GSE93804 Next Generation Sequencing of CNS-infiltrating Tox-sufficient and -deficient OT-1 cells in ODC-OVA mice 7 days after LCMV-OVA infection
Contributors : Doron Merkler ; Nicolas PageSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to compare the transcriptome of CNS-infiltrating OT-1 WT and Tox-deficient cells during effector phase (7 days after infection with LCMV-OVA) (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE93805 Next Generation Sequencing of splenic- and CNS-infiltrating OT-1 cells in ODC-OVA mice upon LCMV-OVA and Lm-OVA infection
Contributors : Doron Merkler ; Nicolas PageSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The goal of this study is to compare the transcriptome of OT-1 cells during priming (3 days after infection) and during effector phase ( 7 days after infection) in ODC-OVA mice after LCMV-OVA and Lm-OVA infection (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE93953 TOX expression governs the encephalitogenic potential of microbe-induced autoreactive CD8+ T cells by reducing immune checkpoint sensitivity
We report that TOX represses a terminal differentiation signature in CD8+ T cells by repressing Id-2 expression (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE96657 Y79 Rb Cell line: CD133 positive vs CD133 negative cancer stem like cells
Contributors : Murali M Balla ; Imran Khan ; Ravi Kiran ; Reddy Kalathur ; Geeta K Vemuganti ; P KondiahSeries Type : Expression profiling by arrayOrganism : Homo sapiensGene expression and pathway analysis of sorted CD133 negative and CD133 positive population (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE99020 Differentially expressed genes between C.elegans with low physical ability and with high physical ability
Contributors : Hong-Gil Nam ; Jeong-Hoon HahmSeries Type : Expression profiling by arrayOrganism : Caenorhabditis elegansAging is an important risk factor for disease and is accompanied by the decline of many physiological characteristics, including physical performance. One of the most powerful tests of physical ability in elderly humans is the short physical performance battery (SPPB) (Guralnik et al., 1994), an assessment of the maximum exercise capacity of lower extremities over a short period of time. A similar metric of maximum velocity (MV) in a short period (30  s) is proposed as an equally informative measu...
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Caenorhabditis elegans Source Type: research

GSE100403 A kinome-wide high-content siRNA screen identifies MEK5-ERK5 signaling as critical for breast cancer cell EMT and metastasis
Contributors : Simona Pavan ; Nathalie Meyer-Schaller ; Ravi K Kalathur ; Meera Saxena ; Gerhard ChristoforiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe have employed a high-content microscopy screen in combination with a kinome and phosphatome-wide siRNA library to identify signaling pathways underlying an EMT of murine mammary epithelial cells and breast cancer cells. This screen identified the MEK5-ERK5 axis as a critical player in TGFb-mediated EMT. Suppression of MEK5-ERK5 signaling completely prevented the morphological and molecular changes occurring during a TGFb-induced...
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE100829 The  C. elegans ortholog of TDP-43 regulates the chromatin localization of the heterochromatin protein 1 homolog, HPL-2
Contributors : Tassa K Saldi   ; Patrick Gonzales ; Alfonso Garrido-Lecca ; Vishantie Dostal ; Christine M Roberts ; Lenoard Petrucelli ; Christopher D LinkSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Caenorhabditis elegansTDP-1 is the  C. elegans ortholog of mammalian TDP-43, which is strongly implicated in the etiology of Frontotemporal Dementia (FTD) and Amyotrophic Lateral Sclerosis (ALS). We discovered that deletion of the tdp-1 gene results in enhanced transcriptional gene silencing leadin...
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Other Caenorhabditis elegans Source Type: research

GSE102401 Effect of monocyte- and osteoclast-derived extracellular vesicles on adipose tissue-derived mesenchymal stem/stromal cells
This article is protected by copyright. All rights reserved. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE102767 GATA2 is Dispensable for Generation of Hemogenic Endothelium But Required for Endothelial-to-Hematopoietic Transition
Contributors : Igor Slukvin ; HyunJun Kang ; Scott Swanson ; Oleg MoskvinSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensUsing loss-of- and restoration-of-function approaches, we found that GATA2 function is mainly focused on enthothelial-to-hematopoietic transition (EHT) other than formation of hemogenic endothelial cells (HECs) in hematopoietic development of human ESCs. In addition, our study found that small portion of hematopoietic progenitors (HPs) can be generated even in the absence of GATA, which was proved to have similar character to that of GATA2-independent HPs lacking CF...
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE104066 Glomerular Transcriptome from NEPUTNE subjects with focal and segemental glomerulosclerosis
Contributors : Sean Eddy ; Viji Nair ; Felix Eichinger ; Laura Mariani ; Sebastian Martini ; Brad Godfrey ; Matthias KretzlerSeries Type : Expression profiling by arrayOrganism : Homo sapiensGlomerular Transcriptome from NEPTUNE subjects with focal and segmental glomerulosclerosis. A number of samples profiled in this analysis were also profiled in Series GSE68127, and Series GSE108113. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE107021 The early expansion of a defective NKG2Apos/CD56dim/CD16neg NK cell subset represents a therapeutic target in haploidentical HSCT
Contributors : Alessandra Roberto ; Clara Di Vito ; Emilia M Mazza ; Silvio Bicciato   ; Enrico Lugli ; Domenico MavilioSeries Type : Expression profiling by arrayOrganism : Homo sapiensNatural Killer (NK) cells are the first lymphocyte population to reconstitute early after non myelo-ablative and T cell-replete haploidentical hematopoietic stem cell transplantations (h-HSCTs) with post-transplant infusion of cyclophosphamide. The present study characterizes the transient and predominant expansion starting from the 2nd week after h-HSCT of a donor-derived unconventional subset of CD56dim/CD16neg (uCD56dim) NK cells ex...
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE108109 Shared molecular targets in the glomerular transcriptome from patients with nephrotic syndrome and ANCA-associated vasculitis
Contributors : Sean Eddy ; Viji Nair ; Sebastian Martini ; Laura Mariani ; Matt Sampson ; Felix Eichinger ; Brad Godfrey ; Matthias KretzlerSeries Type : Expression profiling by arrayOrganism : Homo sapiensGlomerular transcriptome from human kidney biopsies in Neptune and ERCB. A number of samples profiled in this analysis were also profiled in Series GSE68127, and in GSE104066. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE108112 Shared molecular targets in the tubulointerstitial transcriptome from patients with nephrotic syndrome and ANCA-associated vasculitis
Contributors : Sean Eddy ; Viji Nair ; Sebastian Martini ; Laura Mariani ; Matt Sampson ; Felix Eichinger ; Brad Godfrey ; Matthias KretzlerSeries Type : Expression profiling by arrayOrganism : Homo sapiensTubulointerstitial transcriptome from human kidney biopsies in Neptune and ERCB. A number of samples profiled in this analysis were also profiled in Series GSE68127. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE108113 Shared molecular targets in the glomerular and tubulointerstitial transcriptomes from patients with nephrotic syndrome and ANCA-associated vasculitis
Series Type : Expression profiling by arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. A number of samples profiled in this analysis were also profiled in Series GSE68127, and GSE104066. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE109205 Single-cell analysis of progenitor cell dynamics and lineage specification of the human fetal kidney
Contributors : Rajasree Menon ; Cristina Cebri án ; Edgar Otto ; Jason R Spence ; Matthias KretzlerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIn order to shed light on human kidney development, we have used single-cell transcriptomics to characterize gene expression in different cell population, and to study individual cell dynamics and lineage trajectories during development (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE109718 Enhancing human kidney organoid differentiation from pluripotent stem cells with high-throughput automation
In this study, single-cell RNA sequencing identify within organoids previously-undetected parietal and interstitial compartments. We discovered that addition of vascular endothelial growth factor (VEGF) during the differentiation process resulted in an approximately ten-fold increase in endothelial cells, without compromising the formation of the organoids. Although VEGF clearly increased the number of endothelial cells by immunofluorescence, relatively few endothelial cells were captured by scRNA-seq and only a modest increase in endothelial cells was observed. This suggested that either a substantial number of endothelia...
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE109965 Analysis of genetically diverse macrophages reveals local and domain-wide mechanisms that control transcription factor binding and function
Contributors : Verena M Link ; Christopher K GlassSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; Methylation profiling by high throughput sequencing ; OtherOrganism : Mus musculusNon-coding genetic variation is a major driver of phenotypic diversity and allows investigation of mechanisms that control gene expression. Here, we systematically investigated the effects of>50 million variations from five strains of mice on mRNA, nascent transcription, transcription start sites and transcription factor binding in resting and activated macro...
Source: GEO: Gene Expression Omnibus - May 17, 2018 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

GSE109983 Bioactive compound from marine sponge-derived Streptomyces sp. SBT348 inhibits staphylococcal growth and biofilm formation
In this study, we describe the biological activity of a marine sponge-derived Streptomyces sp. SBT348 extract in restraining staphylococcal growth and biofilm formation on polystyrene, glass, medically relevant titan metal and silicone surfaces. A bio-assay guided fractionation was performed to isolate the active compound (C3) from the crude SBT348 extract. Our results demonstrated that C3 effectively inhibits the growth (MIC: 31.25 µg/ml) and biofilm formation (sub-MIC range: 1.95- (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Staphylococcus epidermidis RP62A Source Type: research

GSE110327 TCR signal strength controls thymic differentiation of iNKT cell subsets
Contributors : S H Krovi ; Kent A Riemondy ; Jay R Hesselberth ; Laurent GapinSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThree major phenotypically and functionally distinct invariant Natural Killer T (iNKT) cell subsets (iNKT1, iNKT17 and iNKT2), each with propensity to traffic to different tissues and to secrete different cytokines upon activation, have been defined. These fate assignments can be conferred upon iNKT cells during development in the thymus, but the cues that direct these decisions remain unclear. Here, we show that T cell antigen receptor (TCR) signal strength go...
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE111963 Transcriptome profiling of endothelial cells from wild-type, hhex mutants and hhex-overexpression zebrafish embryos
Contributors : S ébastien Gauvrit ; Stefan GuentherSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioWe used high throughput sequencing to identify differential expression in siblings, hhex mutants and hhex-overexpression endothelial cells at 48 hpf. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Danio rerio Source Type: research

GSE113191 CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia
Contributors : Suming Huang ; Huacheng LuoSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Homo sapiensWe analyzed RNA-seq, ATAC-seq, ChIP-seq and 4C-seq data to find that CTCF binding site located between HOXA7 and HOXA9 genes (CBS7/9) is critical for establishing and maintaining aberrant HOXA9-HOXA13 gene expression in AML. Disruption of the CBS7/9 boundary resulted in spreading of repressive H3K27me3 into the posterior active HOXA chromatin domain that subsequently impaired enhancer/promoter chromatin accessibility and d...
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Other Homo sapiens Source Type: research

GSE113585 Profiling of colorectal tumor-infiltrating CD8 T cells according to their expression status of CD39
Contributors : Yannick Simoni ; Kaibo Duan ; Josephine Lum ; Evan NewellSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHuman tumors are infiltrated by various immune cells, including CD8 T cells. CD8 T cells express unique receptors that can recognize peptides at the host ’s cells, including tumor cells. After probing the antigen specificity of ex-vivo tumor-infiltrating CD8 T cells from human tumors, we hypothesized that expression of CD39 was correlated with tumor-specificity. The present experiment aims at better characterizing ex-vivo CD39+ vs CD39- CD8 T cells . (Source: G...
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE113588 Profiling of lung tumor-infiltrating CD8 T cells according to their expression status of CD39
Contributors : Yannick Simoni ; Kaibo Duan ; Josephine Lum ; Evan NewellSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHuman tumors are infiltrated by various immune cells, including CD8 T cells. CD8 T cells express unique receptors that can recognize peptides at the host ’s cells, including tumor cells. After probing the antigen specificity of ex-vivo tumor-infiltrating CD8 T cells from human tumors, we hypothesized that expression of CD39 was correlated with tumor-specificity. The present experiment aims at better characterizing ex-vivo CD39+ vs CD39- CD8 T cells . (Source: G...
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE113590 Profiling of tumor-infiltrating CD8 T cells according to their expression status of CD39
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 - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114514 Modulation of SF3B1 causes global intron retention and downregulation of the B-cell receptor pathway in chronic lymphocytic leukemia
In this study, we performed RNA-seq analysis to evaluate the global impact of SF3B1 modulator sudemycin D6 (SD6) on alternative splicing. Our analysis revealed significant increases in global intron-retention in SD6-treated CLL cells. Pathway analysis of the genes associated with increased intron-retention suggested that B-cell receptor (BCR), protein ubiquitination, and PI3K signaling pathways were among the top canonical pathways being affected by SD6. The increases in intron-retention were inversely correlated with deceases in mRNA and protein levels of the affected BCR/PI3K pathway molecules such as BLNK, BTK, AKT1, PL...
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114515 Post-slippage cells increase expression of factors associated with SASP.
Contributors : Karen Crasta ; Bing Cheng ; Alex WongSeries Type : Expression profiling by arrayOrganism : Homo sapiensHuman transcriptome analysis of U2OS cells treated with nocodazole or DMSO (Control).The gene expression profiling will reveal senescence-associated genes induced upon nocodazole treatment. Our preliminary data show that antimitotic drugs treatment promote post-slippage senescence. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE114516 Gene expression profiling of hematopoietc stem cells from heterozygous Asxl1 KI mice
Contributors : Masahiro Uni ; Mineo KurokawaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe performed RNA-seq with (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE114523 Genome-wide methylation analysis of ependymoma using Infinium HumanMethylation 450 BeadChip
Contributors : Koichi Ichimura ; Kohei FukuokaSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensGenome wide DNA methylation profiling of ependymomas. The Illumina Infinium 450k Human DNA methylation Beadchip was used to obtain DNA methylation profiles across approximately 485,500 CpGs. Samples included 83 ependymomas. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE114534 Genome-wide DNA methylation of survival outliers of glioblastoma
In this study, we aimed to characterize the global DNA methylation pattern of mainly IDH1 wild type survival outliers of glioblastoma. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by array Homo sapiens Source Type: research

GSE114539 Cohesin interacts with a panoply of splicing factors required for cell cycle progression and genomic organization
Contributors : Jung-Sik Kim ; Xiaoyuan He ; Jie Liu ; Zhijun Duan ; Taeyeon Kim ; Julia Gerard ; Brian Kim ; William S Lane ; William S Noble ; Bogdan Budnik ; Todd WaldmanSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThe cohesin complex regulates sister chromatid cohesion, chromosome organization, gene expression, and DNA repair. Here we report that endogenous human cohesin interacts with a panoply of splicing factors and RNA binding proteins, including diverse components of the U4/U6.U5 tri-snRNP complex and several splicing factors that are commonly mutated in cance...
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114541 Transcriptome profiling of microRNA-mediated neuronal reprogramming with REST repression at day 7
Contributors : Seong W Lee ; Andrew S YooSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEctopic expression of neuronal microRNAs (miRNAs), miR-9/9* and miR-124 (miR-9/9*-124) in adult human fibroblasts has been found to evoke extensive reconfigurations of the chromatin and direct the fate conversion to neurons. We found that miR-9/9* and miR-124 led to the repression of REST, a transcriptional repressor of neuronal genes, during microRNA-mediated neuronal conversion and knockdown of REST enhanced the activation of BAF53b, a mature neuronal marker. Furthermore, time series analysis of...
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114553 Induction of human SST and PV neurons by expressing a single transcription factor LHX6
Contributors : Yuan Fang ; Kai-Heng Fang ; Xin Chen ; Yuanyuan Wang ; Mingyan Lin ; Shi-Bo Xu ; Hai-Qin Huo ; Min Xu ; Lixiang Ma ; Yuejun Chen ; Shuijin He ; Yan LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo systematically explore the effect of LHX6 on neural development and differentiation, we performed RNA-sequencing (RNA-seq) of hPSC-derived GINs at day 50 in vitro.RNAseq results could also confirm alteration of GINs identity with the overexpression of LHX6. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114555 Altered thymic differentiation and modulation of arthritis by invariant NKT cells expressing mutant ZAP70 [RNA-Seq]
Contributors : Meng Zhao ; Mattias N Svensson ; Koen Venken ; Ashu Sethi ; Shu Liang ; Isaac Engel ; Piotr Mydel ; Jeremy Day ; Dirk Elewaut ; Nunzio Bottini ; Mitchell KronenbergSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusVarious subsets of invariant natural killer T (iNKT) cells with different cytokine productions develop in the mouse thymus, but the factors driving their differentiation remain unclear. Here we show that hypomorphic alleles of Zap70 or chemical inhibition of Zap70 catalysis lead to an increase of IFN-g-producing iNKT cells (NKT1 cells), suggesting NKT1 cells may...
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE114559 Human blastocysts of normal and abnormal karyotypes display distinct transcriptome profiles: an analysis of every mono and trisomy
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCharacterization of the transcriptome of normal and abnormal embryos. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 17, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114502 Altered mRNA splicing by mutant p53 activates oncogenic RAS in pancreatic cancer
Contributors : Luisa F Escobar-Hoyos ; Alex Penson ; Robert K Bradley ; Omar Abdel-Wahab ; Steven D LeachSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusIntegrating transcriptomic analyses of both clinical PDAC and PDAC models, we identified that the most common neomorphic TP53 mutation (p53R175H) rewires RNA splicing promoting transcriptome-wide retention of cassette exons bearing cytosine(C)-rich sequences. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE89296 Role of liquid sugar in regulating the hepatic transcriptome in a high fat Western diet model of NAFLD
Contributor : Michael W GreeneSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: The goals of this study are to use hepatic transcriptome profiling (RNA-seq) to examine the role of liquid sugar consumption in the progression of NAFLD.Methods: Hepatic mRNA profiles of 12-week chow (n=4), high fat Western diet (n=5), and high fat Western diet + fructose/sucore in the drinking water (n=5) fed mice were generated by deep sequencing using Illumina GAIIx. The sequence reads that passed quality filters were analyzed at the transcript isoform level with two methods: Burrows –Wheel...
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE98942 Differential expression of oral cancer cell line UM1 and UM2
Contributors : Xiaofeng Zhou ; Anxun WangSeries Type : Expression profiling by arrayOrganism : Homo sapiensUM1 and UM2 are paired cell lines generated from a oral cancer patient [Nakayama, et al Invas. Metast., 18 (1998), pp. 219 –228]. UM1 is highly invasive and exhibits elevated metastatic potential as compared to UM2. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE98974 Adult CNS Myelin Enhances Axonal Outgrowth From Neural Stem Cells
Contributors : Gunnar Poplawski ; Richard Lie ; Matt Hunt ; Hiromi Kumamaru ; Riki Kawaguchi ; Paul Lu ; Michael Schaefer ; Grace Woodruff ; Jacob Robinson ; Jeniffer Dulin ; Cedric Geoffroy ; Lutz Mezel ; Binhai Zheng ; Giovanni Coppola ; Mark TuszynskiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe growth of neural stem cells is strongly enhanced on myelin in vitro and in vivo. To identify the mechanisms associated with this phenome, we compared RNA expression from mouse E12 derived spinal cord cells on stimulation substrates (laminin and myelin) to permissive substrates (PDL). ...
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE100951 Genome-wide maps of Dnmt3a1 binding in WT and Tet1-/- J1 ES cells
Contributors : Sean M Cullen ; Xueqiu Lin ; Wei Li ; Margaret A GoodellSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusBy biotin-streptavidin ChIP, we found that Dnmt3a1 enriched at diatal promoter regions and its binding was elevated by Tet1 deletion. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE100952 Dnmt3a KO CMS-Seq
Series Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusDnmt3a KO vs. WT CMS-Seq in 129S4/SvJae background (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE100953 Genome-wide maps of histone modifications in WT, Dnmt3a-/- and Tet1-/- J1 ES cells.
Contributors : Sean M Cullen ; Xueqiu Lin ; Tianpeng Gu ; Wei Li ; Margaret A GoodellSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusUsing ChIP-seq to assess changes of histone modifications in response to Dnmt3a or Tet1 deficiency. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE100954 Quantitative analysis of WT, Dnmt3a-/-, Dnmt3b-/- and Tet1-/- J1 ES cell transcriptomes
Contributors : Sean M Cullen ; Xueqiu Lin ; Tianpeng Gu ; Wei Li ; Margaret A GoodellSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIn order to figure out the roles of Dnmt3 and Tet1 in gene regulation, we assessed global gene expression changes in Dnmt3aKO, Dnmt3bKO and Tet1KO ES cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE100955 Genome-wide maps of Tet1 binding in [WT, Tet1-Flag] and [Dnmt3a-/-, Tet1-Flag] J1 ES cells
Contributors : Xueqiu Lin ; Tianpeng Gu ; Wei Li ; Margaret A GoodellSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusIn order to assess Tet1 binding, we first generated a Flag tagged Tet1 ES cells and then knocked out Dnmt3a in the [WT, Tet1-Flag] cells. By Tet1 ChIP and Flag ChIP, we showed that Tet1 binding was complementary to Dnmt3a. And Tet1 binding was not affected or slightly increased at majority of its targets. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE100956 WGBS assessment of global methylation alterations in Dnmt3aKO or Dnmt3bKO mouse embryonic stem cells
Contributors : Sean M Cullen ; Xueqiu Lin ; Wei Li ; Margaret A GoodellSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusUsing WGBS we assessed global DNA methylation changes in Dnmt3aKO or Dnmt3bKO mouse embryonic stem cells. Compared with WT cells, Dnmt3aKO cells but not Dnmt3bKO cells showed genome-wide hypomethylation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE100957 Dnmt3a Tet1
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; Methylation 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 - May 16, 2018 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 Mus musculus Source Type: research

GSE101779 Inherited DNA methylation primes the establishment of accessible chromatin during genome activation
Contributors : Guifen Liu ; Wen Wang ; Shengen Hu ; Xiangxiu Wang ; Yong ZhangSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Danio rerioFor animals, epigenetic modifications can be globally or partially inherited from gametes after fertilization, but the mechanism underlying how the inherited epigenetic signatures affect transcriptional regulation during zygotic genome activation (ZGA) remains poorly understood. Here, we performed genome-wide profiling of chromatin accessibility during zebrafish ZGA, which is closely related to zygotic transcriptional regulation. The locations of t...
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Danio rerio Source Type: research

GSE108177 Total RNA-seq of cancer cells with inhibition of DNA and/or histone methylation
Contributors : Hitoshi Ohtani ; Peter A JonesSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensEndogenous Retroviruses (ERVs) silencing mechanism depend on DNA methylation, heterochromatin conformation and the PRC2 complex. However, extensive maps of ERVs distribution and the associated epigenetic marks have not yet been provided in human cancer cells. Our purpose in this study is to investigate ERVs expression changes after inhibition of DNA and/or histone methylations. Total RNA-seq in human colon cancer HCT116 cells following DNA methylation inhibitor treatment or knockdown of indivi...
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE109460 RNA-Seq analysis of JIB-04 effects on global cellular transcription and HIV in 2D10 T cells
Contributors : Muyu Xu ; Max ChangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMeasuring the effects of the compound JIB-04 on global transcription, NFkB pathway-related genes, and integrated HIV proviral DNA. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE112156 Differential expression of host cell genes and their implications in PCV2 infection
We examined the differential gene expression in VR1BL cells in vitro with and without PCV2 infection (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Sus scrofa Source Type: research

GSE112311 Genome-wide maps of histone modifications (SpikeIn) and Suz12 in WT, Dnmt3a-/-, Tet1-/- J1 and DKO ES cells.
Contributors : Sean M Cullen ; Xueqiu Lin ; Tianpeng Gu ; Wei Li ; Margaret A GoodellSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusUsing ChIP-seq to assess changes of histone modifications in response to Dnmt3a or Tet1 deficiency. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 16, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research