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accession-icon GSE96719
Time-dependent regulation of cellular programming of monocytes by NCOR2
  • organism-icon Homo sapiens
  • sample-icon 51 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V3.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2.

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon GSE96703
Time-dependent regulation of cellular programming of monocytes by NCOR2 [Illumina array]
  • organism-icon Homo sapiens
  • sample-icon 51 Downloadable Samples
  • Technology Badge IconIllumina HumanHT-12 V3.0 expression beadchip

Description

Whole transcriptome profiling (Illumina Microarray) of human ex vivo lymphocytes and monocytes, as well as of human monocyte-derived cells generated in vitro by activating CD14+ monocytes with MCSF, GMCSF or the combination of GMCSF and IL4

Publication Title

Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2.

Sample Metadata Fields

Specimen part

View Samples
accession-icon SRP102019
Time-dependent regulation of cellular programming of monocytes by NCOR2 [RNASeq_TK]
  • organism-icon Homo sapiens
  • sample-icon 20 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 1500

Description

Whole transcriptome profiling (RNA-Seq) of a time kinetics experiment containing human monocyte-derived cells, which were activated with IL4 either directly at the start of the culture, or at different hours after an initial activation with GMCSF alone. Cells being activated solely with GMCSF were added as controls Overall design: CD14+ monocytes were FACS-sorted from blood of human healthy donors and later activated in vitro with either GMCSF alone for 72 hours to obtain Mo-GMCSF[IL4 (0h)] cells as controls, with the combination of GMCSF and IL4 for 72 hours or 144 hours to obtain Mo-GMCSF[IL4 (0-72h)] or Mo-GMCSF[IL4 (0-144h)] cells, respectively, or with first GMCSF and then with the combination of GMCSF and IL4 for different durations. For the latter, monocytes were first activated with GMCSF for either 12, 24, 48 or 72 hours, and then with GMCSF plus IL4 until a total activation time of 144 hours. This resulted in Mo-GMCSF[IL4 (12-144h)], Mo-GMCSF[IL4 (24-144h)] , Mo-GMCSF[IL4 (48-144h)] and Mo-GMCSF[IL4 (72-144h)] cells, respectively.

Publication Title

Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2.

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon SRP102092
Time-dependent regulation of cellular programming of monocytes by NCOR2 [RNASeq_KD]
  • organism-icon Homo sapiens
  • sample-icon 6 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 1500

Description

Whole transcriptome profiling (RNA-Seq) was performed on human Mo-GMCSF[IL4 (0-72h)] cells with either NCOR2 being knocked down or corresponding WT cells Overall design: CD14+ monocytes were FACS-sorted from blood of human healthy donors and later activated in vitro with the combination of GMCSF and IL4 for 72h to obtain Mo-GMCSF[IL4 (0-72h)] cells. During the last 24 hours of activation, either siRNAs targeting NCOR2 or scrambled RNAs were added to obtain NCOR2 knock down cells and corresponding WT cells, respectively

Publication Title

Cellular Differentiation of Human Monocytes Is Regulated by Time-Dependent Interleukin-4 Signaling and the Transcriptional Regulator NCOR2.

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon SRP104167
Western diet triggers NLRP3-dependent persistent functional reprogramming of myeloid cells [RNA-Seq]
  • organism-icon Mus musculus
  • sample-icon 24 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 1500

Description

Here we investigated whether sterile triggers of inflammation  induce trained immunity and thereby influence innate immune responses. Western diet (WD) feeding of Ldlr-/- mice induced systemic inflammation, which was undectable in serum soon after mice were shifted back to chow diet (CD). In contrast, myeloid cell responses towards innate stimuli remained broadly augmented. WD induced transcriptomic and epigenomic reprogramming of myeloid progenitor cells, leading to increased proliferation as well as enhanced innate immune and interferon responses towards in vivo LPS challenge. QTL analysis in human monocytes trained with oxidized low-density lipoprotein (oxLDL) and stimulated with LPS suggested inflammasome-mediated trained immunity. Consistently, Nlrp3-/-/Ldlr-/--deficient mice lacked WD-induced systemic inflammation or myeloid progenitor proliferation and reprogramming. Hence, NLRP3 mediates trained immunity following WD and could thereby arbitrate the potentially deleterious effects of trained immunity in inflammatory diseases. Overall design: Examination of GMPs in six different conditions by RNA-seq

Publication Title

Western Diet Triggers NLRP3-Dependent Innate Immune Reprogramming.

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon SRP124807
Western diet triggers NLRP3-dependent persistent functional reprogramming of myeloid cells II [RNA-Seq]
  • organism-icon Mus musculus
  • sample-icon 19 Downloadable Samples
  • Technology Badge IconIllumina HiSeq 1500

Description

Here we investigated whether sterile triggers of inflammation  induce trained immunity and thereby influence innate immune responses. Western diet (WD) feeding of Ldlr-/- mice induced systemic inflammation, which was undectable in serum soon after mice were shifted back to chow diet (CD). In contrast, myeloid cell responses towards innate stimuli remained broadly augmented. WD induced transcriptomic and epigenomic reprogramming of myeloid progenitor cells, leading to increased proliferation as well as enhanced innate immune and interferon responses towards in vivo LPS challenge. QTL analysis in human monocytes trained with oxidized low-density lipoprotein (oxLDL) and stimulated with LPS suggested inflammasome-mediated trained immunity. Consistently, Nlrp3-/-/Ldlr-/--deficient mice lacked WD-induced systemic inflammation or myeloid progenitor proliferation and reprogramming. Hence, NLRP3 mediates trained immunity following WD and could thereby arbitrate the potentially deleterious effects of trained immunity in inflammatory diseases. Overall design: Examination of GMPs in six different conditions by RNA-seq

Publication Title

Western Diet Triggers NLRP3-Dependent Innate Immune Reprogramming.

Sample Metadata Fields

Specimen part, Subject

View Samples
accession-icon GSE7645
Expression data for Saccharomyces cerevisiae oxidative stress response
  • organism-icon Saccharomyces cerevisiae
  • sample-icon 48 Downloadable Samples
  • Technology Badge Icon Affymetrix Yeast Genome S98 Array (ygs98)

Description

Oxidative stress is a harmful condition in a cell, tissue, or organ, caused by an imbalnace between reactive oxygen species and other oxidants and the capacity of antioxidant defense systems to remove them. The budding yeast S. cerevisiae has been the major eukaryotic model for studies of response to oxidative stress.

Publication Title

The genome-wide early temporal response of Saccharomyces cerevisiae to oxidative stress induced by cumene hydroperoxide.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE5940
Gene Expression Profiling of Primary Rat Oligodendrocytes
  • organism-icon Rattus norvegicus
  • sample-icon 9 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Expression 230A Array (rae230a)

Description

Oligodendrocytes undergo extensive changes as they differentiate from progenitors into myelinating cells. To better understand the

Publication Title

Identification of a novel oligodendrocyte cell adhesion protein using gene expression profiling.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE11334
Identification of a miRNA Regulatory Network in FACS-Purified Neuronal Progenitors at the Onset of Rat Neurogenesis
  • organism-icon Rattus norvegicus
  • sample-icon 15 Downloadable Samples
  • Technology Badge Icon Affymetrix Rat Genome 230 2.0 Array (rat2302)

Description

Cortical development is a complex process involving the generation of neuronal progenitors, which proliferate and migrate to form the stratified layers of the maturing cortex. To identify microRNAs (miRNAs) and genes that may be important during early cortical development, we analyzed the expression profiles of rat neuronal progenitors obtained at embryonic day 11 (E11), E12 and E13 using microarrays. Neuronal progenitors were purified from telencephalic dissociates with a positive-selection strategy using surface labeling tetanus-toxin and cholera-toxin and fluorescence-activated cell sorting. We identified classes of miRNAs and mRNAs that were up-regulated or down-regulated in these neuronal progenitors as cortical development progressed from E11 to E13. We present data that supports a regulatory role for miRNAs during the transition from neuronal progenitors into differentiating cortical neurons.

Publication Title

Integrating microRNA and mRNA expression profiles of neuronal progenitors to identify regulatory networks underlying the onset of cortical neurogenesis.

Sample Metadata Fields

No sample metadata fields

View Samples
accession-icon GSE44065
KRAB/KAP1-microRNA cascade regulates erythropoiesis through the stage-specific control of mitophagy
  • organism-icon Mus musculus, Homo sapiens
  • sample-icon 8 Downloadable Samples
  • Technology Badge IconIllumina MouseWG-6 v2.0 expression beadchip

Description

This SuperSeries is composed of the SubSeries listed below.

Publication Title

A KRAB/KAP1-miRNA cascade regulates erythropoiesis through stage-specific control of mitophagy.

Sample Metadata Fields

Specimen part, Cell line

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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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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