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accession-icon GSE89133
The TNF family member TL1A induces IL-22 secretion in committed human TH17 cells via IL-9 induction
  • organism-icon Homo sapiens
  • sample-icon 27 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V4.0 expression beadchip

Description

TL1A contributes to the pathogenesis of several chronic inflammatory diseases, including Inflammatory Bowel Diseases by enhancing TH1, TH17, and TH2 responses. TL1A mediates a strong co-stimulation of these TH subsets particularly of mucosal CCR9+ T cells. However, the signaling pathways that TL1A induces in different TH subsets are incompletely understood. Here, we investigated the function of TL1A on human TH17 cells. TL1A together with TGF- IL-6, and IL-23 enhanced the secretion of IL-17 and IFN- from human CD4+ memory T cells. TL1A induced the expression of the transcription factors BATF and T-bet that correlated with the secretion of IL-17 and IFN-. In contrast, TL1A alone induced high levels of IL-22 in memory CD4+ T cells and committed TH17 cells. However, TL1A did not enhance expression of IL-17A in TH17 cells. Expression of the transcription factor aryl hydrocarbon receptor that regulates expression of IL-22 was not affected by TL1A. We performed transcriptome analysis of TH17 cells to determine genes that are transcriptionally regulated by TL1A. transcriptome analysis revealed increased expression of IL-9 in response to TL1A.

Publication Title

The TNF family member TL1A induces IL-22 secretion in committed human T<sub>h</sub>17 cells via IL-9 induction.

Sample Metadata Fields

Specimen part

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accession-icon GSE11100
Dendritic Cell Vaccine against Glioblastoma Multiforme Patients
  • organism-icon Homo sapiens
  • sample-icon 20 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Human Glioblastoma Multiforme tumors taken before dendritic cell vaccination, the recurrent tumors taken after vaccination and control GBM tumors from non vaccinated patients.

Publication Title

T cells enhance stem-like properties and conditional malignancy in gliomas.

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE97549
Global microarray analysis of ONECUT2 transcription factor overexpression in human prostate cancer cells
  • organism-icon Homo sapiens
  • sample-icon 16 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Treatment of prostate cancer by hormone suppression leads to the appearance of aggressive variants with variable or no dependence on the androgen receptor. Here we show that the developmental transcription factor, ONECUT2, is a master regulator of the AR network that is highly active in castration-resistant prostate cancer (CRPC).

Publication Title

ONECUT2 is a targetable master regulator of lethal prostate cancer that suppresses the androgen axis.

Sample Metadata Fields

Cell line, Treatment

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accession-icon GSE11420
Microarray of Mouse Brain Tumors grown from injections of GL26 cell line
  • organism-icon Mus musculus
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Mouse Genome 430 2.0 Array (mouse4302)

Description

RNA was extracted from the tumors that grew in the brains of mice that were injected with the GL26 cell line. RNA from GL26 cells was also taken. The chip used for all was an affymetrix mouse genome chip (GPL1261). This is the mouse model compliment to a human experiment in which the human chip was used for GBM tumors.

Publication Title

No associated publication

Sample Metadata Fields

No sample metadata fields

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accession-icon GSE52488
Gene expression profiling regulated by PDGF in pBSMCs
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Gene 1.0 ST Array (hugene10st)

Description

To explore global molecular changes in smooth muscle in response to PDGFR activation, primary human bladder smooth muscle cells were treated with 1 nM PDGF-BB (hereafter PDGF) for 0, 4 or 24 h. Total RNA were prepared, and analyzed using expression profiling, and subjected to bioinformatic and functional interrogation.

Publication Title

Integration of proteomic and transcriptomic profiles identifies a novel PDGF-MYC network in human smooth muscle cells.

Sample Metadata Fields

Specimen part

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accession-icon GSE102967
Transcriptome analysis of Blimp1-sufficient (Ctrl) and Blimp1-deficient (CKO) CD4+ Foxp3+ regulatory (Treg) and Foxp3- effector (Teff) T cells
  • organism-icon Mus musculus
  • sample-icon 12 Downloadable Samples
  • Technology Badge IconIllumina MouseWG-6 v2.0 expression beadchip

Description

Comparative analysis of regulation of gene expression by Blimp1 in regulatory and effector CD4+ T cells. The hypothesis tested in the present study was that Blimp1 differentially regualte gene expression in different T cell subsets. Results provide important information of mechanisms underlying regulation of gene expression by Blimp1 in T cells

Publication Title

No associated publication

Sample Metadata Fields

Specimen part

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accession-icon GSE97548
ONECUT2 inhibition by chemical compound treatment in 22Rv1
  • organism-icon Homo sapiens
  • sample-icon 12 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

To evaluate the specificity for inhibition of expression of OC2 target genes we generated microarray data of 22Rv1 cells treated for 4, 6 and 16 hours with the small molecule inhibitor.

Publication Title

ONECUT2 is a targetable master regulator of lethal prostate cancer that suppresses the androgen axis.

Sample Metadata Fields

Cell line, Treatment, Time

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accession-icon GSE75701
Human expression data from iPSCs, motor neurons derived from iPSCs and ESCs, and fetal spinal cords
  • organism-icon Homo sapiens
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

We compare transcriptomic profiles of human induced pluripotent stem cells (iPSCs), motor neurons (MNs) in vitro differentiated from iPSCs or human ESCs containing a HB9::GFP reporter for MNs, and human fetal spinal cords.

Publication Title

ALS disrupts spinal motor neuron maturation and aging pathways within gene co-expression networks.

Sample Metadata Fields

Sex

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accession-icon GSE101149
Microarray expression data from leukemia cell lines RS4;11 and REH with CASC15 KD or KO respectively
  • organism-icon Homo sapiens
  • sample-icon 10 Downloadable Samples
  • Technology Badge Icon Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)

Description

Long non-coding RNAs play a variety of cellular roles, including regulation of transcription and translation, leading to alterations in gene expression. Here, we assess the role of lncRNA CASC15 in RUNX1/AML translocated leukemia. Differentially regulated genes following CASC15 knockdown were enriched for predicted transcriptional targets of the Yin and Yang-1 (YY1) transcription factor. Our findings represent the first characterization of this CASC15 in RUNX1-translocated leukemia, and point towards a mechanistic basis for its action.

Publication Title

No associated publication

Sample Metadata Fields

Cell line

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accession-icon GSE76554
Transcriptomes regulated by NFAT5 in RAW264.7 macrophages
  • organism-icon Mus musculus
  • sample-icon 9 Downloadable Samples
  • Technology Badge IconIllumina MouseWG-6 v2.0 expression beadchip

Description

To explore the function of NFAT5 in macrophage, we performed transcriptome analysis in raw cells.

Publication Title

Transcription factor NFAT5 promotes macrophage survival in rheumatoid arthritis.

Sample Metadata Fields

Specimen part, Cell line

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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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