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accession-icon SRP051659
Detection and Characterization of Gene Expression Differences in Transgenic Glycine max Seeds with RNAseq
  • organism-icon Glycine max
  • sample-icon 36 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2000

Description

Transformation of Glycine max with seed-targeted expression vectors via Agrobacterium causes measurable unscripted gene expression changes in the seed transcriptome Overall design: mRNA was sequenced from three transgenic events expressing three different recombinant proteins in soybean seeds. Three plants were chosen from each as group replicates, and three seeds from each plant as individual biological replicates.

Publication Title

Transcript Polymorphism Rates in Soybean Seed Tissue Are Increased in a Single Transformant of <i>Glycine max</i>.

Sample Metadata Fields

Subject

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accession-icon GSE57947
Identification of genes associated with breast cancer micrometastatic disease in bone marrow using a Patient Derived Xenograft mouse model
  • organism-icon Mus musculus
  • sample-icon 11 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

In this study, using a Patient Derived Xenograft (PDX) system established by transplanting primary tumors from pre-metastatic breast cancer patients we demonstrate that development of distant organ metastases correlates with the presence of Bone Marrow Disseminated Tumor Cells (BM DTCs) in the PDX mice. Comparative gene expression analysis of bone marrow (BM) from tumor bearing PDX mice which developed metastatic disease was carried out with BM from non-tumor bearing controls.

Publication Title

Identifying biomarkers of breast cancer micrometastatic disease in bone marrow using a patient-derived xenograft mouse model.

Sample Metadata Fields

Specimen part

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accession-icon GSE9388
VS94 SAPI AI-2 Temporal study
  • organism-icon Escherichia coli
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix E. coli Genome 2.0 Array (ecoli2)

Description

VS94 gene expression at different time-points in SAPI medium in absence and presence of AI-2 was studied.

Publication Title

Temporal regulation of enterohemorrhagic Escherichia coli virulence mediated by autoinducer-2.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE15248
Biocompatibility and Discovery of the Potential Applications of Magnetite (Fe3O4) Nanoparticles
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina human-6 v2.0 expression beadchip

Description

A Transcriptomics Approach to Study the Biocompatibility and Finding out the Potential Applications of Magnetite (Fe3O4) Nanoparticles

Publication Title

Magnetite (Fe3O4) nanocrystals affect the expression of genes involved in the TGF-beta signalling pathway.

Sample Metadata Fields

Cell line

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accession-icon GSE40654
Does Type of Dietary Fat Matter? Prostate Cancer Xenograft Progression in a SCID Mouse Model with Varying Dietary Fat Sources
  • organism-icon Homo sapiens
  • sample-icon 23 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A 2.0 Array (hgu133a2)

Description

PURPOSE: Previous mouse studies using corn oil (-6) as the dietary fat source suggest that decreasing dietary fat content can slow prostate cancer (PCa) growth. However, other studies, in which the diet was composed around saturated fat, showed no difference in outcomes between high-fat and low-fat diets. The relative effects of other fats, such as fish oil and olive oil, also remain unexplored. To our knowledge, no trial has yet compared the effect of various fats on prostate cancer progression. Therefore, we sought to systematically study the effect of fish oil, olive oil, corn oil, and saturated fat on prostate cancer progression. METHODS: A total of 96 male SCID mice were injected with LAPC-4 human PCa cells. Two weeks following injection, mice were singly-housed and randomized to either a fish oil, olive oil, corn oil, or saturated fat based diet. Animals were euthanized when tumors reached 1,000 mm3. Serum was collected at sacrifice and assayed for PSA, insulin, IGF-1, IGFBP-3, and PGE-2 levels. Tumors were also assayed for PGE-2, and COX-2 levels, and gene array analysis was performed. RESULTS: Mice weights and tumor volumes were equivalent across groups at randomization. Overall, fish-oil consumption was associated with improved survival, relative to all other dietary groups (Log-rank, all p<0.05). We did not detect any significant difference in serum PSA, insulin, IGF-1, IGFBP-3, and PGE-2 levels. Glucose at the time of sacrifice was statistically different between groups, with the fish-oil fed mice having the highest levels of serum glucose (Kruskal-Wallis, p=0.03).

Publication Title

Fish oil slows prostate cancer xenograft growth relative to other dietary fats and is associated with decreased mitochondrial and insulin pathway gene expression.

Sample Metadata Fields

Specimen part

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accession-icon GSE13525
Carboplatin-induced gene expression changes in vitro are prognostic of survival in epithelial ovarian cancer
  • organism-icon Homo sapiens
  • sample-icon 11 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

We performed a time-course microarray experiment to define the transcriptional response to carboplatin in vitro, and to correlate this with clinical outcome in epithelial ovarian cancer (EOC). RNA was isolated from carboplatin and control-treated 36M2 ovarian cancer cells at several time points, followed by oligonucleotide microarray hybridization. Carboplatin induced changes in gene expression were assessed at the single gene as well as at the pathway level. Clinical validation was performed in publicly available microarray datasets using disease free and overall survival endpoints.

Publication Title

Carboplatin-induced gene expression changes in vitro are prognostic of survival in epithelial ovarian cancer.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE36111
Expression data from side population cells of the human OSCC cell line SCC172
  • organism-icon Homo sapiens
  • sample-icon 5 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133A 2.0 Array (hgu133a2)

Description

A cancer stem cell cannot be identified solely based on surface markers as none of the markers used to isolate stem cells in various normal and cancerous tissues is expressed exclusively by stem cells. Our experimental results have also identified additional fractions representing true stem-like cells in oral squamous cell carcinoma (OSCC), refuting the concept that cancer stem cells (CSCs) are a rare population, and we have also developed an in vitro model to explore the stem cell concept in oral epithelial tumorigenesis. This model expounds four distinct fractions within a homogenous cell line SCC172 that is morphologically similar (85% cells expressing CSC markers), yet varying in all functional aspects of cell cycle, dye retention, chemoresistance, tumor-forming potential, self renewal, apoptosis resistance and regulation at molecular levels. Relating to our CSC shift model, we analysed the concept of biological heterogeneity in terms of four fractions SP1, SP2, MP1 and MP2 and associated it with variations among patients in a clinical scenario.

Publication Title

Analysis of MicroRNA-mRNA Interactions in Stem Cell-Enriched Fraction of Oral Squamous Cell Carcinoma.

Sample Metadata Fields

Specimen part, Cell line

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accession-icon GSE32360
Expression data from early Zebrafish embryos after knockdown of mir-34
  • organism-icon Danio rerio
  • sample-icon 17 Downloadable Samples
  • Technology Badge Icon Affymetrix Zebrafish Genome Array (zebrafish)

Description

microRNAs play crucial roles in the early development of an organism. However the regulation of transcription through the action of microRNAs during the initial embyonic development has not been studied.

Publication Title

miR-34 is maternally inherited in Drosophila melanogaster and Danio rerio.

Sample Metadata Fields

Specimen part

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accession-icon SRP009270
MIWI catalysis is required for piRNA amplification-independent LINE1 transposon silencing [deep sequencing]
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer II, Illumina Genome Analyzer IIx

Description

Here we show that MIWI is a small RNA-guided ribonuclease (Slicer) that requires extensive complementarity for target cleavage in vitro. Disruption of its catalytic activity in mice by a single point mutation results in male infertility and displays increased accumulation of LINE1 transposon transcripts. Overall design: MIWI-associated piRNAs from different genotypes were sequenced. Total RNA from purified round spermatids were subjected to Ribozero purification and strand-specific RNAseq lib prepared. Global 5'' RACE library was prepare from indicated genotypes.

Publication Title

Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE32180
MIWI catalysis is required for piRNA amplification-independent LINE1 transposon silencing [microarray]
  • organism-icon Mus musculus
  • sample-icon 8 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Gene 1.0 ST Array (mogene10st)

Description

Here we show that MIWI is a small RNA-guided ribonuclease (Slicer) that requires extensive complementarity for target cleavage in vitro. Disruption of its catalytic activity in mice by a single point mutation results in male infertility and displays increased accumulation of LINE1 transposon transcripts.

Publication Title

Miwi catalysis is required for piRNA amplification-independent LINE1 transposon silencing.

Sample Metadata Fields

No sample metadata fields

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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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