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accession-icon GSE640
Spermatogenesis
  • organism-icon Mus musculus
  • sample-icon 51 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Array (mgu74a), Affymetrix Murine Genome U74A Version 2 Array (mgu74av2)

Description

A multitude of genes expressed solely in meiotic or postmeiotic spermatogenic cells offers a myriad of contraceptive targets.

Publication Title

A multitude of genes expressed solely in meiotic or postmeiotic spermatogenic cells offers a myriad of contraceptive targets.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE72353
A lincRNA connected to cell mortality and epigenetically-silenced in most common human cancers
  • organism-icon Homo sapiens
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

- Gene expression changes linked to two step immortalization of human mammary epithelial cells (HMEC).

Publication Title

A lincRNA connected to cell mortality and epigenetically-silenced in most common human cancers.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE36825
Clonal competition with alternating dominance in multiple myeloma
  • organism-icon Homo sapiens
  • sample-icon 42 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Clonal competition with alternating dominance in multiple myeloma.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE36824
Clonal competition with alternating dominance in multiple myeloma [GEP]
  • organism-icon Homo sapiens
  • sample-icon 42 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Copy number and expression profiling of multiple myeloma patients at multiple stages of their individual clinical course

Publication Title

Clonal competition with alternating dominance in multiple myeloma.

Sample Metadata Fields

Specimen part

View Samples
accession-icon SRP049257
A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin states (RNA-Seq)
  • organism-icon Mus musculus
  • sample-icon 48 Downloadable Samples
  • Technology Badge IconIlluminaHiSeq1500

Description

During hematopoiesis, cells originating from the same stem cell reservoir differentiate into distinct cell types. The mechanisms enabling common progenitors to differentiate into distinct cell fates are not fully understood. Here, we identify chromatin-regulating and cell-fate-determining transcription factors (TF) governing dendritic cell (DC) development by annotating the enhancer and promoter landscapes of the DC lineage. Combining these analyses with detailed over-expression, knockdown and ChIP-Seq studies, we show that Irf8 functions as a plasmacytoid DC epigenetic and fate-determining TF, regulating massive, cell-specific chromatin changes in thousands of pDC enhancers. Importantly, Irf8 forms a negative feedback loop with Cebpb, a monocyte-derived DC epigenetic fate-determining TF. We show that using this circuit logic, differential activity of TF can stably define epigenetic and transcriptional states, regardless of the microenvironment. More broadly, our study proposes a general paradigm that allows closely related cells with a similar set of signal-dependent factors to generate differential and persistent enhancer landscapes. Overall design: Here analyzed 2 experiments, each one contains samples of moDC and pDC ex vivo cultured cells. The first experiment contains 32 samples of moDC and pDC following stimulation with various TLR stimulators. The second experiment contains 8 samples of moDC and pDC following perturbations; Cebpb and Irf8 knock down or over expression.

Publication Title

A negative feedback loop of transcription factors specifies alternative dendritic cell chromatin States.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE829
Laminin binding/non-binding germ cells
  • organism-icon Mus musculus
  • sample-icon 21 Downloadable Samples
  • Technology Badge Icon Affymetrix Murine Genome U74A Version 2 Array (mgu74av2), Affymetrix Murine Genome U74A Array (mgu74a)

Description

Comparison of laminin binding and laminin non-binding germ cells

Publication Title

Defining the spermatogonial stem cell.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE830
Rat germ cells
  • organism-icon Rattus norvegicus
  • sample-icon 18 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Expression 230A Array (rae230a)

Description

Rat germ cells

Publication Title

Defining the spermatogonial stem cell.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE16058
Distinctions between the stasis and telomere attrition senescence barriers in cultured human mammary epithelial cells
  • organism-icon Homo sapiens
  • sample-icon 48 Downloadable Samples
  • Technology Badge Icon Affymetrix HT Human Genome U133A Array (hthgu133a)

Description

Molecular distinctions between the stasis and telomere attrition senescence barriers in cultured human mammary epithelial cells

Publication Title

Molecular distinctions between stasis and telomere attrition senescence barriers shown by long-term culture of normal human mammary epithelial cells.

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon GSE30391
Expression data from human Wharton's jelly stem cells
  • organism-icon Homo sapiens
  • sample-icon 30 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Human umbilical cord Whartons jelly stem cells (WHJSC) are gaining attention as a possible clinical source of mesenchymal stem cells for use in cell therapy and tissue engineering due to their high accessibility, expansion potential and plasticity. However, the cell viability changes that are associated to sequential cell passage of these cells are not known. In this analysis, we have identified the gene expression changes that are associated to cell passage in WHJSC.

Publication Title

Evaluation of the cell viability of human Wharton's jelly stem cells for use in cell therapy.

Sample Metadata Fields

Specimen part

View Samples
accession-icon GSE87629
Genome-wide analysis of B and T cell gene expression during a six-week gluten challenge in patients with celiac disease
  • organism-icon Homo sapiens
  • sample-icon 146 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V3.0 expression beadchip

Description

Dietary gluten proteins (prolamins) from wheat, rye, and barley are the driving forces behind celiac disease, an organ-specific autoimmune disorder that targets both the small intestine and organs outside the gut. In the small intestine, gluten induces inflammation and a typical morphological change of villous atrophy and crypt hyperplasia. Gut lesions improve and heal when gluten is excluded from the diet and the disease relapses when patients consume gluten. Oral immune tolerance towards gluten may be kept for years or decades before breaking tolerance in genetically susceptible individuals. Celiac disease provides a unique opportunity to study autoimmunity and the transition in immune cells as gluten breaks oral tolerance. Seventy-three celiac disease patients on a long-term gluten-free diet ingested a known amount of gluten daily for six weeks. A peripheral blood sample and intestinal biopsies were taken before and six weeks after initiating the gluten challenge. Biopsy results were reported on a continuous numeric scale that measured the villus height to crypt depth ratio to quantify gluten-induced gut mucosal injury. Pooled B and T cells were isolated from whole blood, and RNA was analyzed by DNA microarray looking for changes in peripheral B- and T-cell gene expression that correlated with changes in villus height to crypt depth, as patients maintained or broke oral tolerance in the face of a gluten challenge.

Publication Title

A B-Cell Gene Signature Correlates With the Extent of Gluten-Induced Intestinal Injury in Celiac Disease.

Sample Metadata Fields

Specimen part, Disease, Disease stage, Treatment, Subject

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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