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accession-icon SRP034011
Transcriptomic analysis of Plasmodium PBANKA, PBSLTRiP-KO, PB268-KO parasite infected and uninfected host cell
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIlluminaGenomeAnalyzerIIx

Description

Liver stage of malaria parasite exports SLTRiP and PB268 to the cytosol of parasite infected host cell. To know the host genes perturbed by WT-PBANKA, SLTRiP-KO and PB268-KO parasite growth, we did transcriptomic sequencing of infected host cells. We did mRNA sequencing of four samples for comparative analysis of WT and PB-knockout parasites infected host cells at 22 hours of post sporozoites infection. Overall design: mRNA profiles of Plasmodium PBANKA, PBSLTRiP-KO, PB268-KO parasite infected and uninfected HepG2 cells after 22hrs of sporozoites infections were generated by deep sequencing using Illumina GAIIx.

Publication Title

A Sporozoite- and Liver Stage-expressed Tryptophan-rich Protein Plays an Auxiliary Role in Plasmodium Liver Stage Development and Is a Potential Vaccine Candidate.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE33552
Expression data from MDA-MB-231 cell line treated with Zoledronate, or Fluvastatin, or mock-treated control cells.
  • organism-icon Homo sapiens
  • sample-icon 40 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Statins and bisphosponates (BPs) are two distinct classes of isoprenoid pathway inhibitors targeting HMG-CoA reductase (upstream enzyme) and Farnesyl-pyrophospate synthase (downstream enzyme) respectively. Here we conducted a comparative study of two representatives of these classes, fluvastatin (Fluva) and Zoledronate (Zol), to assess the differences in their in vivo metastatic potentials and pharmacogenomic profiles. Both drugs, being administered after emergence of detectable metastases, appeared to be potent metastasis inhibitors in MDA-MB-231 breast cancer metastasis model. We observed a reduced number of metastatic sites under Fluva, but not Zol treatment. Combinatorial in vivo treatment by Fluva and Zol showed no synergy for these drugs, as reported earlier on the basis of in vitro studies (Budman DR, Oncology 2006), staying in line with similarity of their transcriptomic profiles. Comparison of Zol and Fluva transcriptomic profiles revealed similar patterns of affected genes (describe involved genes functions) through different kinetics (when treated with IC50 determined for 72h treatment, the majority of changes were observed after 24h incubation with Fluva , and only after 48h incubation with Zol at 72h-IC50 or after 24h treatment with its 3 times higher dose). We demonstrated here that targeting different enzymes of the same pathway neither necessarily leads to distinct changes in gene profiles, nor to synergy for in vivo anti-metastatic potential.

Publication Title

Transcriptome analysis and in vivo activity of fluvastatin versus zoledronic acid in a murine breast cancer metastasis model.

Sample Metadata Fields

Cell line, Time

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accession-icon GSE21651
Differential expression for salt and drought stress
  • organism-icon Oryza sativa
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

Leaf samples were used. We exposed young seedlings to NaCl and drought.

Publication Title

Identification of cis-regulatory elements associated with salinity and drought stress tolerance in rice from co-expressed gene interaction networks.

Sample Metadata Fields

Specimen part

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accession-icon SRP127737
Widespread Changes in Transcriptome Profile of Human Mesenchymal Stem Cells Induced by Two-Dimensional (2D) Nanosilicates
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Two-dimensional (2D) nanomaterials, an ultrathin class of materials such as graphene, nanoclays, transition metal dichalcogenides (TMDs), and transition metal oxides (TMOs), have emerged as a new generation of materials due to their unique properties relative to macroscale counterparts. However, little is known about the transcriptome dynamics following exposure to these nanomaterials. Here we investigate the interactions of 2D nanosilicates, a layered clay, with human mesenchymal stem cells (hMSCs) at the whole transcriptome level by high-throughput sequencing (RNA-seq). Analysis of cell-nanosilicate interactions by monitoring change in transcriptome profile uncovers key biophysical and biochemical cellular pathways triggered by nanosilicates. A widespread alteration of genes is observed due to nanosilicate exposure as more than 4,000 genes are differentially expressed. The change in mRNA expression levels reveal clathrin-mediated endocytosis of nanosilicates. Nanosilicate attachment to cell membrane and subsequent cellular internalization activate stress-responsive pathways such as mitogen activated protein kinase (MAPK), which subsequently directs hMSC differentiation towards osteogenic and chondrogenic lineages. This study provides transcriptomic insight on the role of surface-mediated cellular signaling triggered by nanomaterials and enables development of nanomaterials-based therapeutics for regenerative medicine. This approach in understanding nanomaterial-cell interactions, illustrates how change in transcriptomic profile can predict downstream effects following nanomaterial treatment.  Overall design: Examination of affect of 2D nanosilicates on hMSCs

Publication Title

Widespread changes in transcriptome profile of human mesenchymal stem cells induced by two-dimensional nanosilicates.

Sample Metadata Fields

Specimen part, Treatment, Subject

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accession-icon E-MEXP-2506
Transcription profiling by array of rice grown in different light and temperature cycles
  • organism-icon Oryza sativa
  • sample-icon 78 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

Rice (Oryza sativa, ssp. Japonica, cv. Nipponbare 1) plants were grown in a Conviron PGR 15 growth chamber using precise control of temperature, light, and humidity.<br></br>Diurnal (driven) conditions included 12L:12D light cycles and 31C/20C thermocycles in three different combinations. These were: photocycles (LDHH), 12 hrs. light (L)/12 hrs. dark (D) at a constant temperature (31C; HH); photo/thermocycles (LDHC): 12 hrs. light (L) /12 hrs. dark (D) with a high day temperature (31C) and a low night temperature (20C); and thermocycles (LLHC): continuous light (LL) with 12 hrs. high/12 hrs. low temperature (31C, day; 20C, night). Light intensity and relative humidity were 1000 micromol m-2s-2 and 60%, respectively.<br></br>Three-month-old rice plants were entrained for at least one week under the respective condition prior to initiation of each experiment. Leaves and stems from individual rice plants were collected every four hours for 48 hrs in driven (diurnal) conditions followed by a two day freerun spacer under continuous light/temperature followed by two additional days of sampling under the same continuous free run condition.<br></br>

Publication Title

Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules.

Sample Metadata Fields

Age, Specimen part, Time

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accession-icon E-MTAB-275
Transcription profiling by array of rice Indica 93-11 after growth in different light and temperature conditions
  • organism-icon Oryza sativa
  • sample-icon 37 Downloadable Samples
  • Technology Badge Icon Affymetrix Rice Genome Array (rice)

Description

Rice (Oryza sativa, spp. Indica, cv. 93-11) plants were grown in a Conviron PGR 15 growth chamber using precise control of temperature, light, and humidity.<br></br>Diurnal (driven) conditions included 12L:12D light cycles and 31C/20C thermocycles in three different combinations. These were: photocycles (LDHH), 12 hrs. light (L)/12 hrs. dark (D) at a constant temperature (31C; HH); photo/thermocycles (LDHC): 12 hrs. light (L) /12 hrs. dark (D) with a high day temperature (31C) and a low night temperature (20C); and thermocycles (LLHC): continuous light (LL) with 12 hrs. high/12 hrs. low temperature (31C, day; 20C, night). Light intensity and relative humidity were 1000 micromol m-2s-2 and 60%, respectively.<br></br>Three-month-old rice plants were entrained for at least one week under the respective condition prior to initiation of each experiment. Leaves and stems from individual rice plants were collected every four hours for 48 hrs in driven (diurnal) conditions followed by a two day freerun spacer under continuous light/temperature followed by two additional days of sampling under the same continuous free run condition.

Publication Title

Global profiling of rice and poplar transcriptomes highlights key conserved circadian-controlled pathways and cis-regulatory modules.

Sample Metadata Fields

Age, Specimen part, Time

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accession-icon GSE107005
Herpesvirus-encoded microRNAs alter transcriptome of oral keratinocytes
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 2.0 ST Array (hugene20st)

Description

We investigated the impact of on miR-H1 and miR-K12-3-3p- on host transcriptome focusing on gingival epithelial cells that are target sites for various HHV.

Publication Title

Herpesvirus-encoded microRNAs detected in human gingiva alter host cell transcriptome and regulate viral infection.

Sample Metadata Fields

Specimen part

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accession-icon GSE20404
Gene expression signatures of HO-1 in BeWo cells
  • organism-icon Homo sapiens
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

Heme Oxygenase-1 (HO-1) is expressed in many cancers and influences the growth, survivall and metastasis of tumors, however, the molecular mechanisms remains largely unknown. To identify a common mechanism of action of HO-1 in cancer, we studied the global effect of HO-1 on the transcriptome of multiple tumors. Genome-wide expression profiling of HO-1 expressing versus HO-1 silenced cancer cells and a further data mining analysis of the preexisting expression database of 190 human tumors of 14 cancer types led us to identify 14 genes, the expression of which correlated firmly and universally with that of HO-1 (P < 0.001). These genes included regulators of cell plasticity and extracellular matrix remodeling (MMP2, ADAM8, TGF1, BGN, COL21A1, PXDN), signaling (CRIP2, MICB), amino acid transport and glycosylation (SLC7A1 and ST3GAL2), estrogen and phospholipid biosynthesis (AGPAT2 and HSD17B1), protein stabilization (IFI30) and phosphorylation (ALPPL2). PXDN, one of the genes being co-expressed with HO-1, was selected for further analysis. Immunofluorescence and western blotting confirmed positive correlation of PXDN with HO-1 levels in BeWo cancer cells as well as co-localization in invasive extravillous trophoblast cells of first trimester placenta. Loss of HO-1 in BeWo cells correlated with reduced cell adhesion to Collagen type I, Fibronectin and Laminin. The adhesion-promoting effects of HO-1 were dependent on PXDN expression, as loss of PXDN in HO-1 expressing BeWo cells led to reduced cell attachment to Laminin and Fibronectin coated wells.

Publication Title

Transcriptome analysis of human cancer reveals a functional role of heme oxygenase-1 in tumor cell adhesion.

Sample Metadata Fields

Specimen part

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accession-icon GSE87557
Role of annexin A2 in muscle repair
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Repair of injured muscle involves repair of injured myofibers through the involvement of dysferlin and its interacting partners, including annexin. Studies with mice and patients have established that dysferlin deficit leads to chronic inflammation and adipogenic replacement of the diseased muscle. However, longitudinal analysis of annexin deficit on muscle pathology and function is lacking. Here we show that unlike annexin A1, but similar to dysferlin, lack of annexin A2 (AnxA2) causes poor myofiber repair and progressive weakening with age. However, unlike dysferlin-deficient muscle, AnxA2-deficient muscles do not exhibit chronic inflammation or adipogenic replacement. Deletion of AnxA2 in dysferlin deficient mice reduces inflammation, adipogenic replacement, and loss in muscle function caused by dysferlin deficit. These results show that: a) AnxA2 facilitates myofiber repair, b) chronic inflammation and adipogenic replacement of dysferlinopathic muscle requires AnxA2, and c) inhibiting AnxA2-mediated inflammation is a novel therapeutic avenue for dysferlinopathy.

Publication Title

Annexin A2 links poor myofiber repair with inflammation and adipogenic replacement of the injured muscle.

Sample Metadata Fields

Age, Specimen part

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accession-icon GSE109283
Expression data of OsSHMT Arabidopsis
  • organism-icon Arabidopsis thaliana
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Arabidopsis ATH1 Genome Array (ath1121501)

Description

Plants were exposed to NaCl (150mM) stress for 24 hours

Publication Title

Heterologous Expression of Serine Hydroxymethyltransferase-3 From Rice Confers Tolerance to Salinity Stress in &lt;i&gt;E. coli&lt;/i&gt; and Arabidopsis.

Sample Metadata Fields

Age

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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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