GSE160261 Expression data from FITC challenged skin of CLEC4C-DTR mice vs. littermate controls treated with diptheria toxin
Contributors : Hannah L Miller ; Marco ColonnaSeries Type : Expression profiling by arrayOrganism : Mus musculusCLEC4C-DTR exhibit exacerbated contact hypersensitivty to the FITC hapten. Here we assess the transcriptional differences in whole skin of FITC challenged CLEC4C-DTR+ mice and DTR- mice treated with diptheria toxin.Overall, CLEC4C-DTR upregualated 439 genes and downregulated 152 genes compared to transgene negative controls, filtering output on 2 fold expression level difference and FDR (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 28, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE121960 Survival of cells with deregulated MYC requires UVSSA-dependent regulation of RNAPII dynamics
Contributor : Mai SatoSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensCancer cells develop strong genetic dependencies enabling survival under oncogenic stress. MYC is a key oncogene activated across most cancers, and identifying associated synthetic lethality can provide important clues about its activity and potential therapeutic strategies. Based on previously conducted genome-wide screenings we identified UVSSA, a gene involved in transcription-coupled repair whose knockdown decreased cell viability when combined with MYC activation. Synthetic lethal interactions bet...
Source: GEO: Gene Expression Omnibus - October 28, 2020 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE135457 The landscape of RNA Pol II binding reveals a step-wise transition during ZGA
Contributors : Bofeng Liu ; Qianhua Xu ; Qiujun Wang ; Wei XieSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusZygotic genome activation (ZGA) is the first transcription event in life. However, it is unclear how RNA polymerase is engaged in initiating ZGA in mammals. Here, by developing small-scale Tn5-assisted chromatin cleavage with sequencing (Stacc –seq), we investigated the landscapes of RNA polymerase II (Pol II) binding in mouse embryos. We found that Pol II undergoes ‘loading’, ‘pre-confi...
Source: GEO: Gene Expression Omnibus - October 28, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE153282 Primate heart regeneration via migration and fibroblast repulsion by human heart progenitors
Contributors : Gianluca Santamaria ; Alessandra MorettiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Macaca fascicularisIn the present study, scRNAseq was carried out to establish a molecular roadmap for HVP specification and maturation during heart repair as well as HVP properties in response to acute cardiac injury.Transcriptional profiling by scRNAseq was performed at various timepoints during Human ventricular progenitor-differentiation at D0 and D3 towards cardiomyocytes at D21 that were co-cultured on chimeric human- NHP heart slices. scRNAseq was also performed for HVPs an...
Source: GEO: Gene Expression Omnibus - October 28, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Macaca fascicularis Source Type: research

GSE160186 CRM1 inhibitor anti-tumor activity is enhanced with salicylates by S-phase arrest and impaired DNA-damage repair
Contributors : Thomas Witzig ; Jithma Abeykoon ; Surendra DasariSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensChromosome region maintenance protein1 (CRM1) mediates protein export from the nucleus and is a new target for anti-cancer therapeutics. Broader application of KPT-330 (Selinexor), a CRM1 inhibitor approved for myeloma, has been limited by toxicity. We found that combining choline salicylate (CS) with low-doses of KPT-330 (K+CS) had potent synergistic activity across blood and solid organ cancers ex-vivo and in-vivo. Mechanistically, K+CS enhances CRM1 degradation, induces p...
Source: GEO: Gene Expression Omnibus - October 28, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE160187 Do Copper enhance antibiotic resistance (AR) in resistant bacteria and/or induce AR in sensitive bacteria? [RNA-seq]
Contributors : Emmanuel Doelsch ; David Ogunniyi ; Jimmy BreenSeries Type : Expression profiling by high throughput sequencingOrganism : Pseudomonas aeruginosaThe aim of this experiment was to determine if the development of resistance to antibiotics can be driven by the concentration and speciation of Cu. Experimental setup was designed to investigate two hypotheses for which two strains of Gram- bacteria have been selected: - Do TE enhance AR in resistant bacteria? Resistant strain: Bioluminescent Pseudomonas aeruginosa PAO1 (Xen41, Tetracycline resistant) - Do TE induce AR in sensitive bacteria? Sensitive strain: Pseud...
Source: GEO: Gene Expression Omnibus - October 28, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Pseudomonas aeruginosa Source Type: research

GSE160188 Do Copper enhance antibiotic resistance (AR) in resistant bacteria and/or induce AR in sensitive bacteria? [DNA-seq]
Contributors : Emmanuel Doelsch ; David Ogunniyi ; Jimmy BreenSeries Type : Genome variation profiling by high throughput sequencingOrganism : Pseudomonas aeruginosaThe aim of this experiment was to determine if the development of resistance to antibiotics can be driven by the concentration and speciation of Cu. Experimental setup was designed to investigate two hypotheses for which two strains of Gram- bacteria have been selected: - Do TE enhance AR in resistant bacteria? Resistant strain: Bioluminescent Pseudomonas aeruginosa PAO1 (Xen41, Tetracycline resistant) - Do TE induce AR in sensitive bacteria? Sensitive strain:...
Source: GEO: Gene Expression Omnibus - October 28, 2020 Category: Genetics & Stem Cells Tags: Genome variation profiling by high throughput sequencing Pseudomonas aeruginosa Source Type: research

GSE160190 Do Copper enhance antibiotic resistance (AR) in resistant bacteria and/or induce AR in sensitive bacteria?
Series Type : Expression profiling by high throughput sequencing ; Genome variation profiling by high throughput sequencingOrganism : Pseudomonas aeruginosaThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 28, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome variation profiling by high throughput sequencing Pseudomonas aeruginosa Source Type: research

GSE160195 Medication for acromegaly reduces expression of MUC16, MACC1 and GRHL2 in pituitary neuroendocrine tumour tissue
This study aimed to determine differences in transcriptome signatures induced by SSA/DA therapy in PitNET tissue.We selected tumour tissue from twelve patients with somatotrophinomas, with half of the patients receiving SSA/DA treatment before surgery, and the other half treatment naive. Transcriptome sequencing was then carried out to identify differentially expressed genes (DEGs) and their protein-protein interactions, using pathway analyses.We found 34 upregulated and six downregulated DEGs in patients with SSA/DA treatment. Three tumour development promoting factors MUC16, MACC1 and GRHL2, were significantly downregula...
Source: GEO: Gene Expression Omnibus - October 28, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE160206 eEF3 promotes late stages of tRNA translocation on the ribosome
Contributors : Colin Wu ; Rachel GreenSeries Type : OtherOrganism : Saccharomyces cerevisiaeIn addition to the conserved translation elongation factors eEF1A and eEF2, fungi require a third essential elongation factor, eEF3. While eEF3 has been implicated in tRNA binding and release at the A and E sites, its exact mechanism of action is unclear. Here we show that eEF3 acts at the mRNA –tRNA translocation step by promoting the dissociation of the tRNA from the E site, but independent of aminoacyl-tRNA recruitment to the A site. Depletion of eEF3 in vivo leads to a general slow-down in translation elongation due to acc...
Source: GEO: Gene Expression Omnibus - October 28, 2020 Category: Genetics & Stem Cells Tags: Other Saccharomyces cerevisiae Source Type: research

GSE160207 RNA Sequencing Analysis of a Whole Blood Transcriptome in Estonian Families with Osteogenesis Imperfecta
Conclusions: The current pilot study successfully captured the differential expression of inflammation and bone metabolism pathways in OI patients. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 28, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE160213 Identification of RNAs bound in cellulo to miR-491-5p
Contributors : Christophe Denoyelle ; Matthieu Meryet-Figuiere ; Mamy AndrianteranagnaSeries Type : OtherOrganism : Homo sapiensWe purified all RNAs in direct interaction with biotinylated versions of miR-491-5p or a control miRNA in the cytoplasmic compartment (see protocol) of IGROV1-R10 chemoresistant human ovarian cancer cell line. Input and purified RNA were deep-sequenced in order to calculate an enrichment score able to identify which transcripts were bound in cellulo by miR-491-5p (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 28, 2020 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE160221 Network-based integration of multi-omics data identifies the determinants of miR-491-5p effects
Series Type : Expression profiling by array ; OtherOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 28, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by array Other Homo sapiens Source Type: research

GSE160228 Dynamic single-cell RNA sequencing identifies immunotherapy persister cells following PD-1 blockade
We report results of transcriptional profiling of ex vivo MC38 murine organotypic tumor spheroids following programmed death-1 (PD-1) blockade compared to isotype control IgG treatment by bulk and single-cell RNA-sequencing after 6 days of treatment. Additionally, we report results from single-cell RNA-sequencing of MC38 tumors treated in vivo with PD-1 blockade versus isotype control IgG to validate ex vivo workflow. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 28, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE160229 Targeted high-resolution chromosome conformation capture at genome-wide scale in mouse erythroid cells
Contributors : Damien J Downes ; Jim R HughesSeries Type : OtherOrganism : Mus musculusChromosome conformation capture (3C) provides an adaptable tool through which to study diverse biological questions. Currently, 3C techniques provide either low-resolution interaction profiles across the entire genome, e.g. HiC, or high-resolution interaction profiles at up to several hundred loci, e.g. NG Capture-C and 4C-seq. Generation of high-resolution, genome-wide interaction profiles can feasibly be achieved through efficiency improvements to current high-resolution methods. To this end we systematically tested and removed areas i...
Source: GEO: Gene Expression Omnibus - October 28, 2020 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research

GSE160082 Transcriptional responses of Escherichia coli to ceragenins and antimicrobial peptides
Contributors : Gabriel Mitchell ; Michael A Marletta ; Jeffery S CoxSeries Type : Expression profiling by high throughput sequencingOrganism : Escherichia coliHere we report the results of a study comparing the global transcriptional responses of Escherichia coli to two well-studied CAMPs, LL37 and colistin, and two ceragenins with related structures, CSA13 and CSA131. We found that E. coli responds similarly to both CAMPs and ceragenins by inducing a Cpx envelope stress response. However, whereas E. coli exposed to CAMPs increased expression of genes involved in colanic acid biosynthesis, bacteria exposed to ceragenins sp...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Escherichia coli Source Type: research

GSE110287 Histone acetylation targeting to transcribed chromatin through RNAPII
In this study we resolve this question. Using both immunoblot analysis and chromatin immunoprecipitation-sequencing (ChIP-seq) in S. cerevisiae, we show that the majority of histone acetylation is dependent on transcription. Loss of histone H4 acetylation upon transcription inhibition is partially explained by depletion of histone acetyltransferases (HATs) from gene bodies, implicating transcription in HAT targeting. Despite this, HAT occupancy alone poorly predicts histone acetylation, suggesting that HAT activity is regulated at a step post-recruitment. Collectively, these data show that the majority of histone acetylati...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE122224 Omics multi-layers networks and identification of the key genes and miRNAs involved in fat storage and metabolism: systems biology approach
Contributors : Maryam Bakherad ; Abolfazl BahramiSeries Type : Expression profiling by high throughput sequencingOrganism : Gallus gallusIn spite of the importance of fat metabolism in different species, there has been little success dissecting the inreactome basis of fat storage. To better understand the molecular basis of fat metabolism, we study transcriptome profiling of abdominal fat between chicken with either good or poor genetic merit for meat quality. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Gallus gallus Source Type: research

GSE129582 Subcellular RNA fractions of HSV-1 infected primary human fibroblasts including infection with delta-Vhs mutant
Contributors : Adam Whisnant ; Thomas Hennig ; Marco Michalski ; Andrzej Rutkowski ; Lara Djakovic ; Marie-Sophie Friedl ; Bhaskar Jha ; Marisa Baptista ; Anne L'Hernault ; Florian Erhard ; Caroline C Friedel ; Lars D ölkenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPrimary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain 17 or its vhs null mutant at a multiplicity of infection (MOI) of 10. Subcellular RNA fractions including total RNA, cytoplasmic RNA, nucleoplasmic RNA and chromatin-associated RNA were prepared and subjected to RN...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE129715 Total and newly transcribed (4sU-RNA) RNA of primary human fibroblasts infected with the vhs-null mutant of HSV-1
Contributors : Caroline C Friedel ; Lara Djakovic ; Andrzej J Rutkowski ; Marie-Sophie Friedl ; Thomas Hennig ; Adam W Whisnant ; Michael Kluge ; Florian Erhard ; Lars D ölkenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPrimary human foreskin fibroblasts (HFF) were infected with vhs-null mutant of HSV-1 strain 17 at a multiplicity of infection (MOI) of 10. Newly transcribed RNA was labelled by adding 500 µM 4-thiouridine (4sU) to the cell culture media for 1h. Total cellular RNA was isolated using Trizol. Newly transcribed RNA was purified following the protocol describe...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE130069 mRNA profiling of Pontin WT and RA under glucose starvation
Contributors : Young-Suk Yu ; Hijai R Shin ; Kyoung-Jae Won ; Sung-Hee BaekSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo determine which genes are affected by methylated Pontin, we performed RNA-sequencing (RNA-seq) in Pontin WT and RA MEFs after glucose starvation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE132920 H3K4me3 ChIPmentation on HSV-1 infected primary human fibroblasts
Contributors : Caroline C Friedel ; Lara Djakovic ; Andrzej J Rutkowski ; Marie-Sophie Friedl ; Thomas Hennig ; Adam W Whisnant ; Michael Kluge ; Florian Erhard ; Lars D ölkenSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensPrimary human fetal foreskin fibroblasts (HFFFs) were infected with wild-type simplex virus 1 (HSV-1) strain 17 at a multiplicity of infection (MOI) of 10. ChIPmentation libraries were prepared starting with 500,000 cells per condition following the protocol described by Christian Schmidl et al, Nature Methods 2015 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE138102 G9a plays distinct roles in maintaining DNA methylation, retrotransposon silencing and chromatin looping
In this study, we observe widespread DNA methylation loss in G9a depleted and catalytic mutant embryonic stem cells. Furthermore, we define how G9a regulates chromatin accessibility, epigenetic modifications and transcriptional silencing in both catalytic dependent and independent manners. Reactivated retrotransposons provide alternative promoters and splice sites leading to upregulation of neighboring genes and production of chimeric transcripts. Moreover, while topologically associated domains and compartments A/B definitions are largely unaffected, the loss of G9a leads to altered chromatin states, aberrant CTCF and coh...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Methylation profiling by high throughput sequencing Other Mus musculus Source Type: research

GSE139434 BET protein inhibition disrupts transcription without altering enhancer-promoter interactions [Next generation Capture-C]
Contributors : Nicholas T Crump ; Erica Ballabio ; Thomas A MilneSeries Type : OtherOrganism : Homo sapiensIn higher eukaryotes, enhancers are DNA sequences that allow for the complex temporal and tissue-specific regulation of genes. Although it is not entirely clear how enhancer-promoter interactions can increase gene expression, this proximity has been observed in multiple systems at multiple loci and is thought to be essential for the maintenance of gene expression. Here, we show that treatment of cells with inhibitors of BET proteins can have a strong impact on transcription but very little impact on enhancer-promoter ...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE139435 BET protein inhibition disrupts transcription without altering enhancer-promoter interactions [ChIP-seq]
Contributors : Nicholas T Crump ; Thomas A MilneSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensIn higher eukaryotes, enhancers are DNA sequences that allow for the complex temporal and tissue-specific regulation of genes. Although it is not entirely clear how enhancer-promoter interactions can increase gene expression, this proximity has been observed in multiple systems at multiple loci and is thought to be essential for the maintenance of gene expression. Here, we show that treatment of cells with inhibitors of BET proteins can have a strong impact on transcription bu...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE139436 BET protein inhibition disrupts transcription without altering enhancer-promoter interactions [RNA-seq]
Contributors : Nicholas T Crump ; Laura Godfrey ; Thomas A MilneSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIn higher eukaryotes, enhancers are DNA sequences that allow for the complex temporal and tissue-specific regulation of genes. Although it is not entirely clear how enhancer-promoter interactions can increase gene expression, this proximity has been observed in multiple systems at multiple loci and is thought to be essential for the maintenance of gene expression. Here, we show that treatment of cells with inhibitors of BET proteins can have a strong impact on transcription ...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE139437 BET protein inhibition disrupts transcription without altering enhancer-promoter interactions
Series Type : Expression profiling by high throughput sequencing ; Other ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE140068 Chromatin-associated RNA of HSV-1 infected primary human fibroblasts including infection with vhs mutants
Contributors : Caroline C Friedel ; Adam W Whisnant ; Lara Djakovic ; Andrzej J Rutkowski ; Marie-Sophie Friedl ; Michael Kluge ; Somesh Sai ; Ramon Oliveira Vidal ; Thomas Hennig ; Sascha Sauer ; Florian Erhard ; Lars D ölkenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPrimary human foreskin fibroblasts (HFF) were infected with wild-type herpes simplex virus 1 (HSV-1) strain 17 or its vhs null mutant, or with BAC-derived viruses expressing either a wild-type or catalytically inactive vhs with the D195N mutation at a multiplicity of infection (MOI) of 10. Chromatin-associated ...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE141609 Evolution of CpH methylation in vertebrate brains
Contributors : Alex de Mendoza ; Ozren Bogdanovic ; Ryan ListerSeries Type : Expression profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Apis mellifera ; Branchiostoma lanceolatum ; Callorhinchus milii ; Danio rerio ; Gallus gallus ; Lethenteron camtschaticum ; Monodelphis domestica ; Octopus bimaculoides ; Ornithorhynchus anatinusThe brain requires complex mechanisms of genome regulation to encode and store behavioural information. In mammals, DNA methylation deposited at non-CG dinucleotides characterises brain epigenomes. However, it is unclear to what extent this n...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Methylation profiling by high throughput sequencing Apis mellifera Branchiostoma lanceolatum Callorhinchus milii Danio rerio Gallus gallus Lethenteron camtschaticum Monodelphis domestica Source Type: research

GSE143360 Characterization of Atlantic salmon head kidney extracellular vesicles
We report the miRNA profile of extracellular vesicles released from Atlantic salmon head kidney white blood cells that have been cultured for 1 day or 5 days. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Salmo salar Source Type: research

GSE143796 Neuronal Activity Increases Translocator Protein (TSPO) Levels in the Adult Mouse Brain
Conclusions: Neuronal activity has the potential to modify TSPO expression in the adult central nervous system. These findings challenge the general assumption that altered TSPO levels unequivocally mirrors ongoing neuroinflammation and emphasize the need to consider non-inflammatory interpretations in some physiological or pathological contexts. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE146128 Functional Dissection of Transcription Factor Networks Governing Haematopoietic Progenitor States
Contributors : Iwo Kucinski ; Nicola K Wilson ; Sarah J Kinston ; Rebecca Hannah ; Berthold GottgensSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusBlood is generated by a constant stream of differentiating haematopoietic progenitor cells. The process is controlled by an immensely complex gene regulatory networks. These have been difficult to comprehend using correlative evidence and limited systematic functional data. Hoxb8-FL cell line is a model system of lympho-myeloid progenitors, which self-renews in vitro and is...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE147204 RNA-seq data from three Saccharomyces cerevisiae strains with different protein productivity
Contributors : Qi Qi ; Rosemary Yu ; Jens NielsenSeries Type : Expression profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeThe budding yeast Saccharomyces cerevisiae is a popular host to be used to produce recombinant proteins. Here we studied three yeast strains with different productivity using the RNA-seq data to elucidate the mechanisms for improving protein production. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE147270 Kinetic modeling of stem cell transcriptome dynamics to identify regulatory modules of normal and disturbed neuroectodermal differentiation
Contributors : Nils Bl üthgen ; Marcel LeistSeries Type : Expression profiling by arrayOrganism : Homo sapiensThousands of transcriptome data sets are available, but approaches for their use in dynamic cell response modelling are sparse, especially for processes affected simultaneously by two orthogonal influence variables. We approached this problem for neuroepithelial development of human pluripotent stem cell (differentiation variable), in the presence or absence of valproic acid (signaling variable). Using few basic assumptions (sequential differentiation states of cells; discrete on/off states for individual gene...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE147666 Identification of genes showing an age related expression in iNKT1, 2, and 17 cells of BALB/c thymus
In this study we applied RNA high-throughput seqencing to compare the global gene expression of young adult and aged iNKT subset in thymus of BALB/c mice.We found that only a small number of genes exerted a profound and statistically significant up- or downregulation upon ageing whereas a plethora of minor changes in the gene expression pattern were evident. However, significant age-related differences in expression of a variety of genes such as Histone genes, Gzma, CD25 and others mightcorrelate with functional adaptations to the drastically altering thmyus micro-environment during aging. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE153158 RNA sequencing of NF-kB knockout (KO) U937 cells
Contributors : Dilip Kumar ; Vipin Narang ; Amit SinghalSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTranscription factors of NF-kB family play central roles in inflammatory responses. However, most of our current understanding on these factors are based on in vitro context specific studies and animal models, and human specific cellular and pathophysiological functions at molecular level are poorly understood. Here, we have designed a new oligomer based lentiviral pgRNAs-CRISPR-Cas9 knock-out (KO) approach and performed RNA-seq on 11 independent clones representing p50, p52, p65, c...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE156455 Transcriptional programs of circuit assembly in the Drosophila visual system
Contributors : Yerbol Z Kurmangaliyev ; Lawrence S ZipurskySeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterPrecise patterns of synaptic connections between neurons are encoded in their genetic programs. Here we used single-cell RNA sequencing to profile neuronal transcriptomes at multiple stages in the developing Drosophila visual system. We devised an efficient strategy for profiling neurons at multiple time points in a single pool, thereby minimizing batch effects and maximizing the reliability of time-course data. A transcriptional atlas spanning multiple stages was gene...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Drosophila melanogaster Source Type: research

GSE156806 Gene expression of UC organoids and UC model organoids (long-term inflammation model) derived from human colonic organoids
Contributors : Kiichiro Tsuchiya ; Sho WatanabeSeries Type : Expression profiling by arrayOrganism : Homo sapiensGene expression changes of human colon orgnaoids by 60weeks of inflammatory stimulation in vitro (long-term inflammed organoids) and after 10weeks from the removal of stimulation (inflammation-removed organoids). GSEA analysis was performed about RNA1-9 (Organoids #1). For the reproducibility of the analysis, GSEA was performed in triplicate. The key molecule for long-term inflammation was extracted from RNA10-12 (Organoids #2).The comparison of gene expression of organoids derived from normal(RNA1-3) and UC muc...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE157952 Genome binding/occupancy profiling of methylated Pontin under glucose starvation
Contributors : Young-Suk Yu ; Hijai R Shin ; Kyoung-Jae Won ; Sung-Hee BaekSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusTo determine where methylated Pontin is recruited, we performed ChIP-sequencing (ChIP-seq) in WT MEFs after glucose starvation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE159308 Gene expression profile of Cxcl12-DsRed+ stromal cells from E15.5, P5, and P10 livers.
Contributors : Lei Ding ; Yeojin LeeSeries Type : Expression profiling by arrayOrganism : Mus musculusThe study is designed to identify transcriptional differences of CD45-Ter119-Cxcl12-DsRed+ stromal cells at different develomental stages. 50,000 CD45-Ter119-Cxcl12-DsRed+ stromal cells from freshly prepared livers of E15.5, P5 and P10 Cxcl12DsRed/+ mice were sorted into Trizol by flow cytometry. Total RNA was isolated and amplified with the WT-Ovation Pico RNA Amplification system (Nugen) as the manufacturer ’s instructions. Sense strand complementary DNA was generated using the WT-Ovation Exon Module (Nugen). Then,...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE159806 Regulatory T cells support breast cancer progression by opposing IFN- γ -dependent functional reprogramming of myeloid cells
Contributors : Nicholas M Clark ; Leandro M Mart ínez ; Steven Murdock ; James T deLigio ; Amy L Olex ; Comfort Effi ; Mikhail G Dozmorov ; Paula D BosSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRegulatory T (Treg) cell infiltration of solid tumors often correlates with poor prognosis, but their tumor suppressive function lacks mechanistic understanding. Through a combination of transgenic mice, cell fate mapping, adoptive transfer and co-injection strategies, we demonstrate that Treg cell ablation-dependent anti-tumor effects in murine breast cancer require intratumoral re...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE160001 FOXA1-dependent responses of the HER2+ SKBR-3 cell line to lapatinib
Contributors : Gary L Johnson ; Steven P AngusSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSKBR-3 HER2+ breast cancer cells were treated with 25 nM Dharmacon siGENOME non-targeting (NT) siRNA control pool or siRNA pool targeting FOXA1 for 48h, then treated with either DMSO or 300nM lapatinib for 24h. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE160018 Adaptive responses of the HER2+ SKBR-3 and BT474m1 cell lines to lapatinib and JQ1
Contributors : Gary L Johnson ; Steven P AngusSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSKBR-3 or BT474m1 HER2+ breast cancer cells were treated with either DMSO, 300nM lapatinib, 300nM JQ1, or lapatinib and JQ1 in combination for 48h. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE160024 RNA-seq analysis of Ralstonia solanacearum treated with nitrosative and oxidative stress
Contributors : Connor G Hendrich ; Alicia N Truchon ; Beth L Dalsing ; Caitilyn AllenSeries Type : Expression profiling by high throughput sequencingOrganism : Ralstonia solanacearumRalstonia solancearum causes bacterial wilt disease on diverse plant hosts. R. solanacearum cells enter a host from soil or infested water through the roots, then multiply and spread in the water-transporting xylem vessels. Despite the low nutrient content of xylem sap, R. solanacearum grows extremely well inside the host, using denitrification to respire in this hypoxic environment. R. solanacearum growth in planta also depends on the successf...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Ralstonia solanacearum Source Type: research

GSE160037 Simultaneous silencing of Aurora-A and UHRF1 inhibits colorectal cancer cell growth by regulating the expression of DNMT1 and STAT1
Contributors : Jing Han ; Xin Chen ; Laili Chu ; Na Sun ; Chennan Wang ; Rongqing Li ; Zhen Jiang ; Xing Ge ; Junnian Zheng ; Jing Yang ; Takayuki IkezoeSeries Type : Expression profiling by arrayOrganism : Homo sapiensAurora-A has attracted a great deal of interest as a potential therapeutic target. However, the outcomes of inhibitors targeting Aurora-A are not as favorable as expected, and the basis of their ineffectiveness remains unknown. Here, we found that signal transducer and activator of transcription 1 (STAT1) was highly expressed in colorectal cancer (CRC) xenograft mouse models that were resistant to alisertib,...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE160038 Using a Zebrafish Model to Identify Cellular Responses to Uropathogenic E. coli Bacteremia
Contributors : Ashley Rawson ; Vijay Saxena ; Hongyu Gao ; Jenaya Hooks ; Xiaoling Xuei ; Patrick McGuire ; Takashi Hato ; David S Hains ; Ryan Anderson ; Andrew L SchwadererSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioUrinary tract infections (UTIs) are the second most common infections encountered in the pediatric population, second only to respiratory tract infections. UTIs are also a major cause of morbidity and mortality. UTIs can often ascend causing infection in the upper urinary tract or even progress to bacteremia or urosepsis. Urosepsis accounts for 10-30% of septic shock ...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Danio rerio Source Type: research

GSE160061 FGF9 Promotes Mouse Spermatogonial Stem Cell Proliferation Mediated by p38 MAPK Signaling [single-cell RNA-seq]
Conclusions: Taken together, this data indicates that FGF9 is an important regulator of SSC proliferation, operating through p38 MAPK phosphorylation and upregulating Etv5 and Bcl6b in turn. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE160062 FGF9 Promotes Mouse Spermatogonial Stem Cell Proliferation Mediated by p38 MAPK Signaling [bulk RNA-seq]
Conclusions: Taken together, this data indicates that FGF9 is an important regulator of SSC proliferation, operating through p38 MAPK phosphorylation and upregulating Etv5 and Bcl6b in turn. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE160063 FGF9 Promotes Mouse Spermatogonial Stem Cell Proliferation Mediated by p38 MAPK Signaling
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE160064 Radiation-induced damage to prepubertal Pax7+ skeletal muscle stem cells drives lifelong deficits in myofiber size and nuclear number
Contributors : J F Bachman ; J V ChakkalakalSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDuring prepubertal development, muscle stem cells (satellite cells, SCs) actively contribute to myofiber growth. Because some SCs are active during this time, they may be particularly susceptible to damage. Using a Small Animal Radiation Research Platform (SARRP), we investigated the effects of local fractionated radiation treatment on prepubertal SCs. Immediately after this regimen, there was a reduction in SC number. Although surviving SCs had deficiencies in function, some myogenic potential...
Source: GEO: Gene Expression Omnibus - October 26, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research