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accession-icon GSE34139
Molecular pathology of the ARF induced by choline deficiency and of the protection afforded by fish oil
  • organism-icon Rattus norvegicus
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Gene 1.0 ST Array (ragene10st)

Description

Male weanling Wistar rats from the Animal Facility at the Center for Experimental and Applied Pathology were divided into 4 groups and fed the following diets: 1) choline-deficient diet with VO [corn and hydrogenated oils) as lipids (CDVO); 2) choline-supplemented diet with VO as lipids (CSVO); 3) choline-deficient diet with MO as lipid (CDMO); and 4) choline-supplemented diet with MO as lipid (CSMO). Authors have adhered to appropriate NIH Guide for the Care and Use of Laboratory Animals. It is known that female rats are more resistant than male rats to AKI. Animals were sacrificed after receiving the experimental diets for 6 days. The left kidney was fixed in formaldehyde-buffer and stained with hematoxiline-eosin for histopathological analysis. The right kidney was cryopreserved for microarray analysis. Cryopreserved kidney was wrapped with aluminum foil and broken with a hammer previously wrapped with tape paper on a counter covered in aluminum. The pieces of the kidney were located in a mortar with liquid nitrogen to keep cryopreservation and were pulverized with a pestle. Nitrogen was added as it evaporated. The tissue was broken up to be completely pulverized. Powder was placed with a spatula in a cryotube supported on a dry ice with a layer of aluminum above. Before proceeding with another sample and to avoid contamination, the mortar, the pestle and the spatula were washed with tap water, distilled water and then alcohol. The tape of the hammer, the aluminum on the counter and the latex gloves were also replaced by new ones. Total RNA was purified from 30 milligrams of frozen rat kidney pools, using RNeasy Mini Kit [Qiagen GmbH, Hilden, Germany) according to the manufacturer's instructions. The biological concentration, integrity and quality of the RNA obtained were performing using NanoDrop 2000c (Thermo Fisher Scientific, Delaware, USA) and RIN (RNA Integrity Number). Five hundred nanograms of total RNA were processed and hybridized to Affymetrix GeneChip Rat Gene 1.0 ST Array (Affymetrix Inc, Singapore, Singapore), according to Ambion WT Expression Kit instructions (Ambion Inc, Texas, USA). Total RNA obtained during the tissue extraction was processed to obtain a double strand cDNA. After that we performed a in-vitro transcripition to generate antisence cRNA (aRNA). This aRNA was used to generate a single-stranded DNA (ss-DNA) using random primers and the dUTP +dNTP mix. The resulting single-stranded DNA (ss-DNA) containing the unnatural uracilbase is then treated with Uracil DNA Glycosylase, which specifically removes the uracilresidue from the ss-DNA molecules. In the same reaction, the APE 1 enzyme then cleaves the phosphodiester backbone where the base is missing, leaving a 3-hydroxyland a 5-deoxyribose phosphate terminus. Before this prosses, shorts ss-DNA fragments were labeled by terminal deoxynucleotidyl transferase (TdT) that covalently linked the 3-hydrosyl phosphate terminus whit Biotin Allonamide Triphosphate. The GeneChip Rat Gene 1.0 ST Array enables whole-genome, gene-level expression studies for well-characterized genes. It is a single GeneChip-brand array comprised of more than 722 254 unique 25-mer oligonucleotide features accounting for more than 27 342 gene-level probe sets. Results were scanned with GeneChip Scanner 3000 7G (Affymetrix Inc, Tokyo, Japan), and normalized by RMA algorithm using Affymetrix Expression Console Software. In addition, call values were retrieved by MAS5 algorithm, and only genes with a p (present) call value were used in the analysis. Differentially expressed genes were identified using limma (www.bioconductor.org) and p adjusted values and absolute log fold change greater than 1.5 were used for gene selection.

Publication Title

Molecular pathology of acute kidney injury in a choline-deficient model and fish oil protective effect.

Sample Metadata Fields

Sex, Specimen part

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accession-icon GSE30683
ETV5 Mediated Downstream Gene Activation in Spermatogonial Stem Cells
  • organism-icon Mus musculus
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Insight into mechanisms controlling gene expression in the spermatogonial stem cell (SSC) will improve our understanding of the processes regulating spermatogenesis and aid in treating problems associated with male infertility.

Publication Title

Spermatogonial stem cell self-renewal requires ETV5-mediated downstream activation of Brachyury in mice.

Sample Metadata Fields

Specimen part, Treatment

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accession-icon GSE15652
GDNF-Regulated Gene Expression in Cultures of Rat Spermatogonial Stem Cells
  • organism-icon Rattus norvegicus
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

Expression of GDNF-regulated genes was studied in cultures of self-renewing rat spermatogonial stem cells established from 8-10 day old rat pups maintained in a defined serum free medium. GDNF is the primary regulator of spermatogonial stem cell self renewal in the rat.

Publication Title

Identification of glial cell line-derived neurotrophic factor-regulated genes important for spermatogonial stem cell self-renewal in the rat.

Sample Metadata Fields

Specimen part

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accession-icon GSE42726
Expression profile of adult Drosophila melanogaster expressing a self-replicating RNA of Sindbis virus
  • organism-icon Drosophila melanogaster
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Drosophila Genome 2.0 Array (drosophila2)

Description

Alphaviruses establish a persistent infection in arthropod vectors, which is essential for effective transmission of the virus to vertebrate hosts. The development of persistence in insects is not well understood, although it is thought to involve the innate immune response. Using a transgenic fly system (SINrep) expressing a self-replicating viral genome, we have previously demonstrated the antiviral response of the Drosophila Imd (Immune Deficiency) and Jak-STAT innate immunity pathways.

Publication Title

An antiviral role for antimicrobial peptides during the arthropod response to alphavirus replication.

Sample Metadata Fields

Specimen part

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accession-icon GSE31726
Expression analysis of G9C8 clone and NOD.G9C8 tg CTLs
  • organism-icon Mus musculus
  • sample-icon 4 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Diabetogenic CD8+ G9C8 clone cells and the T cells from a transgenic mouse bearing the same TCR as the clone, displayed differences in their ability to induce disease in vivo.Microarray analysis was done to identify the molecular basis for such differences between the two sets of CD8 T cells.

Publication Title

Cytotoxic mechanisms employed by mouse T cells to destroy pancreatic β-cells.

Sample Metadata Fields

Specimen part, Disease

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accession-icon GSE14222
Gene Expression Profiling of the SSC-Enriched Thy1+ and SSC-Depleted Thy1- Fractions of Prepubertal Mouse Testes
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

Self-renewal and differentiation of spermatogonial stem cells (SSCs) provides the foundation for testis homeostasis, yet mechanisms that control their functions in mammals are poorly defined. We used microarray transcript profiling to identify specific genes whose expression are augmented in the SSC-enriched Thy1+ germ cell fraction of mouse pup testes. Comparisons of gene expression in the Thy1+ germ cell fraction to the Thy1-depeleted testis cell population identified 202 genes that are expressed 10-fold or higher in Thy1+ cells. This database provided a mining tool to investigate specific characteristics of SSCs and identify novel mechanisms that potentially influence their functions.

Publication Title

Colony stimulating factor 1 is an extrinsic stimulator of mouse spermatogonial stem cell self-renewal.

Sample Metadata Fields

No sample metadata fields

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accession-icon SRP113020
Neoplastic pancreas cells enter a quasi-mesenchymal state with increased oncogenic potential following transient TGF-ß exposure
  • organism-icon Mus musculus
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 2500

Description

Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease and a major health problem in the United States. While the cytokine TGF-ß has been implicated in PDAC development, it can exert bot pro- and anti-tumorigenic effects that are highly context dependent and incompletely understood. To better characterize the responses of neoplastic pancreas cells to TGF-ß, three-dimensional (3D) cultures of KrasG12D-expressing mouse pancreatic epithelial cells were employed. While active exposure to exogenous TGF-ß caused the KrasG12D cells to growth arrest, its subsequent removal allowed the cells to enter a hyper-proliferative, quasi-mesenchymal (QM) and progenitor-like state. This transition was highly stable and maintained by autocrine TGF-ß signaling. Transient pulses of TGF-ß have been observed during pancreatitis, a major risk factor for PDAC, and may therefore serve to convert pre-existing KrasG12D-expressing cells into QM cells. While untreated KrasG12D cells formed simple cysts in vivo, QM cells formed ductal structures resembling human PanINs. Furthermore, markers of the QM state are expressed in human PDAC and are associated with worse outcomes. These data suggest that the QM state plays a role in PDAC development and may selectively contribute to more aggressive PDAC subtypes. This work therefore provides novel molecular insights into both PDAC development and the complex role of TGF-ß in tumorigenesis. Overall design: Three technical replicates per experimental group from one isolate were analyzed by RNA sequencing

Publication Title

Pre-neoplastic pancreas cells enter a partially mesenchymal state following transient TGF-β exposure.

Sample Metadata Fields

Subject

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accession-icon SRP006999
Sequencing of microRNA in spermatogonial stem cell enriched cell populations.
  • organism-icon Mus musculus
  • sample-icon 5 Downloadable Samples
  • Technology Badge IconIllumina Genome Analyzer II

Description

MicroRNAs (miRs) play a key role in the control of gene expression in a wide array of tissue systems where their functions include the regulation of self-renewal, cellular differentiation, proliferation, and apoptosis. However, the functional importance of individual miRs in controlling spermatogonial stem cell (SSC) homeostasis has not been investigated. Using high-throughout sequencing, we profiled the expression of miRs in the Thy1+ testis cell population, which is highly enriched for SSCs, and the Thy1- cell population, composed primarily of testis somatic cells. In addition, we profiled the global expression of miRs in cultured germ cells, also enriched for SSCs. Our results demonstrate that miR-21, along with miR-34c, -182, -183, -146a, -465a-3p, -465b-3p, -465c-3p, and -465c-5p are preferentially expressed in the Thy1+ SSC-enriched population, as compared to Thy1- somatic cells, and we further observed that Thy1+ SSC-enriched testis cells and SSC-enriched cultured germ cells share remarkably similar miR expression profiles. Overall design: Spermatogonial Stem Cell enriched cell populations (freshly isolated and short-term cultured) and somatic cell populations were isolated from C57B/L6 mouse donors and subjected to small RNA isolation and sequencing.

Publication Title

MicroRNA-21 regulates the self-renewal of mouse spermatogonial stem cells.

Sample Metadata Fields

Specimen part, Cell line, Subject

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accession-icon GSE18914
Prepubertal Human Spermatogonia and Mouse Gonocytes Share Conserved Gene Expression of Germline Stem Cell Regulatory
  • organism-icon Mus musculus, Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Full title: Prepubertal Human Spermatogonia and Mouse Gonocytes Share Conserved Gene Expression of Germline Stem Cell Regulatory Molecules

Publication Title

Prepubertal human spermatogonia and mouse gonocytes share conserved gene expression of germline stem cell regulatory molecules.

Sample Metadata Fields

Age

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accession-icon SRP057452
Nucleotide stress induction of HEXIM1 suppresses melanoma by modulating cancer cell-specific gene transcription [RNA-Seq1]
  • organism-icon Homo sapiens
  • sample-icon 24 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq2500

Description

Cancer metabolism has been actively studied to gain insights into tumorigenic survival mechanisms and susceptibilities. In melanoma, we identify HEXIM1, a transcription elongation regulator, as a novel melanoma suppressor that participates in nucleotide stress regulation. HEXIM1 expression is low in melanoma. Its overexpression suppresses melanoma while its inactivation accelerates tumor onset in vivo. HEXIM1 responds to nucleotide stress. Knockdown of HEXIM1 rescues neural crest and melanoma nucleotide stress phenotypes in vivo. Mechanistically, under nucleotide stress, HEXIM1 is induced to form an inhibitory complex with P-TEFb, the kinase that initiates transcription elongation, to pause transcription at tumorigenic genes. The resulting alteration in gene expression also causes anti-tumorigenic transcripts to bind to and be stabilized by HEXIM1. HEXIM1 therefore plays an important role in inhibiting cancer cell-specific gene transcription while also facilitating anti-cancer gene expression. Our study reveals a novel role for HEXIM1 in coupling nucleotide metabolism with transcriptional regulation in melanoma. Overall design: RNA-seq analysis of human A375 melanoma cells treated with either DMSO or 25 µM A771726 for 0-72 hrs.

Publication Title

Stress from Nucleotide Depletion Activates the Transcriptional Regulator HEXIM1 to Suppress Melanoma.

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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