

Publication Title

Identification of candidate long noncoding RNAs associated with left ventricular hypertrophy.

Sample Metadata Fields

Specimen part

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accession-icon GSE58370
The Enzyme-Like Domain of Arabidopsis Nuclear Beta-Amylases is Critical During DNA Sequence Recognition and Transcriptional Activation
  • organism-icon Arabidopsis thaliana
  • sample-icon 27 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Plant BZR1-BAM transcription factors contain a -amylase (BAM)-like domain, characteristic of proteins involved in starch breakdown. The enzyme-derived domains appear to be non-catalytic, but determine the function of the Arabidopsis thaliana BZR1-BAMs (BAM7 and BAM8) during transcriptional initiation. Microarray experiments with plants overexpressing different mutant versions of the proteins show that only functional BZR1-BAM variants deregulate gene expression and cause leaf developmental abnormalities. Transcriptional changes caused by overexpression of the BZR1 domain alone indicate that the BAM domain increases selectivity for the preferred cis-regulatory element BBRE (BZR1-BAM Responsive Element).

Publication Title

The Enzyme-Like Domain of Arabidopsis Nuclear β-Amylases Is Critical for DNA Sequence Recognition and Transcriptional Activation.

Sample Metadata Fields

Age, Specimen part, Treatment

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accession-icon GSE9570
Expression data from embryonic rat kidney timepoints and a budded WD-MM recombination tissue
  • organism-icon Rattus norvegicus
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

Here we compared the expression of an engineered kidney tissue, created by recombining an in vitro budded Wolffian duct with fresh E13 metanephric mesenchyme, with that of three in vivo rat embryonic kidney timepoints (E13, E18, and week 4)

Publication Title

Staged in vitro reconstitution and implantation of engineered rat kidney tissue.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP016623
De novo piRNA cluster formation in the Drosophila germline triggered by transgenes containing a transcribed transposon fragment
  • organism-icon Drosophila melanogaster
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

PIWI interacting RNAs (piRNAs) provide defense against transposable element (TE) expansion in the germline of metazoans. piRNAs are processed from the transcripts encoded by specialized heterochromatic clusters enriched in damaged copies of transposons. How these regions are recognized as a source of piRNAs is still elusive. The aim of this study is to determine how transgenes that contain a fragment of the LINE-like I transposon lead to an acquired TE resistance in Drosophila. We show that such transgenes, being inserted in unique euchromatic regions which normally do not produce small RNAs, become de novo bidirectional piRNA clusters that silence I-element activity in the germline. Strikingly, small RNAs of both polarities are generated from the entire transgene and flanking genomic sequences — not only from the transposon fragment. Chromatin immunoprecipitation analysis shows that in ovaries the trimethylated histone 3 lysine 9 (H3K9me3) mark associates with transgenes producing piRNAs. We show that transgene-derived hsp70 piRNAs stimulate in trans cleavage of cognate endogenous transcripts with subsequent processing of the non-homologous parts of these transcripts into piRNAs. Overall design: The fractions of small RNAs (19-29 nt) from ovaries of wild type and 11 transgenic lines of Drosophila melanogaster were sequenced using Illumina HiSeq 2000.

Publication Title

De novo piRNA cluster formation in the Drosophila germ line triggered by transgenes containing a transcribed transposon fragment.

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon GSE18043
Priming integrin alpha5 promotes human mesenchymal stromal cell osteoblast differentiation and osteogenesis
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Human adult mesenchymal stromal cells (hMSC) have the potential to differentiate into chondrogenic, adipogenic or osteogenic lineages, providing a potential source for tissue regeneration. An important issue for efficient bone regeneration is to identify factors that can be targeted to promote the osteogenic potential of hMSCs. Using transcriptomic analysis, we found that integrin alpha5 (ITGA5) expression is upregulated during dexamethasone-induced hMSCs osteoblast differentiation. Gain-of-function studies showed that ITGA5 promotes the expression of osteoblast phenotypic markers as well as in vitro osteogenesis in hMSCs. Downregulation of endogenous ITGA5 using shRNA blunted osteoblast marker expression and osteogenic differentiation. Pharmacological and molecular analyses showed that the enhanced hMSCs osteoblast differentiation induced by ITGA5 was mediated by activation of FAK/ERK1/2-MAPKs and PI3K signaling pathways. Remarkably, activation of ITGA5 using a specific antibody that primes the integrin or a peptide that specifically activates ITGA5 was sufficient to enhance ERK1/2-MAPKs and PI3K signaling and to promote osteoblast differentiation and osteogenic capacity of hMSCs. We also demonstrate that hMSCs engineered to over-express ITGA5 exhibited a marked increase in their osteogenic potential in vivo. These findings not only reveal that ITGA5 is required for osteoblast differentiation of adult human MSCs but also provide a novel targeted strategy using ITGA5 agonists to promote the osteogenic capacity of hMSCs, which may be used for tissue regeneration in bone disorders where the recruitment or capacity of MSCs is compromised.

Publication Title

Priming integrin alpha5 promotes human mesenchymal stromal cell osteoblast differentiation and osteogenesis.

Sample Metadata Fields

Sex, Age, 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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