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    Results: 1 to 20 of 18365

    1.

    high-throughput transciptome study for rhesus macaque

    (Submitter supplied) In this study, we successfully identified the causal gene underlying the phenotype of extreme high insulin level in a founder population of rhesus macaque. To further reveal the molecular mechanism, especially the effect of mutated gene on transcriptome profile, we performed paired-end, strand-specific, polyA-postive RNA-Seq in two tissues (fat and muscle) of both case and control monkeys.
    Organism:
    Macaca mulatta
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL14954
    10 Samples
    Download data:
    GEO (RPKM), SRA SRP071778
    Series
    Accession:
    GSE79223
    ID:
    200079223
    2.

    NUCLEAR FATE OF YEAST SNORNA IS DETERMINED BY COTRANSCRIPTIONAL RNT1 CLEAVAGE

    (Submitter supplied) We show that in S. cerevisiae pre-snoRNA processing by the endonuclease Rnt1 occurs co-transcriptionally, removing the m7G cap to facilitate the formation of box C/D snoRNA. Failure to remove m7G cap from box C/D pre-snoRNA affects 3’ end processing, ribonucleoprotein complex formation and causes mislocalization to the cytoplasm. Consequently, Rnt1-dependent 5’ end processing of box C/D snoRNA is critical for snoRNA-dependent methylation of ribosomal RNA. more...
    Organism:
    Saccharomyces cerevisiae
    Type:
    Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Other
    Platforms:
    GPL18249 GPL21656
    11 Samples
    Download data:
    GEO (BED, BW), SRA SRP096186
    Series
    Accession:
    GSE93240
    ID:
    200093240
    3.

    RNA sequencing of white adipose tissue of lean and obese mice

    (Submitter supplied) We report differential expressed genes in white adipose tissue of mice fed with a low-fat diet or a high-fat diet.
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL19057
    18 Samples
    Download data:
    GEO (TXT), SRA SRP139599
    Series
    Accession:
    GSE112999
    ID:
    200112999
    4.

    Clinker: visualizing fusion genes detected in RNA-seq data

    (Submitter supplied) Genomic profiling efforts have revealed a rich diversity of oncogenic fusion genes, and many are emerging as important therapeutic targets. While there are many ways to identify fusion genes from RNA-seq data, visualising these transcripts and their supporting reads remains challenging. Clinker is a bioinformatics tool written in Python, R and Bpipe, that leverages the superTranscript method to visualise fusion genes. more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL18573
    6 Samples
    Download data:
    GEO (CSV)
    Series
    Accession:
    GSE113504
    ID:
    200113504
    5.

    Mesenchymal TNFR2 promotes the development of polyarthritis and comorbid heart valve stenosis.

    (Submitter supplied) This study demonstrates that arthritis and heart valve stenosis comorbidity, the most common condition among RA and SpA patients, share common mesenchymal requirements converging in the pathogenic activation of resident mesenchymal origin fibroblasts in the TnfARE mouse model. TNFR2 signaling, in this context, orchestrates the molecular mechanisms underlying arthritis and heart valve stenosis manifestation by regulating fibroblasts pathogenic activation status, cell proliferation and pro-inflammatory milieu. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL18635
    18 Samples
    Download data:
    GEO (TXT), SRA SRP127399
    Series
    Accession:
    GSE108451
    ID:
    200108451
    6.

    Transcriptome analysis of immortalized and transformed human IMR90 fibroblasts

    (Submitter supplied) RNA polymerase (Pol) III transcribes small untranslated RNAs that are essential for cellular homeostasis and growth. Its activity is regulated by inactivation of tumor suppressor proteins and overexpression of the oncogene c-MYC, but the concerted action of these tumor-promoting factors on Pol III transcription has not yet been assessed. In order to comprehensively analyse the regulation of Pol III transcription during tumorigenesis we employ a model system that relies on the expression of five genetic elements to achieve cellular transformation. more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL11154
    6 Samples
    Download data:
    GEO, SRA SRP102731
    Series
    Accession:
    GSE99212
    ID:
    200099212
    7.

    Liver transcriptome analysis reveals extensive transcriptional plasticity during acclimation to low salinity in Cynoglossus semilaevis

    (Submitter supplied) Background: Salinity is an important abiotic stress that influences the physiological and metabolic activity, reproduction, growth and development of marine fish. It has been suggested that half-smooth tongue sole (Cynoglossus semilaevis), a euryhaline fish species, use a large amount of energy to maintain osmotic pressure balance when exposed to fluctuations in salinity. To delineate the molecular response of C. more...
    Organism:
    Cynoglossus semilaevis
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL24671
    6 Samples
    Download data:
    GEO (TXT, XLS), SRA SRP133777
    Series
    Accession:
    GSE111312
    ID:
    200111312
    8.

    TLR4 deficiency reduces inflammatory signaling by reprogramming macrophage lipid metabolism

    (Submitter supplied) Chronic inflammation is a hallmark of obesity and is linked to the development of numerous diseases. The activation of toll-like receptor 4 (TLR4) by long-chain saturated fatty acids (lcSFAs) is an important process in understanding how obesity initiates inflammation. While experimental evidence supports an important role for TLR4 in obesity-induced inflammation in vivo, via a mechanism thought to involve direct binding to and activation of TLR4 by lcSFAs, several lines of evidence argue against lcSFAs being direct TLR4 agonists. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL17021
    10 Samples
    Download data:
    GEO (TXT), SRA SRP110574
    Series
    Accession:
    GSE100526
    ID:
    200100526
    9.

    Gene expression profiling study by RNA-seq for identifying gene signatures associated with castration-refractory prostate cancer (CRPC) development.

    (Submitter supplied) The objective of this study is to identify gene signature associated with castration-refractory prostate cancer (CRPC) development. We carried out RNA-seq based transcriptome profiling using 45 prostate samples with various disease progression steps such as benign prostate hyperplasia (BPH), primary cancer of prostate (CaP), advanced CaP and CRPC. Via various statistical analyses, we identified significant gene set associated with each progression step and observed that AR was the only gene feature associated with all progression steps, indicating that AR is the crucial mediator of and has a diverse activity across the CaP progressions. more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL11154
    45 Samples
    Download data:
    GEO (TXT), SRA SRP073789
    Series
    Accession:
    GSE80609
    ID:
    200080609
    10.

    RNA-Sequencing of 2,4-D treated Brachypodium distachyon roots containing NLS

    (Submitter supplied) In this study we treated Brachypodium distachyon roots with synthetic auxin, 2,4-D, to induce nodule-like structures (NLS) and performed RNA-seq to assess transcriptome changes during NLS formation.
    Organism:
    Brachypodium distachyon
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL21050
    6 Samples
    Download data:
    GEO (TXT), SRA SRP104182
    Series
    Accession:
    GSE97940
    ID:
    200097940
    11.

    Epigenetic regulation by BAF (mSWI/SNF) complexes limits neural stem cell proliferation by suppressing Wnt signaling in late cortical neurogenesis

    (Submitter supplied) We have analyzed changes in gene expression, histone 3 lysine 4 dimethyl (H3K4me2) and histone 3 lysine 37 trimethyl (H3K27me3) levels in the embryonic cortex at E17.5 resulting from conditional deletion of BAF complex - i.e., double knockout of BAF155 and BAF170, in late cortical progenitors utilizing Cre expression under human GFAP (hGFAP) promoter (dcKO_hGFAP-Cre). Moreover, we also analyzed gene expression in WT E17.5 cortex treated with vehicle and Wnt inhibitor together with that of in dcKO_hGFAP-Cre cortex treated with Wnt inhibitor. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
    Platform:
    GPL13112
    36 Samples
    Download data:
    GEO (TXT, XLS), SRA SRP124677
    Series
    Accession:
    GSE106711
    ID:
    200106711
    12.

    The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Saccharomyces cerevisiae
    Type:
    Expression profiling by high throughput sequencing; Other
    Platform:
    GPL17342
    6 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE113489
    ID:
    200113489
    13.

    The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops [iCLIP]

    (Submitter supplied) The DEAD-box RNA helicase Dbp2p is highly conserved in eukaryotes and has been implicated in transcription, ribosome biogenesis, mRNP assembly, nuclear export, and lncRNA function. How Dbp2p functions in these seemingly unrelated biological roles is not known. An important step towards addressing this question is the determination of cellular RNA binding sites of Dbp2p. Here, we identify transcriptome-wide RNA binding sites of Dbp2p from Saccharomyces cerevisiae using denaturing tandem affinity purification followed by UV-crosslinking. more...
    Organism:
    Saccharomyces cerevisiae
    Type:
    Expression profiling by high throughput sequencing; Other
    Platform:
    GPL17342
    2 Samples
    Download data:
    GEO (TXT), SRA SRP141644
    Series
    Accession:
    GSE113488
    ID:
    200113488
    14.

    The DEAD-box protein Dbp2p is linked to non-coding RNAs, the helicase Sen1p, and R-loops [RNA-Seq]

    (Submitter supplied) The DEAD-box RNA helicase Dbp2p is highly conserved in eukaryotes and has been implicated in transcription, ribosome biogenesis, mRNP assembly, nuclear export, and lncRNA function. How Dbp2p functions in these seemingly unrelated biological roles is not known. An important step towards addressing this question is the determination of cellular RNA binding sites of Dbp2p. Here, we identify transcriptome-wide RNA binding sites of Dbp2p from Saccharomyces cerevisiae using denaturing tandem affinity purification followed by UV-crosslinking. more...
    Organism:
    Saccharomyces cerevisiae
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL17342
    4 Samples
    Download data:
    GEO (TXT), SRA SRP141643
    Series
    Accession:
    GSE113487
    ID:
    200113487
    15.

    Prerequisite Barcoding of Cell-Type-Restricted Enhancers by ESC Transcription Factors in ESCs Licenses Their Robust Developmental Activation

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Mus musculus
    Type:
    Genome binding/occupancy profiling by high throughput sequencing; Other; Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing
    Platforms:
    GPL13112 GPL21103 GPL17021
    26 Samples
    Download data:
    GEO (BEDGRAPH, BIGWIG, TXT)
    Series
    Accession:
    GSE81681
    ID:
    200081681
    16.

    Prerequisite Barcoding of Cell-Type-Rpecific Enhancers by ESC Transcription Factors in ESCs Licenses Their Robust Developmental Activation [RNA-seq]

    (Submitter supplied) While cell-type-restricted enhancers are initially detected following cooperative binding of positionally-determined DNA binding transcription factors during determination/differentiation, it remains unknown whether there are preceding events in embryonic stem cells (ESCs) that are functionally important to activate cell-type-restricted enhancer networks. Here, using murine macrophages as a model, we report that, while largely devoid of characteristic enhancer marks (H3K4me1, H3K4me2, H3K27Ac, H3K27me3 and p300) in ESCs, macrophage enhancers are activated as transcription units mainly by the binding of a single, at most two, ESC transcription factors. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL21103
    5 Samples
    Download data:
    GEO (BEDGRAPH), SRA SRP102284
    Series
    Accession:
    GSE96903
    ID:
    200096903
    17.

    Single cell RNA-seq analysis of K27M-mutant glioma

    (Submitter supplied) To understand the diversity of expression states within K27M-mutant gliomas, we profiled 4058 single cells, primarily from 6 K27M-mutant gliomas, by single cell RNA-seq
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL18573
    4058 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE102130
    ID:
    200102130
    18.

    Electrophilic stress induced by dimethyl itaconate regulates IkB-zeta-mediated inflammatory responses

    (Submitter supplied) Interplay between metabolic state of the cell and its ability to undergo immunological activation has been recently recognized as a treasure chest of novel fundamental regulatory principles. Itaconate, and its membrane permeable derivative dimethyl itaconate (DI) were recently shown to selectively inhibit subset of cytokines during macrophage activation (e.g. Il1b, il6, Il12b but not TNF), yet the precise mechanism of this effect remained unclear. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL17021
    8 Samples
    Download data:
    GEO (TXT), SRA SRP114712
    Series
    Accession:
    GSE102190
    ID:
    200102190
    19.

    A stress response that monitors and regulates mRNA structure is central to cold-shock adaptation

    (Submitter supplied) Temperature influences the structural and functional properties of cellular components, necessitating stress responses to restore homeostasis following temperature shift. The heat shock circuitry is well understood, but that controlling the E. coli cold-shock adaptation program is not. We found that during the growth arrest phase (acclimation) that follows shift to low temperature, protein synthesis increases and ORF-wide mRNA secondary structure decreases. more...
    Organism:
    Escherichia coli; Escherichia coli str. K-12 substr. MG1655
    Type:
    Expression profiling by high throughput sequencing; Other
    4 related Platforms
    55 Samples
    Download data:
    GEO (TXT, WIG), SRA SRP117035
    Series
    Accession:
    GSE103421
    ID:
    200103421
    20.

    RNA-seq analysis dataset: FACS-sorted Ptf1a-lineage cells from E14.5 hypothalamus of Ptf1a hetero and homozygous mice

    (Submitter supplied) Because Ptf1a is a transcription factor, this protein should regulate transcription of various genes in Ptf1a-expressing cells of the hypothalamus. To detect those downstream genes, we purified cells in the Ptf1a-lineage from the hypothalamus at E14.5 by FACS sorting, subsequently performed RNA-seq analysis and obtained 706 differentially expressed genes. 386 genes had lower and 320 had higher expression in Ptf1a-lineage cells from homozygous Ptf1a deficient mice. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL19057
    8 Samples
    Download data:
    GEO (XLSX)
    Series
    Accession:
    GSE112935
    ID:
    200112935

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