GSE51025 Cooperative Transcription Factor Induction Mediates Hemogenic Reprogramming
Contributors : Andreia M Gomes ; Betty Chang ; Carlos-Filipe Pereira ; Kateri Moore ; Ihor R LemischkaSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensDuring development, hematopoietic stem/progenitor cells (HSPCs) arise fromspecialized endothelial cells by a process termed endothelial-to-hematopoietictransition (EHT). The genetic program driving human HSPC emergence remains largely unknown. We previously reported that the generation of hemogenic precursor cells from mouse fibroblasts recapitulates developmental hematop...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE83944 Circadian oscillations of cytosine modification in humans contribute to epigenetic variability, aging, and complex disease
Conclusions: Our findings suggest that loss of balance between cytosine methylation and demethylation during the circadian cycle can be a potential mechanism for complex disease. Additional experiments, however, are required to investigate the possible involvement of confounding effects, such as hidden cellular heterogeneity. Circadian rhythmicity, one of the key adaptations of life forms on Earth, may contribute to frailty later in life. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE93232 Analysis of transcriptome between clv3 and mpclv3
Contributors : Zhong Zhao ; Linjie Luo ; Jian ZengSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaThe targets of AUXIN REPONSE FACTOR5/MONOPTEROS (ARF5/MP) were reported in many studies which mainly concerned to the flower initiation. But most of these targets are expressed in periphery zone (PZ), how MP regulate the stem-cell activity is unclear. In order to specifically identify the targets of MP in stem cells, as clv3 mutant enrich lots of stem cells, thus we performed transcriptomes of clv3 and mpclv3. This method will enhance the resolution of MP targets specific in stem ...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE99583 Human iPSC derived glomeruli facilitate accurate modelling of podocytopathy
Contributor : Belinda PhipsonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPodocytes are the highly specialised cells within the glomeruli of the kidney that maintain the filtration barrier by forming interdigitating foot processes and slit-diaphragms. Disruption to these features result in proteinuria. Studies into podocyte biology and disease has been hampered by a paucity of in vitro models of this non-proliferative cell type. Here we characterise sieved glomeruli from kidney organoids derived from human pluripotent stem cells. Compared to conditionally immortalised podocytes, or...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE100401 Characterizing the nuclease accessibility of DNA in human cells to map higher order structures of chromatin
Contributors : Uwe Schwartz ; Sarah Diermeier ; Josef Exler ; Rodrigo Maldonado ; Gernot L ängstSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensPackaging of DNA into chromatin regulates DNA accessibility and consequently all DNA-dependent processes. The nucleosome is the basic packaging unit of DNA forming arrays that are suggested, by biochemical studies, to fold hierarchically into ordered higher-order structures of chromatin. This organization has been recently questioned using microscopy techniques, proposing an irregular structure. To address the principles of ...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE101059 Transcriptome analysis of a red-flowered white clover mutant
Contributors : Heshan Zhang ; Yang LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Trifolium repensTranscriptomes analysis of the petals from a red-flowered white clover mutant (red flowers) and its shade-treated counterpart (white flowers) grown under shaded conditions was performed using high-throughput sequencing. We obtained 121,626,564 and 130,577,944 clean reads in red-flowered mutant and treated counterpart, respectively. Of these clean reads, we respectively gained 125,350 and 99,638 unigene sequencces in two groups. As a result, a total of 157,964 unigenes were obtained with an averag...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Trifolium repens Source Type: research

GSE102048 Profiling proliferative cells and their progeny in damaged murine hearts
Contributors : Kai Kretzschmar ; Yorick Post ; Marie Bannier-H élaouët ; Jarno Drost ; Onur Basak ; Vivan S Li ; Maaike van den Born ; Danielle Versteeg ; Lieneke Kooijman ; Stefan van der Elst ; Johan H van Es ; Eva van Rooij ; Hans CleversSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe significance of cardiac stem cell (CSC) populations for cardiac regeneration remains disputed. Here, we apply the most direct definition of stem cell function (the ability to replace lost tissue through cell division) to interrogate the existence of CSCs. By single-cell mRNA sequencing...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE102114 Differential expression of long non ‑coding RNA and mRNA in children with Henoch‑Schönlein purpura nephritis
Contributors : Shuang Pang ; Jun ZhangSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensLong non ‑coding RNAs (lncRNAs) serve an essential role in regulating immunological functions. However, their impact on Henoch‑Schönlein purpura nephritis (HSPN), has remained elusive. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE103208 Ginkgo biloba induces different gene expression signatures of oncogenic pathways in malignant and non-malignant cells of the liver
Contributors : Carolin Czauderna ; Mayrel P Dominguez ; Darko Castven ; Diana Becker ; Luis Z Rodriguez ; Monika Herr ; Dennis Strand ; Susanne Strand ; Stefanie Heilmann-Heimbach ; Luis Gomez-Quiroz ; Peter R Galle ; Jens U MarquardtSeries Type : Expression profiling by arrayOrganism : Homo sapiensGinkgo biloba (EGb761) is a widely used botanical drug with diverse biological properties. Several reports indicate that EGb761 confers both preventive effects as well as anti-tumorigenic properties in a variety of tumors, including hepatocellular carcinoma (HCC). We here evaluate a differential functional and mechanistic effect...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE105900 RNA-Sequencing of Control KD and KD for Ime4-dMettl14, Fl(2)d, Vir, Nito, CG7358 in S2R+ cells
Contributors : Tina Lence ; Nastasja Kreim ; Jean-Yves RoignantSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterN6-methyladenosine (m6A) is an abundant RNA modification in eukaryotes, playing crucial roles in multiple biological processes. m6A is catalyzed by the activity of Mettl3, which depends on additional proteins whose precise functions remain poorly understood. Here we identified Flacc/Zc3h13 as a novel interactor of m6A methyltransferase complex components in Drosophila and mouse. Like other components, Flacc controls m6A levels and is involved in sex determination i...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Drosophila melanogaster Source Type: research

GSE106613 Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA binding factor Rbm15/Spenito to other components of the m6A machinery
Contributors : Philip Knuckles ; Tina Lence ; Irmgard U Haussmann ; Dominik Jacob ; Nastasja Kreim ; Marco Biggiogera ; Marc Helm ; Marc B ühler ; Sarah H Carl ; Irene Masiello ; Tina Hares ; Rodrigo Villaseñor ; Daniel Hess ; Miguel A Andrade-Navarro ; Matthias Soller ; Jean-Yves RoignantSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusm6A is catalyzed by the activity of Mettl3, which depends on additional proteins whose precise functions remain poorly understood. Here we identified Zc3h13 as a novel interactor of m6A methyltransferase complex components in mouse. Like ot...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE106614 Zc3h13/Flacc is required for adenosine methylation by bridging the mRNA binding factor Rbm15/Spenito to other components of the m6A machinery
Series Type : Expression profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Drosophila melanogaster ; Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Methylation profiling by high throughput sequencing Drosophila melanogaster Mus musculus Source Type: research

GSE107717 RNASEQ Analysis of sh-TRC and sh-MIR100HG in the triplex negative breast cancer
Contributors : Shaowei Wang ; Baowei JiaoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPurpose:The goals of this study are using next generation sequencing to identify differentially expressed genes by analyzing knockdown of MIR100HG in triple-negative breast cancer (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE109477 Genome-wide chromatin analysis of Ewing sarcoma (ChIP-seq)
In this study, we apply epigenomic analysis to characterize the transcription dysregulation in this cancer, focusing on the investigation of super-enhancer and its associated transcriptional regulatory mechanisms. We demonstrate that super-enhancer-associated transcripts are significantly enriched in EWS-FLI1 target genes, contribute to the aberrant transcriptional network of the disease, and mediate the exceptional sensitivity of Ewing sarcoma to transcriptional inhibition. Through integrative analysis, we identify MEIS1 as a super-enhancer-driven oncogene, which co-operates with EWS-FLI1 in transcriptional regulation, an...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE111992 Human iPSC-derived glomeruli provide an advanced model to interrogate podocyte biology and accurately recapitulate podocytopathy
Contributors : Andrew Lonsdale ; Lorna HaleSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPodocytes are highly specialised cells within the glomeruli of the kidney that maintain the filtration barrier by forming interdigitating foot processes and slit-diaphragms. Disruption to these features result in proteinuria and glomerulosclerosis. Studies into podocyte biology and disease have previously relied on conditionally immortalised cell lines due to the non- proliferative nature of this cell type. Here we describe an advanced model to study both podocyte and glomerular biology using is...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE111997 Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin
Contributors : Aimee Flores ; Bill LowrySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe sought to determine whether Ldh activity in SCC tumors is a marker of the cell type from which these cells arise, or a key metabolic activity important for tumor initiation or progression. Here we show that genetic abrogation of Ldh enzyme activity in HFSC-mediated tumorigenesis had no effect on tumor number, time to tumor formation, tumor proliferation, epithelial to mesenchymal transition in tumors, gene expression in tumors, tumor pathology, or the immune response to tumors. (Source: GEO: Gen...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE112858 Evolution of maternal and zygotic mRNA complements in the early Drosophila embryo
Contributors : Joel Atallah ; Susan E LottSeries Type : Expression profiling by high throughput sequencing ; Third-party reanalysisOrganism : Drosophila ananassae ; Drosophila erecta ; Drosophila mauritiana ; Drosophila melanogaster ; Drosophila miranda ; Drosophila mojavensis ; Drosophila persimilis ; Drosophila pseudoobscura ; Drosophila santomea ; Drosophila sechellia ; Drosophila simulans ; Drosophila virilis ; Drosophila willistoni ; Drosophila yakubaThe earliest stage of animal development is controlled by maternally deposited mRNA transcripts and proteins. Once the zygote is able to transcribe its own genome, matern...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Third-party reanalysis Drosophila ananassae Drosophila erecta Drosophila mauritiana Drosophila melanogaster Drosophila miranda Drosophila mojavensis Drosophila persimilis Drosophila pseu Source Type: research

GSE113997 Sensory neuron lineage mapping and manipulation in the Drosophila olfactory system
Contributors : Phing C Chai ; Steeve Cruchet ; Leonore Wigger ; Richard BentonSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterWe assessed the differential expression of genes in the adult antennae of pnt RNAi and control flies to understand how the expressions of olfactory receptors could change in response to cell fate alteration in the antennae. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Drosophila melanogaster Source Type: research

GSE115127 ADAR1-editing in HeLa, p150-KO and ADAR1-KO transcriptomes
Contributors : Christian K Pfaller ; Roberto CattaneoSeries Type : Expression profiling by high throughput sequencing ; Third-party reanalysisOrganism : Homo sapiensRNAseq analysis of cell lines with ADAR1-p150 and ADAR1-p110 knock-outs and primary human tissue samples (from GSE57353 and GSE99392 data sets) to identify sites of ADAR1 editing (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Third-party reanalysis Homo sapiens Source Type: research

GSE115128 Editing of measles virus genomic RNA by ADAR1
Contributors : Christian K Pfaller ; Roberto CattaneoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNAseq analysis of purified measles virus RNA grown in standard HeLa cells, p150KO or ADAR1KO cells (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE115129 ADAR1-editing of cellular and measles virus-derived duplex RNA
Series Type : Expression profiling by high throughput sequencing ; Third-party reanalysisOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Third-party reanalysis Homo sapiens Source Type: research

GSE115524 HiChIRP reveals RNA-associated chromosome conformation
Contributors : Maxwell R Mumbach ; Jeffrey M Granja ; Ryan A Flynn ; Ansuman T Satpathy ; Adam J Rubin ; Caitlin M Roake ; Jimmy K Guo ; Yanyan Qi ; David G Gennert ; Shadi Shams ; Bryan H Louie ; Michael R Corces ; Steven E Artandi ; Paul A Khavari ; Maninjay K Atianand ; Katherine A Fitzgerald ; William J Greenleaf ; Howard Y ChangSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Homo sapiens ; Mus musculusModular domains of lncRNAs can serve as scaffolds to bring distant regions of the linear genome into spatial proximity. Here we present HiChIRP, a method leveraging novel ...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Other Homo sapiens Mus musculus Source Type: research

GSE116404 Differential RNA-seq analysis of control vs. dnFGFR2b-expressing mouse otocysts reveals targets of FGFR2b signaling at the beginning of inner ear morphogenesis
Contributor : Suzanne L MansourSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusInduction of dnFGFR2bfor 3 partially overlapping intervals at the early stages of otocyst morphogenesis revealed expected and novel up and downregulated genes that were validated by in situ hybridization analysis. Cell cyle genes were enriched in the downregulated datasets and human hearingloss genes were enriched in the upregulated datasets. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116707 Aging alters the epigenetic asymmetry of HSC division [scATAC-Seq]
Contributor : Medhanie MulawSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusHematopoietic stem cells (HSCs) balance self-renewal and differentiation to maintain homeostasis. With aging, the frequency of polar HSCs decreases. Cell polarity in HSCs is controlled by the activity of the small RhoGTPase Cdc42. Here we demonstrate, using a comprehensive set of paired daughter cell analyses that include single cell 3D-confocal imaging, single cell transplants, single cell RNA-seq as well as single cell ATAC-seq, that the outcome of HSC divisions is strongly linked to the polari...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE116708 Aging alters the epigenetic asymmetry of HSC division [scRNA-Seq]
Contributor : Medhanie MulawSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHematopoietic stem cells (HSCs) balance self-renewal and differentiation to maintain homeostasis. With aging, the frequency of polar HSCs decreases. Cell polarity in HSCs is controlled by the activity of the small RhoGTPase Cdc42. Here we demonstrate, using a comprehensive set of paired daughter cell analyses that include single cell 3D-confocal imaging, single cell transplants, single cell RNA-seq as well as single cell ATAC-seq, that the outcome of HSC divisions is strongly linked to the polarity status befo...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116712 Aging alters the epigenetic asymmetry of HSC division
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy 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 - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE117227 Rad53- and Chk1-Dependent DNA Damage Response Pathways Cooperatively Promote Fungal Pathogenesis and Modulate Antifungal Drug Susceptibility
Contributors : Kwang-Woo Jung ; Sangyong Lim ; Yong-Sun BahnSeries Type : Expression profiling by high throughput sequencingOrganism : Cryptococcus neoformans var. grubiiTo elucidate the signaling circuitry downstream of Rad53, we compared transcriptome profiles between wild type and rad53 Δ mutant strains post radiation exposure using RNAseq analysis. Of total 6,962 genes, 5,087 and 4,768 genes showed statistically different expression levels in the wild type and rad53Δ mutant strains, respectively, post radiation exposure (P-value cutoff of
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Cryptococcus neoformans var. grubii Source Type: research

GSE117258 RNA Sequencing Analysis of Nestin-creERT2, NG2-creERTM, and Synapsin-cre Tumors
Contributors : Sheila R Alcantara Llaguno ; Daochun Sun ; Zilai Wang ; Luis F ParadaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRNA sequencing analysis was performed on glioma primary tissue harvested from different mouse models (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE117271 Bulk RNA-sequencing of cell types isolated by FACS from normal human prostates
Contributors : Douglas W Strand ; Gervaise H Henry ; Chad M VezinaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDifferential expression of prostatic cell types were determined using RNA-sequencing of FACS sorted cell types from normal human prostates. The cell types sequenced were basal epithelia, luminal epithelia, a heterogeneous fibromuscular stroma and a poorly understood "other" epithelial population. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE117403 Single Cell RNA-sequencing of cell types isolated by FACS from normal human prostates
Contributors : Douglas W Strand ; Gervaise H Henry ; Chad M VezinaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSingle-cell RNA-sequencing was conducted on specific cell types and heterogeneous viable cells (sorted by FACS) in order to determine a cellular atlas of the normal human prostate. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE117485 RNA-Seq in two Ewing sarcoma cell lines: A673 and SKNMC
In this study, we apply epigenomic analysis to characterize the transcription dysregulation in this cancer, focusing on the investigation of super-enhancer and its associated transcriptional regulatory mechanisms. We demonstrate that super-enhancer-associated transcripts are significantly enriched in EWS-FLI1 target genes, contribute to the aberrant transcriptional network of the disease, and mediate the exceptional sensitivity of Ewing sarcoma to transcriptional inhibition. Through integrative analysis, we identify MEIS1 as a super-enhancer-driven oncogene, which co-operates with EWS-FLI1 in transcriptional regulation, an...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE118041 Transcriptional response to PORCN inhibition using an orthotopic model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II)
Contributors : Nathan Harmston ; Babita Madam ; Enrico Petretto ; David M VirshupSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTimecourse RNA-seq of response to PORCN inhibition, using ETC-159, in an orthotopic model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE118108 Gene expression profiling of PBMCs in dairy cows pre- and post-partum
Contributors : Sabine Mann ; Anja Sipka ; Jennifer K GrenierSeries Type : Expression profiling by high throughput sequencingOrganism : Bos taurusThe transition to lactation challenges dairy cows metabolically. Immune dysfunction and infectious disease risk is the hallmark of this transition period. Transcriptome data of PBMC shows differentially expressed pathways postpartum. Metabolically stressed cows show upregulation of innate immune pathways and inflammation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Bos taurus Source Type: research

GSE118179 Transcriptional response to PORCN inhibition using a subcutaneous model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II)
Contributors : Nathan Harmston ; Babita Madam ; Enrico Petretto ; David M VirshupSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSRP136970 - PRJNA448481 - RNA-seq of response to PORCN inhibition, using ETC-159,in a subcutanenous model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE118190 Transcriptional response to PORCN inhibition using an in vitro model of RNF43 mutant pancreatic adenocarcinoma (HPAF-II)
Contributors : Nathan Harmston ; Babita Madam ; Enrico Petretto ; David M VirshupSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSRP136961 - PRJNA448457 - RNA-seq of response to PORCN inhibition, using ETC-159, in vitro of RNF43 mutant pancreatic adenocarcinoma (HPAF-II). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE118231 Transcriptional response to PORCN inhibition using an HPAF-II orthotopic model upon MYC perturbation
Contributors : Nathan Harmston ; Babita Madam ; Enrico Petretto ; David M VirshupSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSRP137043 - PRJNA448654 - Timecourse RNA-seq response to PORCN inhibition using an HPAF-II orthotopic model with different MYC states (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120716 A cellular anatomy of the normal adult human prostate and prostatic urethra
Series Type : Expression 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 - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE121891 Single cell RNAseq of mouse olfactory bulb reveals cellular heterogeneity and activity dependent molecular census of adult-born neurons
Contributors : Matthew C Hill ; James F Martin ; Benjamin R ArenkielSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCellular heterogeneity within the mammalian brain poses a challenge towards understanding its complex functions. Within the olfactory bulb (OB), odor information is processed by subtypes of inhibitory interneurons whose heterogeneity and functionality is influenced by ongoing adult neurogenesis. To investigate this cellular heterogeneity, and to better understand the developmental programs of adult-born neurons, we utilized single cell RNA sequencing and computational mo...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE122072 Shortening the half-life of Cas9 maintains its gene editing ability and reduces neuronal toxicity
Contributors : Su Yang ; Shihua Li ; Xiao-Jiang Li ; James M BillingsleySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusVirus-mediated expression of CRISPR/Cas9 has been actively used for genome editing in animal models of genetic disorders, including neurological diseases, but the consequences of overexpressing bacterial Cas9 in the mammalian brain remain unknown. Through RNA-seq analysis, we found that virus-mediated expression of Cas9 caused systematic changes in genes involved in neuronal functions. We also generated a short-lived version of Cas9, which maintains its genome editin...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE122099 Molecular pathway analysis towards understanding tissue vulnerability in spinocerebellar ataxia type 1
Conclusions: The findings from this study suggest that different mechanisms of neurodegeneration are at work in the SCA1 inferior olive and cerebellum. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE122589 Transcription factor activity and nucleosome organisation in mitosis
Contributors : Nick Owens ; Pablo NavarroSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Mus musculusMitotic bookmarking transcription factors (BFs) maintain the capacity to bind to their targets during mitosis, despite major rearrangements of the chromatin. While they were thought to propagate gene regulatory information through mitosis by statically occupying their DNA targets, it has recently become clear that BFs are highly dynamic in mitotic cells. This represents both a technical and a conceptual challenge to study and under...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE122853 RNA-seq analysis asociated with the infection of bovine papillomavirus
This study aims to identify possible molecular mechanisms that are behind the pathological processes associated with bovine papillomatosis through the identification of genes related to the development of the lesions. For this, next-generation RNA sequencing was used to assess differentially expressed genes in infected by BPV and non-infected bovines. Three animals with papillomatosis lesion and three without papillomatosis lesion were studied. The Galaxy platform was used to analyze the data generated by the sequencing. The Illumina output files were converted to FASTQ format. Quality evaluation was performed using FastQC...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Bos taurus Source Type: research

GSE123072 Biotic stress-induced priming and de-priming of transcriptional memory in apple.
Contributors : Kay Gully ; Jean-Marc Celton ; Alexandre Degrave ; Marie-Noelle Brisset ; Etienne Bucher ; Sandrine Balzergue ; Muriel Bahut ; Sandra PelletierSeries Type : Expression profiling by arrayOrganism : Malus domesticaIn order to identify primed (and memorized) genes resulting from BTH and/ or flg22 application, we performed a series of microarray-based transcription profiles. 14 days after propagation plants were treated the first time with the indicated treatment and second time 17 days after propagation with the indicated treatment. Plants were harvested and RNA was extracted 31 days after propagation. BTH was ...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Malus domestica Source Type: research

GSE123073 Biotic stress-induced priming and de-priming of transcriptional memory in Arabidopsis
Contributors : Kay Gully ; Jean-Marc Celton ; Alexandre Degrave ; Marie-Noelle Brisset ; Etienne Bucher ; Sandrine Balzergue ; Muriel Bahut ; Sandra PelletierSeries Type : Expression profiling by arrayOrganism : Arabidopsis thalianaIn order to identify primed (and memorized) genes resulting from BTH and/ or flg22 application, we performed a series of microarray-based transcription profiles. 7 days after germination Arabidopsis plants were treated the first time with the indicated treatment and second time 10 days after germination with the indicated treatment. Plants were harvested and RNA was extracted 21 days after germi...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Arabidopsis thaliana Source Type: research

GSE123188 GR mutation in mice changes the genome-wide epigenome of placental tissue in a highly sex-specific manner
Contributors : M Schmidt ; E Lax ; Z Zhou ; A Ruder ; A Ludiro ; F Lapert ; A Macedo da Cruz ; P Sandrini ; T Calzoni ; A Luoni ; R Massart ; MA Riva ; P Gass ; M SzyfSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusWe found that the GR mutation leads to a complete change of the DNA methylation landscape in fetal placenta of c57/bl6n mice in a highly sex-specific manner. The genome-wide capture-sequencing analysis revealed enrichments in genes related to a broad range of biological functions associated with basic signaling pathways and neurological development, but also with diseases ...
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE123246 SRC-2/NCOA genomic binding in decidualizing human endometrial stromal cells
Contributors : John P Lydon ; Francesco J DeMayo ; Maria M SzwarcSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensWhole genome binding profile of SRC-2/NCOA2 in human endometrial stromal cells (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE123247 NLRP2 promotes proinflammatory and chemotactic responses in proximal tubular epithelial cells
In this study, we investigated the functional role of NLRP2 in proximal tubular epithelial cells by overexpressing it in human conditionally immortalized cells obtained from urine of a healthy subject. We found that NLRP2 markedly upregulates proinflammatory and chemotactic responses as well as downregulates interferon-mediated signaling pathways. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE123269 VEGAS: A Platform for Continuous Directed Evolution in Mammalian Cells (RNAseq)
Contributor : English G JustinSeries Type : Expression profiling by high throughput sequencingOrganism : Sindbis virusSindbis virus is a mutagenic ssRNA arbor virus. The structural genome component of this virus can be exchanged for any transgene of
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Sindbis virus Source Type: research

GSE123274 Endo-siRNAs repress expression of SINE1B during in vitro maturation of porcine oocyte
Contributors : Qingran Kong ; Jiaming ZhangSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Sus scrofaWe performed small RNA-seq on Dicer KD and control porcine oocyte, and report endo-siRNAs corresponding to SINE1B are significantly down-regulated by Dicer knockdown and are essential for in vitro maturation of porcine oocyte (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Sus scrofa Source Type: research

GSE123275 Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes at LncRNA and mRNA and miRNA levels between Hep2 cells with stable transfection of MYCT1 and non-transfection of MYCT1
Contributor : Wei-Neng FuSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensPurpose: To obtain the differentially expressed LncRNA, mRNAs and miRNAs between the two groups of cells.Results: We identified 174 LncRNAs, 327 mRNAs and 235 miRNAs differentially expressed in MYCT1-overexpressed Hep2 cells compared to the controls. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - December 4, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research