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Integration of genome-wide analysis to characterize long noncoding RNAs in diverse immune cell types of the stage IV melanoma patients

ABSTRACT: We investigated the expression profiles in the CD4+, CD8, and CD14+ peripheral blood cells (PBLs) of the stage IV melanoma patients and the healthy donors.

ORGANISM(S): Homo sapiens

PROVIDER: GSE104744 | GEO | 2018/10/10

REPOSITORIES: GEO

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Integration of genome-wide analysis to characterize long noncoding RNAs in diverse immune cell types of the stage IV melanoma patients

Project description:Integration of genome-wide analysis to characterize long noncoding RNAs in diverse immune cell types of the stage IV melanoma patients

| PRJNA413744 | ENA

Gene expression profiles in bone marrow of human gastric adenocarcinoma at stage III and stage IV

Project description:A secreted factor in bone marrow associated with metastatic gastric cancer was indentified through expression profiling in bone marrow of stage III and stage IV gastric adenocarcinoma. In the study presented here, bone marrow samples from patients with stage III or stage IV gastric adenocarcinoma were used to acquire expression profiles.

2013-10-22 | E-GEOD-41801 | biostudies-arrayexpress

Gene expression profiles in bone marrow of human gastric adenocarcinoma at stage III and stage IV

2013-10-22 | GSE41801 | GEO

Asthma IV

Project description:Asthma IV

| PRJNA540484 | ENA

Gene Expression Profiling-Based Identification of Molecular Subtypes in Stage IV Melanoma with Different Clinical Outcome

Project description:This SuperSeries is composed of the following subset Series: GSE22153: Gene Experssion Profiling-Based Identification of Molecular Subtypes in Stage IV Melanoma with Different Clinical Outcome (test set) GSE22154: Gene Experssion Profiling-Based Identification of Molecular Subtypes in Stage IV Melanoma with Different Clinical Outcome (validation set) Refer to individual Series

2010-06-08 | E-GEOD-22155 | biostudies-arrayexpress

Epigenomic profiles of Brachypodium distachyon mutants deficient in RNA polymerase IV (Pol IV)

Project description:Monocot grass species (Poaceae) express a diverse set of multisubunit RNA polymerase enzymes, including Pol II, Pol IV and Pol V. To better understand this functional diversity, we have charted Pol IV function in the model Brachypodium distachyon. Intriguingly, pol IV null mutations in Poaceae crops disrupt growth, reproductive development and seed set. In order to investigate how Pol IV controls vegetative growth and TE activity in these grasses, we have isolated B. distachyon mutant alleles for Pol IV’s largest subunit, NRPD1. We obtained the germplasm in which to screen for these pol IV mutations from the B. distachyon community's sodium azide (NaN) and T-DNA insertion collections.

2024-03-04 | GSE243693 | GEO

Extracellular microvesicle microRNAs as predictive biomarkers for targeted therapy in Stage IV cutaneous malignant melanoma

Project description:We analyzed the value of microRNAs (miRNAs) in plasma-derived extracellular microvesicles (EV) as biomarkers for treatment outcome in Stage IV CMM patients receiving MAPK inhibitors (MAPKis).

2017-08-03 | GSE102166 | GEO

Single-cell RNA-seq data for control and POU IV-misexpressed Ciona intestinalis embryos at late tailbud (LTB) stage

Project description:Purpose: Understand how the misexpression of key sensory cell determinant POU IV affects cell type specification of various sensory neurons in the peripheral nervous system in Ciona. Methods: CesA>POU IV (2.5ng/l) + CesA>GFP (5.0ng/l) injected eggs and control eggs were fertilized side by side, and allowed to develop to the late tailbud stage (13.5h after fertilization at 18°C). For each sample, 120 morphologically normal embryos were used for single cell RNA-seq assays. Dissociation of the embryos and single cell RNA-seq assays by 10x Genomics chromium system were done as described in 9. Horie R. et al., Shared evolutionary origin of vertebrate neural crest and cranial placodes. Nature 560, 228-232 (2018). Results: Misexpression of POU IV leads to the formation of Synthetic Cell Types that exhibit properties of other sensory neurons, especially those of bipolar tail neurons (BTNs) and a synthetic gene battery that is not found in any wildtype sensory neuron.

2021-12-29 | GSE192645 | GEO

Integrative Genome-Wide Analysis of Long Noncoding RNAs in Diverse Immune Cell Types of Melanoma Patients.

Project description: Not available

| S-EPMC6072578 | biostudies-literature

Polymerase IV Plays a Crucial Role in Pollen Development in Capsella

Project description:In Arabidopsis thaliana, DNA-dependent RNA polymerase IV (Pol IV) is required for the formation of transposable element (TE)-derived small RNA (sRNA) transcripts. These transcripts are processed by DICER-LIKE3 into 24-nt small interfering RNAs (siRNAs) that guide RNA-directed DNA methylation. In the pollen grain, Pol IV is also required for the accumulation of 21/22-nt epigenetically activated siRNAs (easiRNAs), which likely silence TEs via post-transcriptional mechanisms. Despite this proposed role of Pol IV, its loss of function in Arabidopsis does not cause a discernable pollen defect. Here, we show that the knockout of NRPD1, encoding the largest subunit of Pol IV in the Brassicaceae species Capsella rubella, caused post-meiotic arrest of pollen development at the microspore stage. As in Arabidopsis, all TE-derived siRNAs were 2 depleted in Capsella nrpd1 microspores. In the wild-type background, the same TEs produced 21/22-nt and 24-nt siRNAs; these processes required Pol IV activity. Arrest of Capsella nrpd1 microspores was accompanied by the deregulation of genes targeted by Pol IV-dependent siRNAs. TEs were much closer to genes in Capsella rubella compared to Arabidopsis thaliana, perhaps explaining the essential role of Pol IV in pollen development in Capsella. Our discovery that Pol IV is functionally required in Capsella microspores emphasizes the relevance of investigating different plant models.

2020-01-23 | GSE136847 | GEO

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