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    Results: 1 to 20 of 15780

    1.

    Comparison of Liver Tumor Models to Regenerating Liver Tissues

    (Submitter supplied) To identify genes and pathways sepcific to tumorigenesis, we harvested tissues from two different liver tumor models as well as regenerating tissues. Genes significantly different in the two tumor models, but not in regenerating tissues, were used for further investigation
    Organism:
    Mus musculus; Rattus norvegicus
    Type:
    Expression profiling by high throughput sequencing
    Platforms:
    GPL13112 GPL14844
    17 Samples
    Download data:
    GEO (TXT), SRA SRP066975
    Series
    Accession:
    GSE75677
    ID:
    200075677
    2.

    RNA-sequencing of Adult Zebrafish Inner Ear Hair Cells

    (Submitter supplied) To understand the basic biological properties of inner ear hair cells (HCs) from non-mammalian vertebrates, we examined the transcriptome of adult zebrafish auditory and vestibular HCs. GFP-labeled HCs were isolated from inner-ear sensory epithelia of a pou4f3 promoter-driven GAP-GFP line of transgenic zebrafish. One thousand HCs and 1,000 non-sensory surrounding cells (nsSCs) were separately collected for each biological replicate, using the suction pipette technique. more...
    Organism:
    Danio rerio
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL18413
    6 Samples
    Download data:
    GEO (XLSX), SRA SRP113243
    Series
    Accession:
    GSE101693
    ID:
    200101693
    3.

    Gene expression profiling of mouse macrophages following long noncoding RNA Malat1 knockdown

    (Submitter supplied) We applied next-generation sequencing to investigate the gene expression profiles in mouse bone-marrow derived macrophages with or without long noncoding RNA-Malat1 knockdown. We identified a number of differentially regulated genes in cells with Malat1 knockdown.
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL19057
    4 Samples
    Download data:
    GEO (TXT), SRA SRP125035
    Series
    Accession:
    GSE106913
    ID:
    200106913
    4.

    Histone exchange assay in loss of DOT1

    (Submitter supplied) Strain background is Saccharomyces cerevisiae wzy42 histone mutant strain with pWZ403 Myc-HHT2-HHF2 plasmid and pGAL1/10 FLAG-HHT1-HHF1 integrated gene. Cells were grown in YP+2% raffinose until mid-log (OD600=0.5) and arrested with alpha factor. When most of Cells were in G1 phase, added galactose (final conc. 2%) and harvested cells after 1 hour. Fixed cells were harvested by centrifugation at 4 Celcius degrees and the cell pellets were washed by 15mL of pH7.5 TBS buffer per a conical tube. more...
    Organism:
    Saccharomyces cerevisiae
    Type:
    Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
    Platform:
    GPL17342
    35 Samples
    Download data:
    GEO (BIGWIG, WIG), SRA SRP123464
    Series
    Accession:
    GSE106450
    ID:
    200106450
    5.

    Gene expression profiling of mouse macrophages following IRF2 knockdown

    (Submitter supplied) We applied next-generation sequencing to investigate the gene expression profiles in mouse bone-marrow derived macrophages with or without IRF2 knockdown. We identified a number of differentially regulated genes in cells with IRF2 knockdown.
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL19057
    4 Samples
    Download data:
    GEO (XLSX), SRA SRP124976
    Series
    Accession:
    GSE106895
    ID:
    200106895
    6.

    Non-synchronized cell cycle transcriptomics in U2OS and HeLa cancer cells

    (Submitter supplied) Sorting U2OS and HeLa cells genetically modified with the Fucci System allowed us to separate cells according to cell cycle progression followed by RNA Sequencing to characterize the oscillating transcriptome in cells without the need for chemical synchronization.
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL11154
    15 Samples
    Download data:
    GEO (CSV), SRA SRP119610
    Series
    Accession:
    GSE104736
    ID:
    200104736
    7.

    Kdm2b regulates somatic reprogramming through variant PRC1 complex dependent function

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
    Platform:
    GPL19057
    63 Samples
    Download data:
    GEO
    Series
    Accession:
    GSE94160
    ID:
    200094160
    8.

    Comparative Genomic Analysis of Hematopoietic System Using High Throughput Single Cell Sequencing

    (Submitter supplied) Traditional single-cell RNA-seq technologies have shown limitations for large scale experiments.Here, we report Microwell-seq, a low-cost, low-contamination and high-throughput scmRNA-seq method with extremely simple devices. Using the method, we profiled 80000 single human hematopoietic stem and progenitor cells and identify 47 transcriptionally distinct subpopulations. We propose a revised the adult human hematopoietic hierarchy dominated by unipotent progenitors. more...
    Organism:
    Mus musculus; Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platforms:
    GPL11154 GPL13112
    14 Samples
    Download data:
    GEO (TXT), SRA SRP094955
    Series
    Accession:
    GSE92274
    ID:
    200092274
    9.

    The Aneuploid Multiple Myeloma 3D Genome Reveals Spatial Genome Disorganization Associated with Copy Number Variations and Gene Expression

    (Submitter supplied) Hi-C technique has been widely applied to study the three-dimensional architecture of the whole genome. Genome structures such as compartment A/B, TAD (topologically associated domain) and chromatin loops can be identified from Hi-C data in both normal cells of human and other species, and are found to be associated with features such as epigenetic markers, DNA-binding proteins and gene expression. But such technique had been rarely used in cancer studies. Here we used Hi-C to study the aneuploid cancer genomic architecture in multiple myeloma cells. Our results indicate that Hi-C interaction matrix of cancer cells is affected by CNVs and should be adjusted for copy number. After correcting this CNV bias, we found a significant overlapping between the boundaries of CNV blocks and boundaries of TADs, which suggests that TAD boundaries are fragile sites for CNV breakpoints. In addition, the compartment A/B switching is associated with differential gene expression, from which we found important genes that are related with multiple myeloma. We build a 3D structure model of the aneuploidy genome and found that there are great changes both in the whole genome spatial interactome and local chromosome territories. In summary, our research builds the first 3D genome interaction maps of multiple myeloma and the first time notice this CNV-driven bias in Hi-C studies, which may deepen our understanding of changes in cancer 3D genome.
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing; Genome variation profiling by high throughput sequencing
    Platform:
    GPL16791
    12 Samples
    Download data:
    GEO (FPKM_TRACKING, TAR, TXT), SRA SRP090786
    Series
    Accession:
    GSE87585
    ID:
    200087585
    10.

    Role of FGFR1 in neuronal devlopment

    (Submitter supplied) Purpose: The goal was to study the effects of nFGFR1 on neuronal progenitor cells, by analyzing different effects of FGFR1 mutants through RNA-seq.
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL16791
    15 Samples
    Download data:
    GEO (TXT)
    Series
    Accession:
    GSE103307
    ID:
    200103307
    11.

    SOX10 Single Transcription Factor Based Fast and Efficient Generation of Oligodendrocytes from Human Pluripotent Stem Cells

    (Submitter supplied) We report the use of a single transcription factor, SOX10, for the generation of oligodendrocytes from human pluripotent stem cells. We further used RNA sequencing to compare the oligodendrocytes derived from pluripotent stem cells to different primary cells. It was revealed that oligodendrocytes derived from pluripotent stem cells are representative of intermediate oligodendrocytes during embryonic development.
    Organism:
    Homo sapiens
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL18573
    12 Samples
    Download data:
    GEO (TXT), SRA SRP125095
    Series
    Accession:
    GSE106984
    ID:
    200106984
    12.

    Metabolic regulation of filamentous fungi is tailored for secondary secondary metabolite production

    (Submitter supplied) We investigated the metabolism of six secondary metabolite producing fungi of the Penicillium genus, during nutrient depletion in the stationary phase of batch fermentations and assessed conserved metabolic responses across species using genome-wide transcriptional profiling. Coexpression analysis revealed that expression of secondary metabolite biosynthetic genes correlates with expression of genes associated with pathways responsible for generation of precursor metabolites for secondary metabolism. more...
    Organism:
    Penicillium coprophilum; Penicillium decumbens; Penicillium polonicum; Penicillium nalgiovense; Penicillium steckii; Penicillium flavigenum
    Type:
    Expression profiling by high throughput sequencing
    6 related Platforms
    36 Samples
    Download data:
    GEO (TXT), SRA SRP125096
    Series
    Accession:
    GSE106983
    ID:
    200106983
    13.

    Enhancer-binding of Brd4 controls cell differentiation

    (Submitter supplied) The epigenomic reader Brd4 is an important drug target for cancers. However, its role in cell differentiation and animal development remains largely unclear. Using two conditional knockout mouse strains and derived cells, we demonstrate that Brd4 controls cell identity gene induction and is essential for adipogenesis and myogenesis. Brd4 co-localizes with lineage-determining transcription factors (LDTFs) on active enhancers during differentiation. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
    Platform:
    GPL17021
    34 Samples
    Download data:
    GEO (TXT, WIG), SRA SRP107492
    Series
    Accession:
    GSE99101
    ID:
    200099101
    14.

    Differential gene expression in the intestine of sea cucumber (Apostichopus japonicus) under low and high salinity conditions

    (Submitter supplied) Sea cucumber, Apostichopus japonicus is a very important species for aquaculture, and its behavior and physiology can respond to the initial change in salinity. It is important to understand the molecular responses of A. japonicus when exposed to ambient changes in salinity In this study, RNA-seq provided a general overview of the gene expression profiles of the intestine of A. japonicus exposed to high salinity (SD40), normal salinity (SD30) and low salinity (SD20) environment.
    Organism:
    Apostichopus japonicus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL23583
    9 Samples
    Download data:
    GEO (FASTA, TXT), SRA SRP117073
    Series
    Accession:
    GSE103466
    ID:
    200103466
    15.

    Lysophosphatidylcholine regulates sexual stage differentiation in the human malaria parasite Plasmodium falciparum

    (Submitter supplied) Purpose: The goal of this study was to identify genes associated with increased sexual differentiation in P. falciparum. Method: RNAseq analysis of two different P. falciparum strains (NF54 and Pf2004/164tdTom) cultured under sexual differentiation-inducing (-SerM) and non-inducing (-SerM/LysoPC and -SerM/Serum) conditions Results: We found a total of 342 genes significantly induced in response to LysoPC depletion, thereby determining changes associated with sexual differentiation and limiting Kenndedy pathway substrates.
    Organism:
    Plasmodium falciparum
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL19269
    26 Samples
    Download data:
    GEO (TXT), SRA SRP118517
    Series
    Accession:
    GSE104114
    ID:
    200104114
    16.

    YY1 is a structural regulator of enhancer-promoter loops [scRNA-seq]

    (Submitter supplied) There is considerable evidence that chromosome structure plays important roles in gene control, but we have limited understanding of the proteins that contribute to structural interactions between gene promoters and their enhancer elements. Large DNA loops that encompass genes and their regulatory elements depend on CTCF-CTCF interactions, but most enhancer-promoter interactions do not depend on this structural protein. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL17021
    2 Samples
    Download data:
    GEO (CLOUPE, CSV), SRA SRP116928
    Series
    Accession:
    GSE103574
    ID:
    200103574
    17.

    Polycomb Repressive Complex 2 methylates Elongin A to regulate transcription

    (Submitter supplied) This SuperSeries is composed of the SubSeries listed below.
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing; Genome binding/occupancy profiling by high throughput sequencing
    Platform:
    GPL17021
    42 Samples
    Download data:
    GEO (BW)
    Series
    Accession:
    GSE104660
    ID:
    200104660
    18.

    Polycomb Repressive Complex 2 methylates Elongin A to regulate transcripiton [BrU-RNA-seq]

    (Submitter supplied) Polycomb repressive complex 2 (PRC2-EZH2) methylates histone H3 at lysine 27 (H3K27) and is required to maintain gene repression during development. Misregulation of PRC2 is linked to a range of neoplastic malignancies, which is believed to involve methylation of H3K27. However, the full spectrum of non-histone substrates of PRC2 that might also contribute to PRC2 function is not known. We characterized the target recognition specificity of PRC2 and used the resultant data to screen for novel potential targets. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL17021
    10 Samples
    Download data:
    GEO (BW, TXT), SRA SRP119476
    Series
    Accession:
    GSE104658
    ID:
    200104658
    19.

    Polycomb Repressive Complex 2 methylates Elongin A to regulate transcripiton [RNA-seq]

    (Submitter supplied) Polycomb repressive complex 2 (PRC2-EZH2) methylates histone H3 at lysine 27 (H3K27) and is required to maintain gene repression during development. Misregulation of PRC2 is linked to a range of neoplastic malignancies, which is believed to involve methylation of H3K27. However, the full spectrum of non-histone substrates of PRC2 that might also contribute to PRC2 function is not known. We characterized the target recognition specificity of PRC2 and used the resultant data to screen for novel potential targets. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL17021
    28 Samples
    Download data:
    GEO (BW, TXT), SRA SRP119473
    Series
    Accession:
    GSE104657
    ID:
    200104657
    20.

    Non-monotonic changes in Progenitor Cell Behavior and Gene expression during aging of the Adult Neural Stem Cell Niche

    (Submitter supplied) Neural stem cell activity in the ventricular-subventricular zone (V-SVZ) decreases with aging, thought to occur by a unidirectional decline. However, by analyzing the V-SVZ transcriptome of male mice at 2, 6, 18 and 22 months, we found that most of the genes that change significantly over time show a reversal of trend, with a maximum or minimum expression at 18 months. In vivo, MASH1+ progenitor cells decrease in number and proliferation between 2-18 months, but these increased between 18-22 months. more...
    Organism:
    Mus musculus
    Type:
    Expression profiling by high throughput sequencing
    Platform:
    GPL17021
    12 Samples
    Download data:
    GEO (XLSX), SRA SRP119471
    Series
    Accession:
    GSE104651
    ID:
    200104651

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