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    Results: 1 to 20 of 16765

    1.

    Sex Differences in the Late First Trimester Human Placenta Transcriptome

    (Submitter supplied) This study is the first characterization of the first trimester placenta transcriptome, highlighting similarities and differences among the sexes in ongoing human pregnancies resulting in live births. Sexual dimorphism may contribute to pregnancy outcomes, including fetal growth and birth weight, which was seen in our cohort, with males significantly heavier than females at birth. This transcriptome provides a basis for development of early diagnostic tests of placental function that can indicate overall pregnancy heath, fetal-maternal health, and long term adult health.
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL18573
    39 Samples
    Download data:
    GEO (TXT), SRA SRP128898
    Series
    Accession:
    GSE109082
    ID:
    200109082
    2.

    A Macrophage Colony-Stimulating Factor-Producing gamma-delta T Cell Subset Prevents Malarial Parasitemic Recurrence

    (Submitter supplied) Despite evidence that gd T cells play an important role during malaria, their precise role remains unclear. During murine malaria induced by Plasmodium chabaudi infection and in human P. falciparum infection, we found that gd T cells expanded rapidly after resolution of acute parasitemia, in contrast to ab T cells that expanded at the acute stage and then declined. Single-cell sequencing showed that TRAV15N-1 gd T cells were clonally expanded in mice and had convergent complementarity-determining region 3 sequences. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL21103
    8 Samples
    Download data:
    GEO, SRA SRP127469
    Series
    Accession:
    GSE108478
    ID:
    200108478
    3.

    Aberrant mRNA m6A methylation promotes the progression of endometrial cancer by altering Akt activity

    (Submitter supplied) The N6-methyladenosine (m6A) methylation of mRNA is an emerging gene regulatory mechanism that controls the stability and translation of methylated transcripts in development and cell differentiation. Here, we show that aberrant m6A methylation plays key roles in the progression of endometrial cancer. About 70% of endometrial tumors exhibit reduced m6A methylation due to either mutation in METTL14 (~10%) or decreased expression of METTL3 (~60%). more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL20301
    32 Samples
    Download data:
    GEO (BED), SRA SRP097578
    Series
    Accession:
    GSE93911
    ID:
    200093911
    4.

    RNA sequencing of sorted cells from mouse PDAC

    (Submitter supplied) Pancreatic ductal adenocarcinoma (PDAC) is characterized by the presence of abundant desmoplatic stroma primarily composed of cancer-associated fibroblasts (CAFs). It is generally accepted that CAFs stimulate tumor progression and might be implicated in drug resistance and immunosuppression. Here, we have compared the transcriptional profile of PDGFRα+ CAFs isolated from genetically engineered mouse PDAC tumors with that of normal pancreatic fibroblasts (NPFs) to identify genes potentially implicated in their pro-tumorigenic properties. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL13112
    18 Samples
    Download data:
    GEO, SRA SRP125006
    Series
    Accession:
    GSE106901
    ID:
    200106901
    5.

    Dyw2-DYW2_OTP100: Identification of the transcriptome defects (nuclear and organelles) of the T-DNA KO mutants of DYW2 and OTP100

    (Submitter supplied) ngs2016_08_dyw2-dyw2-Identification of the transcriptome defects (nuclear and organelles) of the T-DNA KO mutants of DYW2 and OTP100-TheT-DNA KO mutations are embryo-ethal for DYW2 and OTP100 so the homozygous mutants were produced by a temporal embryo-specific complementation using the promoter of ABI3. The resulting homozygous mutants were compared to their WT siblings. The T-DNA lines were GK_332A07 for DYW2 and SAIL_784_A11 for OTP100
    Organism:
    Arabidopsis thaliana
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL19580
    12 Samples
    Download data:
    GEO (TXT), SRA SRP110017
    Series
    Accession:
    GSE100298
    ID:
    200100298
    6.

    Transcriptomic signatures connected to the essential fatty acid limitation in Daphnia magna

    (Submitter supplied) The availability of polyunsaturated fatty acids (PUFAs) in food items influences the fitness of organisms at higher trophic levels. Omega 3 and omega 6 fatty acids are essential compounds that cannot be synthesised de novo in these animals. Especially the omega 3 PUFA eicosapentaenoic acid (EPA) is an important molecule, as it is a limiting nutritional component for growth and reproduction in numerous marine and freshwater zooplankton species. more...
    Organism:
    Daphnia magna
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL24325
    15 Samples
    Download data:
    GEO (TXT), SRA SRP109969
    Series
    Accession:
    GSE107545
    ID:
    200107545
    7.

    RNA G-quadruplex secondary structure promotes alternative splicing via the RNA binding protein hnRNPF

    (Submitter supplied) It is generally thought that splicing factors regulate alternative splicing through binding to RNA consensus sequences. In addition to these linear motifs, RNA secondary structure is emerging as an important layer in splicing regulation. Here we demonstrate that RNA elements with G-quadruplex forming capacity promote exon inclusion. Destroying G-quadruplex forming capacity while keeping G-tracts intact abrogates exon inclusion. more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL20301
    4 Samples
    Download data:
    GEO, SRA SRP125893
    Series
    Accession:
    GSE107542
    ID:
    200107542
    8.

    The activation of the NF-κB-JNK pathway is independent of the PI3K-Rac1-JNK pathway involved in the bFGF-regulated human fibroblast cell migration

    (Submitter supplied) Wound healing is a complex process that repairs organ-tissues including skin after injury. Cell migration is an important process of wound healing and fibroblast growth factor bFGF has been reported to accelerate cell migration. However, knowledge of how bFGF regulates cell migration is limited. Here, we used human foreskin fibroblast primary cells and RNA-Seq based transcriptome analysis to isolate bFGF-regulating signal pathways that regulate cell migration. more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL17303
    6 Samples
    Download data:
    GEO (TXT), SRA SRP052771
    Series
    Accession:
    GSE65193
    ID:
    200065193
    9.

    WOX11 recruits a histone H3K27me3 demethylase to promote gene expression during shoot development in rice

    (Submitter supplied) WUSCHEL-related homeobox (WOX) genes are key regulators of meristem activity and plant development, the chromatin mechanism of which to reprogram gene expression remains unclear. Histone H3K27me3 is a chromatin mark of developmentally repressed genes. How the repressive mark is removed from specific genes during plant development is largely unknown. Here, we show that WOX11 interacts with the H3K27me3 demethylase JMJ705 to activate gene expression during shoot development in rice. more...
    Organism:
    Oryza sativa Japonica Group
    Type:
    Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
    Platforms:
    GPL13834 GPL23876
    9 Samples
    Download data:
    GEO, SRA SRP118965
    Series
    Accession:
    GSE104306
    ID:
    200104306
    10.

    Transcriptional profiling of putative J protein Jjj1 in Candida glabrata

    (Submitter supplied) In the present study the gene encoding the putative J protein Jjj1 was deleted in a susceptible dose dependent clinical isolate resulting in decreased susceptibility to fluconazole compared to wild type. When JJJ1 was deleted in combination with the transcription factor PDR1 the fluconazole susceptibility was consistently only one fold higher from the strain deleted for PDR1 alone. Expression profiling was conducted to determine which genes have altered expression in the absence of JJJ1 and which of these alterations are dependent on PDR1 expression.
    Organism:
    [Candida] glabrata
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL24070
    6 Samples
    Download data:
    GEO, SRA SRP119236
    Series
    Accession:
    GSE104476
    ID:
    200104476
    11.

    RNA seq of pancreatic cancer-associated fibroblasts

    (Submitter supplied) Transcriptomic profiling of pancreatic cancer-associated fibroblasts (CAFs) was done to evaluate the expression of GPCRs. The same was also done for normal pancreatic stellate cells, so as to evaluate whether a population of GPCRs shows increased expression in CAFs vs their normal precursors. We report the discovery of a novel GPCR in CAFs; we demonstrate this GPCR helps to drive the cross-talk between CAFs and cancer cells, enhancing the growth of pancreatic cancer cells.
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL18573
    4 Samples
    Download data:
    GEO, SRA SRP113156
    Series
    Accession:
    GSE101665
    ID:
    200101665
    12.

    Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of human U2OS cells under mild replication stress by low dose aphidicolin (APH)

    (Submitter supplied) To detect transcripts before and after APH treatment, we subjected total RNA isolated from U2OS cells expressing human FANCD2-3xFLAG to next generation sequencing.
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL11154
    2 Samples
    Download data:
    GEO, SRA SRP119207
    Series
    Accession:
    GSE104465
    ID:
    200104465
    13.

    Keap1 knockdown in melanocytes induces cell proliferation and survival via HO-1-associated β-catenin signaling

    (Submitter supplied) Nrf2-Keap1 signaling pathway protects cells against photo-oxidative stress. Yet in recent works, its role in melanogenesis together with cell protection functions against oxidative stress has been gaining interest. However, its effect on melanogenesis still has contradictory results from different studies. The aims of our study were to investigate the effect of Keap1 silencing in melanocyte on melanogenesis and its associated mechanism. more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL18573
    2 Samples
    Download data:
    GEO (WIG), SRA SRP097448
    Series
    Accession:
    GSE93895
    ID:
    200093895
    14.

    The translation termination factor GSPT1 is a phenotypically relevant off-target of heterobifunctional phthalimide degraders

    (Submitter supplied) Protein degradation is an emerging therapeutic strategy with a unique molecular pharmacology that enables the disruption of all functions associated with a target. This is particularly relevant for proteins depending on molecular scaffolding, such as transcription factors or receptor tyrosine kinases (RTKs). To address tractability of multiple RTKs for chemical degradation by the E3 ligase cereblon (CRBN), we synthesized a series of phthalimide degraders based on the promiscuous kinase inhibitors sunitinib and PHA665752. more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL18573
    9 Samples
    Download data:
    GEO
    Series
    Accession:
    GSE108763
    ID:
    200108763
    15.

    RNA sequencing analysis of gene expression in rat hippocampus exposed to chronic stress and albiforin treatment

    (Submitter supplied) We performed high-throughput profiling of gene expression in rat hippocampus in response to chronic unpredictable mild stress (CUMS) and albiflorin treatment. Total 415 differentially expressed genes (DEGs) were identified in rat hippocampus in response to albiflorin treatment compared with CUMS rats treated with saline (CUMS-Sal). We conducted the integrated metabolomics and transcriptomics analysis and found the correction of 16 biochemical pathways by albiflorin such as sphingolipids, phospholipids, tryptophan metabolism, fatty acid oxidation, and purine and pyrimidine metabolism. more...
    Organism:
    Rattus norvegicus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL22396
    12 Samples
    Download data:
    GEO
    Series
    Accession:
    GSE109445
    ID:
    200109445
    16.

    RNAseq comparison of HSV-1 KOS vs n199 infected cells

    (Submitter supplied) The abundance of HSV mRNAs was determines over 16h of infection in wt (KOS) and n199 (ICP22 mutant) infected cells. ICP22 is an immediate early gene of HSV that affects gene expression
    Organism:
    Human alphaherpesvirus 1; Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL23890
    12 Samples
    Download data:
    GEO
    Series
    Accession:
    GSE109420
    ID:
    200109420
    17.

    Transcriptome profiles of mouse embryonic stem cells cultured in different conditions by RNA-seq analysis

    (Submitter supplied) Pluripotent mouse embryonic stem cells (ESCs) were originally derived and stably maintained on feeder cells such as inactivated mouse embryo fibroblasts, and can generate complete ESC-pups by tetraploid embryo complementation (TEC), the most stringent functional test of naive pluripotency. Remarkably, 2i (inhibitors of Mek and Gsk3β signaling) medium with LIF in the absence of serum and feeders was developed to achieve ground state of mouse ESCs, and also has been successfully used for derivation of germline competent ESCs in other species such as rat. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL23479
    8 Samples
    Download data:
    GEO
    Series
    Accession:
    GSE109418
    ID:
    200109418
    18.

    Reduced Abd-B Hox function during kidney development results in lineage infidelity

    (Submitter supplied) In this study, in order to better understand shared core Hox functions, we examined kidney development in mice with frameshift mutations of multiple Abd-B type Hox genes. The resulting phenotypes included dramatically reduced branching morphogenesis of the uretreric bud, premature depletion of nephron progenitors and abnormal development of the stromal compartment. Most unexpected, however, we also observed a cellular level lineage infidelity in nephron segments.
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL17021
    4 Samples
    Download data:
    GEO
    Series
    Accession:
    GSE109404
    ID:
    200109404
    19.

    A toxicogenomics approach to screen chlorinated flame retardants tris(2-chloroethyl) phosphate and tris(2-chloroisopropyl) phosphate for potential health effects

    (Submitter supplied) Tris(2-chloroethyl) phosphate (TCEP) is a pervasive flame retardant that has been identified as a chemical of concern given its health effects and therefore its use has since been tightly regulated. Tris(2-chloroisopropyl) phosphate (TCIPP), an analogue of TCEP, is believed to be its replacement. However, compared to TCEP, little is known of the toxicological impacts of TCIPP. We used RNA sequencing as unbiased and sensitive tool to identify and compare effects on a transcriptome level of TCEP and TCIPP in the human hepatocellular carcinoma cell line, HepG2. more...
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL18460
    15 Samples
    Download data:
    GEO
    Series
    Accession:
    GSE109463
    ID:
    200109463
    20.

    AICDA-induced epigenetic plasticity accelerates germinal center-derived lymphomagenesis

    (Submitter supplied) Epigenetic heterogeneity is emerging as a significant phenotypic feature of tumors. In diffuse large B-cell lymphomas (DLBCLs), increased cytosine methylation heterogeneity is associated with poor clinical outcome, yet the biological mechanisms driving epigenetic heterogeneity remain unclear. Activation-induced cytidine deaminase (AICDA), an enzyme that deaminates and facilitates demethylation of DNA methyl-cytosines in germinal center (GC) B-cells, is required for DLBCL pathogenesis and linked to inferior clinical outcomes. more...
    Organism:
    Homo sapiens; Mus musculus
    Type:
    Methylation profiling by high throughput sequencing; Expression profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing
    Platforms:
    GPL11154 GPL13112 GPL17021
    88 Samples
    Download data:
    GEO (TXT), SRA SRP100105
    Series
    Accession:
    GSE95013
    ID:
    200095013

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