GSE98547 RAP2 Mediates Mechanotransduction to Hippo pathway
Contributors : Zhipeng Meng ; Yunjiang QiuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMammalian cells are surrounded by the extracellular matrix (ECM), which regulates intercellular signal transduction and provides structural support to cells. Mechanical forces generated by ECM play a key role in regulating cell behaviors including survival, growth, mobility, and differentiation. However, it is unclear how mechanical forces are sensed by cells and transmit biochemical signals to cell fate-determining transcription factors such as YAP (Yes-associated protein) and TAZ (transcription...
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE100987 The changed piRNA profiles of GC-1 cells exposure to 500 nM MC-LR.
Contributors : Ling Zhang ; Xiaodong HanSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Mus musculusWe treated GC-1 cells with 500 nM or 0 nM of MC-LR for 24 h.Next, total RNA from GC-1 cells of these two groups were extracted using TRIzol Reagent. The two small RNA libraries were prepared using the Illumina small RNA preparation kit and were deep-sequenced. After adapter sequences were trimmed, 10,824,057, and 11,566,902 small RNA reads that were smaller than 45 nucleotides were obtained from control group and MC-LR group, respectively. The sequences that correspond to known piRNAs were dete...
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Mus musculus Source Type: research

GSE103776 Effect of liquid cultivations on N2 and AB1 strains of C. elegans
Contributors : Irem Celen ; Jung H Doh ; Chandran R SabanayagamSeries Type : Expression profiling by high throughput sequencingOrganism : Caenorhabditis elegansAbrupt environment changes can elicit an array of genetic effects. However, many of these effects can be overlooked by functional genomic studies conducted in static laboratory conditions. We studied the transcriptomic responses of Caenorhabditis elegans under single generation exposures to drastically different culturing conditions. In our experimental scheme, P0 worms were maintained on terrestrial environments (agar plates), F1 in aquatic cultures, and F2 back to...
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Caenorhabditis elegans Source Type: research

GSE104029 Skeletal muscle Nr4a1 hypomethylation and gene induction reduce insulin sensitivity in sedentary maternal high-fat offspring
Contributors : Evert M van Schothorst ; Sara Schumann ; Inge van der Stelt ; Dorien van Dartel ; Susanne KlausSeries Type : Expression profiling by arrayOrganism : Mus musculusMaternal high-fat consumption has negative effects on the offspring ’s obesity/diabetes susceptibility and we hypothesize that epigenetic modifications in the skeletal muscle are partly responsible for this phenotype. To detect genes affected by maternal nutrition, offspring of low-fat (LF) and high-fat (HF) diet fed dams (C57BL/6 mice) received LF diet upon weani ng and were sacrificed at an age of 6 or 25 weeks. M. quadriceps gene expression ...
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE106942 Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions in various Arabidopsis genetic backgrounds [ChIP-seq]
We report genome-wide binding targets of REF6, a H3K27me3 demethylase and also high-throughput profiling of histone modifications of H3K27me3 in Arabidopsis flowers. Using chromatin-immunoprecipitation followed by high-throughput sequencing, we mapped thousands of binding targets of REF6 in flowers and in addition, we used a second fixative, DSG to capture more indirect targets of REF6. In order to investigate the function of indirect binding of REF6 represented H3K27me3 demethylase, the binding targets of DNA binding domain deleted REF6 were identified in the triple mutant background in which REF6 and its two homologs wer...
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE106943 Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions as well as expression analysis in various Arabidopsis genetic backgrounds [RNA-seq]
We report genome-wide binding targets of REF6, a H3K27me3 demethylase and also high-throughput profiling of histone modifications of H3K27me3 in Arabidopsis flowers. To further investigate the downstream targets of REF6 represented H3K27me3 demethylase, we performed RNA-seq using single, double mutant and triple mutant. Using chromatin-immunoprecipitation followed by high-throughput sequencing, we mapped thousands of binding targets of REF6 in flowers and in addition, we used a second fixative, DSG to capture more indirect targets of REF6. In order to investigate the function of indirect binding of REF6 represented H3K27me...
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE106944 Genome-wide mapping of demethylase, REF6 binding targets and H3K27me3 marked regions as well as expression analysis in various Arabidopsis genetic backgrounds
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE108138 Systematic assessment of next-generation sequencing for quantitative small RNA profiling: A-to-I editing pools
Contributor : Muneesh TewariSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : synthetic constructSmall RNA-seq is increasingly being used for profiling of small RNAs. Quantitative characteristics of long RNA-seq have been extensively described, but small RNA-seq involves fundamentally different methods for library preparation, with distinct protocols and technical variations that have not been fully and systematically studied. Using common sets of reference samples, we evaluated the accuracy, reproducibility and bias of small RNA-seq library preparation for five distinct protocols and across ni...
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing synthetic construct Source Type: research

GSE112686 Effect of hyperfractionated irradiation (HFRT) of prostate primary basal cells (PrEPs) on the transcriptome
Contributors : Fabian Guggenberger ; Harmen J van de Werken ; Holger H Erb ; Giuseppe Cappellano ; Kristina Trattnig ; Florian Handle ; Sarah Peer ; Georg Sch äfer ; Guido Jenster ; Zoran Culig ; Ira-Ida Skvortsova ; Frédéric R SanterSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe irradiated PrEPs derived from four patients undergoing radical prostatectomy according to a HFRT protocol (20 single treatments). Transcriptome was analysed by NextGen sequencing. Gene expression profiling revealed a dysregulation of 3468 genes at mRNA level (1470 upregulated and 1998 d...
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE113819 Expression data from human jejunum before and one month after Roux en Y Gastric Bypass (RYGB)
Contributors : Nicholas Stylopoulos ; Danny Ben-ZviSeries Type : Expression profiling by arrayOrganism : Homo sapiensRYGB reconfigures the intenstine such that food enters the jejunum after passing only a small gastric pouch. This new anatomy places the jejunum as the first part of the intestine that interacts with the food, with little to no gastric digestion, causing dramatic changes in jejunal morphology. Baseline is defined as the biopsy during RYGB. Patients are obese.We used microarrays to study the global programme of gene expression before and 1 month after RYGB, with biopsies taken from the same location the stoma...
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE113821 mRNA Seq of mouse tissues 9 days or 9 weeks after RYGB or sham surgery [9 days]
In this study we sought to characterize the acute response to RYGB surgery using diet induced obese mice. Controls were sham operated mice. Mice were age, sex, weight and diet matched. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE113822 mRNA Seq of mouse tissues 9 weeks after RYGB or sham surgery [9 weeks]
In this study we sought to characterize the long tern response to RYGB surgery using diet induced obese mice. Controls were sham operated mice. Mice were age, sex, weight and diet matched. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE113823 Time-dependent molecular responses differ between gastric bypass and dieting but are conserved across species
Series Type : Expression profiling by array ; Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Expression profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE116307 Combined systemic disruption of MET and EGFR signaling causes liver failure in normal mice
Conclusion: The present study demonstrates that in addition to controlling the regenerative response, MET and EGFR synergistically control baseline liver homeostasis in normal mice in such a way that their combined disruption leads to liver failure and death.We used microarrays to detail the global programme of gene expression in Delta MET + EGFRi mice liver vs control mice liver (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE116649 Megadomains and superloops form dynamically during X-chromosome inactivation but are dispensable for silencing and escape
Contributor : John E FrobergSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Mus musculusThe mammalian inactive X-chromosome (Xi) is structurally distinct from all other chromosomes and serves as a model for higher order chromosome organization. The Xi lacks strong topologically associated domains and is instead organized into megadomains and superloops mediated in part by the noncoding loci, Dxz4 and Firre. Their functional significance is presently unclear, though one study suggests that they permit Xi genes to escape sil...
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Other Mus musculus Source Type: research

GSE116720 Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions [4C]
Contributors : Zhou Yu ; Huanwei Huang ; Ting ChenSeries Type : OtherOrganism : Mus musculuswe report that regional expression of the Hoxc genes is regulated by antagonistic switch between repression and activation epigenetic modification. In freshly isolated dermal cells from P50 telogen Wt/Wt ear skin, no enrichment of H3K27ac was detected at Hoxc cluster, consistent with their lack of expression; in contrast, robust peaks of this marker are observed in 3 ’ region of the Hoxc cluster in dorsal skin dermal cells. Secondly we looked at H3K27 trimethylation (H3K27me3), a marker for polycomb-dependent gene repression, ...
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research

GSE116721 Gene expression, epigenetic modification, and chromatin landscape of skin dermal cells in different body positions [ChIP-Seq]
Contributors : Zhou Yu ; Huanwei Huang ; Ting ChenSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculuswe report that regional expression of the Hoxc genes is regulated by antagonistic switch between repression and activation epigenetic modification. In freshly isolated dermal cells from P50 telogen Wt/Wt ear skin, no enrichment of H3K27ac was detected at Hoxc cluster, consistent with their lack of expression; in contrast, robust peaks of this marker are observed in 3 ’ region of the Hoxc cluster in dorsal skin dermal cells. Secondly we looked at H3K27 trimethylation (H...
Source: GEO: Gene Expression Omnibus - July 9, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE110435 Expression profiling in exosomal miRNAs of patients with late-onset acute graft-versus-host disease in Allogeneic Hematopoietic Stem Cell Transplantation
Contributor : Tomohiro UmezuSeries Type : OtherOrganism : Homo sapiensRecent studies have demonstrated exosomal microRNAs are potential in facilitating molecular diagnosis. Currently, little is known about the underlying mechanism of late-onset acute GVHD (LA GVHD). Identification of altered differential expression profiling of miRNAs in exosome will be useful for understanding role of miRNA in the LA GVHD. The purpose of this study is to investigate the relevance of miRNAs in exosome derived from patients developing LA GVHD after allogeneic HSCT. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 8, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE116701 Analysis of Wild Type and Leptin-overexpressing Pig PBMC Transcriptomes
Contributors : Xiang Chen ; Hongjiang WeiSeries Type : Expression profiling by high throughput sequencingOrganism : Sus scrofaPurpose: To find the difference between leptin-overexpressing and wt pig.Methods: Peripheral blood mononuclear cells (PBMCs) mRNA profiles of 6-month-old wild-type (WT) and leptin-overexpressing pig were generated by deep sequencing. Sequencing libraries were constructed according to the protocol for the Illumina TruSeq Sample preparation kit. Sequencing was performed on the Illumina X Ten sequencer. Library construction and sequencing were performed at the Genergy Biotech Co., Ltd. (Shanghai).Resul...
Source: GEO: Gene Expression Omnibus - July 7, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Sus scrofa Source Type: research

GSE86495 Metabolic signaling directs the reciprocal lineage decisions of αβ and γδ T cells
We report that mTORC1 couples microenvironmental cues with metabolic programs in orchestrating reciprocal development of two fundamentally distinct lineages, αβ and γδ T cells. Loss of mTORC1 impairs αβ but promotes γδ T cell development, and disrupts metabolic remodeling of oxidative and glycolytic metabolism. Mechanistically, reactive oxygen species (ROS) controlled by mTORC1 serves as a key metabolic signal, and perturbation of redox homeostas is impinges upon fate decisions. Furthermore, singlecell RNA sequencing and genetic dissection reveal that mTORC1 links developmental...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE97090 RNA sequencing of Dorsal Root Ganglia upon axonal injury, in presence or absence of NAC (N-acetyl cysteine), and upon H2O2 nerve treatment
Contributors : Arnau A Hervera ; Ilaria Palmisano ; Matt C Danzi ; Simone Di GiovanniSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: A) compare the response to an axonal injury in the peripheral vs central nervous system B) clarify the mechanism of Reactive Oxygen Species-dependent axonal regenerationResults: we found that after peripheral axonal injury there is a higher number of differentially expressed genes with respect to central injury. Moreover,inflammation related genes and regeneration-associated genes were differentially regulated after peripheral injury and H2O2, b...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE98321 Epididymal white adipose tissue expression data from WT and Abhd15-ko mice on normal chow diet at refed state
Contributors : Juliane G Bogner-Strauss ; Wenmin Xia ; Ariane R Pessentheiner ; Melina Amor ; Evelyn Walenta ; Hubert Hackl ; Thomas R ülickeSeries Type : Expression profiling by arrayOrganism : Mus musculusAbhd15 is mainly expressed in white adipose tissues and highly upregulated upon adipogenesis. Abhd15 expression is correlated with insulin resistance in obese humans, however its physiological function remains unknown. We used the microarray technology to gain insight into ABHD15 ’s physiological function by identifying dysregulated genes in eWAT from Abhd15-ko mice in comparison to WT mice.We used microarray...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE98996 Transcriptome analysis the citrus rootstocks of Ziyang xiangcheng (Citrus junos Sieb.) and Poncirus trifoliate (Poncirus trifoliata (L.) Raf.) under saline-alkali stress
Contributors : Juxun Wu ; Hualin YiSeries Type : Expression profiling by high throughput sequencingOrganism : Citrus junos ; Citrus sinensis ; Citrus trifoliataSalt stress, especially saline-alkali stress, has seriously negative effect on citrus production. Ziyang xiangcheng (Citrus junos Sieb.) (Cj) has been reported as a saline-alkali stress and iron deficiency tolerant citrus rootstock. However, the molecular mechanism of its saline-alkali stress tolerance is still not clear. Two citrus rootstocks and one navel orange scion, Cj, Poncirus trifoliate (Poncirus trifoliata (L.) Raf.) (Pt) and ‘Lane Late’ navel o...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Citrus junos Citrus sinensis Citrus trifoliata Source Type: research

GSE106953 Dysregulated circRNAs in plasma from active tuberculosis patients
Contributors : Zhengjun Yi ; Yurong Fu ; Kunshan gao ; Ruifang LiSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensRole of circRNAs in active tuberculosis (TB) remains unknown. The present study was aimed to determine plasma circRNA expression profile in active TB patients to identify potential biomarker by circRNA microarrays. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE107918 Drug sensitivity screening and genomic characterization of 45 HPV-negative head and neck carcinoma cell lines for novel biomarkers of drug efficacy [CGH]
Contributors : Tatiana Lepikhova ; Piia-Riitta Karhemo ; Riku Louhimo ; Bhagwan Yadav ; Astrid Murum ägi ; Evgeny Kulesskiy ; Mikko Kivento ; Harri Sihto ; Reidar Grenman ; Stina Syrjänen ; Olli Kallioniemi ; Tero Aittokallio ; Krister Wennerberg ; Heikki Joensuu ; Outi MonniSeries Type : Genome variation profiling by genome tiling arrayOrganism : Homo sapiensThere is an unmet need for effective targeted therapies for patients with advanced head and neck squamous cell carcinoma (HNSCC). We correlated gene expression, gene copy numbers and point mutations in 45 human papillomavirus negative HNSCC cell lines with t...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by genome tiling array Homo sapiens Source Type: research

GSE108061 Drug sensitivity screening and genomic characterization of 45 HPV-negative head and neck carcinoma cell lines for novel biomarkers of drug efficacy [gene expression]
Contributors : Tatiana Lepikhova ; Piia-Riitta Karhemo ; Riku Louhimo ; Bhagwan Yadav ; Astrid Murum ägi ; Evgeny Kulesskiy ; Mikko Kivento ; Harri Sihto ; Reidar Grenman ; Stina Syrjänen ; Olli Kallioniemi ; Tero Aittokallio ; Krister Wennerberg ; Heikki Joensuu ; Outi MonniSeries Type : Expression profiling by arrayOrganism : Homo sapiensThere is an unmet need for effective targeted therapies for patients with advanced head and neck squamous cell carcinoma (HNSCC). We correlated gene expression, gene copy numbers and point mutations in 45 human papillomavirus negative HNSCC cell lines with the drug sensitivity ...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE108062 Drug sensitivity screening and genomic characterization of 45 HPV-negative head and neck carcinoma cell lines for novel biomarkers of drug efficacy
Series Type : Genome variation profiling by genome tiling array ; Expression profiling by arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by genome tiling array Expression profiling by array Homo sapiens Source Type: research

GSE109599 Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum
Conclusion: Overall, this study allows us to characterize at a genome-wide level cis-regulatory regions likely to play an essential function in the developmental transitions and in clonally variant gene expression in P. falciparum. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Plasmodium falciparum Source Type: research

GSE110588 Single cell and pooled embryo RNA-seq of of early Ciona embryos
Contributors : Michael S Levine ; Nicholas TreenSeries Type : Expression profiling by high throughput sequencingOrganism : Ciona intestinalisThis dataset provides gene expression levels of single cell and pooled embryos as part of a study on zygotic genome activation in Ciona embryogenesis. The single cell RNA-seq data suggested that Cyclin B3 was a key mediator of this process. This was confirmed by performing RNA-seq on pooled RNA isolated from embryos where Cyclin B3 was knocked down (using morpholinos) or overexpressed (using mRNA injections). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Ciona intestinalis Source Type: research

GSE111643 CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [RNA-seq]
Contributors : Michael Gapinske ; Alan Luu ; Jackson Winter ; Wendy S Woods ; Kurt Kostan ; Nikhil Shiva ; Jun S Song ; Pablo Perez-PineraSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCRISPR gene editing has revolutionized biomedicine and biotechnology by providing a simple means to engineer genes in vivo by introducing mutations at target sites in the genomic DNA of living cells. However, given the stochasticity of cellular DNA repair mechanisms and the potential for introducing mutations at off-target sites, technologies capable of introducing targeted changes with increased preci...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE111644 CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [gDNA]
Contributors : Michael Gapinske ; Alan Luu ; Jackson Winter ; Wendy S Woods ; Kurt Kostan ; Nikhil Shiva ; Jun S Song ; Pablo Perez-PineraSeries Type : OtherOrganism : Homo sapiensCRISPR gene editing has revolutionized biomedicine and biotechnology by providing a simple means to engineer genes in vivo by introducing mutations at target sites in the genomic DNA of living cells. However, given the stochasticity of cellular DNA repair mechanisms and the potential for introducing mutations at off-target sites, technologies capable of introducing targeted changes with increased precision, such as cytidine deaminase single-base ...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE111645 CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors [off-targets]
Contributors : Michael Gapinske ; Alan Luu ; Jackson Winter ; Wendy S Woods ; Kurt Kostan ; Nikhil Shiva ; Jun S Song ; Pablo Perez-PineraSeries Type : OtherOrganism : Homo sapiensCRISPR gene editing has revolutionized biomedicine and biotechnology by providing a simple means to engineer genes in vivo by introducing mutations at target sites in the genomic DNA of living cells. However, given the stochasticity of cellular DNA repair mechanisms and the potential for introducing mutations at off-target sites, technologies capable of introducing targeted changes with increased precision, such as cytidine deaminase single-base ...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE111646 CRISPR-SKIP: Programmable Gene Splicing with Single Base Editors
Series Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Homo sapiens Source Type: research

GSE112622 Species-specific endogenous  retroviruses drive widespread, heritable changes in the oocyte methylome
Contributors : Julie Brind'Amour ; Hisato Kobayashi ; Julien R Albert ; Kenjiro Shirane ; Akihiko Sakashita ; Aaron B Bogutz ; Tasuku Koike ; Mohammad M Karimi ; Louis L Lefebvre ; Tomohiro Kono ; Matthew C LorinczSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculus ; Rattus norvegicusDe novo  DNA methylation (DNAme) occurs coincident with transcription during mouse oogenesis. As many oocyte transcripts originate in Long Terminal Repeats (LTRs), which are divergent across species, we examined whether polymorphic LTR-i...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Rattus norvegicus Source Type: research

GSE112982 Metabolic signaling directs the reciprocal lineage decisions of αβ and γδ T cells
Contributors : Kai Yang ; Daniel B Blanco ; Xiang Chen ; Hongbo ChiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDevelopment of ab and gd T cells requires coupling of environmental signals with metabolic and redox regulation by mTORC1 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE113764 Transcriptome of human white and brown adipose tissue biopsies
Contributors : Mueez U Din ; Teema Saari ; Juho Raiko ; Nobu Kudomi ; Stefanie F Maurer ; Tobias Fromme ; Ez-Zoubir Amri ; Martin Klingenspor ; Olof Solin ; Pirjo Nuutila ; Kirsi A VirtanenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe analyzed coding transcript abundance in paired biopsies of white and brown adipose tissue obtained from the supraclavicular region of 15 healthy subjects.In a prior experiment measuring 18F-deoxyglucose uptake by PET-CT, 9 subjects displayed active brown fat and 6 did not. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE113810 Compounds released by the biocontrol yeast Hanseniaspora opuntiae protect plants against Corynespora cassiicola and Botrytis cinerea
Contributors : Mariana Ferreira Saab ; Damien Formey ; Martha Torres ; Wendy Arag ón ; Emir Alejandro Padilla ; Alexandre Tromas ; Christian Sohlenkamp ; Kátia R Freitas Schwan-Estrada ; Mario SerranoSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaPlant diseases induced by fungi are one of the most important limiting factors during pre- and post-harvest food production. For decades, synthetic chemical fungicides have been used to control these diseases, however, increase on worldwide regulatory policies and the demand to reduced their application, have led to sea...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE114075 Biogenesis of a young, 22-nt microRNA in Phaseoleae species by precursor-programmed uridylation
Contributors : Blake C Meyers ; Qili FeiSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Arabidopsis thaliana ; Cajanus cajan ; Vigna radiataPhased, secondary siRNAs (phasiRNAs) represent a class of small RNAs in plants generated via distinct biogenesis pathways, predominantly dependent on the activity of 22 nt miRNAs. Most 22 nt miRNAs are processed by DCL1 from miRNA precursors containing an asymmetric bulge, yielding a 22/21 nt miRNA/miRNA* duplex. Here we show that miR1510, a soybean miRNA capable of triggering phasiRNA production from numerous NB-LRRs, previously described as 21 nt in its...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Arabidopsis thaliana Cajanus cajan Vigna radiata Source Type: research

GSE115172 Increased lactate secretion by cancer cells sustains non-cell-autonomous adaptive resistance to MET and EGFR targeted therapies.
Contributors : Diego Pasini ; Karrin J Ferrari ; Daniel Fernandez-PerezSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMicroenvironment is known to influence cancer drug response and sustain resistance to therapies targeting receptor-tyrosine kinases. However if and how tumor microenvironment can be altered during treatment, contributing to resistance onset is not known. Here we show that, under prolonged treatment with tyrosine kinase inhibitors (TKIs), EGFR- or MET-addicted cancer cells displayed a metabolic shift towards increased glycolysis and lactate production. We identified se...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116625 Salt-responsive miRNAs and target genes of Salix matsudana Koidz
Contributors : Renying Zhuo ; Xiaojiao Han ; Yunxing Zhang ; Dong XuSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Salix matsudanaIn order to screening the responsive miRNAs and target genes of willow under salt stress, the 30-day-old plants were exposed to the salt solution (100 mmol L-1 NaCl) for 0 h and 2 d. then RNA isolated from root and stem tissues for the same time point were mixed respectively in equal amounts for small RNA (sRNA) sequencing. sRNAs with 16 –30 nt were separated from 1 µg total RNA by size fractionation. Subsequently, the selected sRNA fragments were liga...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Salix matsudana Source Type: research

GSE116630 Dynamic Patterns of Threat-associated Gene Expression in the Amygdala and Blood
Contributors : Adriana Lori ; Stephanie Maddox ; Sumeet Sharma ; Ra ül Andero ; Kerry J Ressler ; Alicia K SmithSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: Identification the biological response to fear and stress in both brain and blood is vital for investigators performing peripheral studies of psychiatric traits. The goal of this study was to determine genes responsive to fear conditioning (FC), a well-characterized rodent model of threat-exposure, in the presence or absence of prior stress history, providing insight into the physiological processes underlying tr...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116632 AHR ChIP-seq in lymphoblastoid cell line
Contributors : Richard M Weinshlboum ; Drew R Neavin ; Jeong-Heon Lee ; Zhenqing Ye ; Liewei WangSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensChIP-seq was done on one lymphoblastoid cell lines for vehicle control, or 3-MC agonist treatment to identify AHR binding regions throughout the genome. We identified 17,688 common binding peaks between all ChIP treatments (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE116635 Identifying Intestine Specific Homeobox gene ISX as a biomarker and therapeutic target for metastatic pancreatic cancer: developing spontaneous progression models displaying stage-specific genomic changes
Conclusions: Based on genetic analysis of a same-lineage genetic background cell models, this study identifies a novel molecular pathway underlying the progression of pancreatic cancer disease. This study shows that Intestine Specific Homeobox (ISX) gene is a novel biomarker unique to pancreatic cancer progression. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116636 Novel Race-specific Genetic and Epigenetic Determinants of ADT-Resistance in African American Prostate Cancer
Conclusions: Our study represents the first detailed analysis of African American ADT resistant miRNome, with biologic replicates, generated by miRNA-seq technology. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE116637 RNA-seq of eight lymphoblastoid cell lines after AHR ligand treatments
Contributors : Richard M Weinshlboum ; Drew R Neavin ; Liewei WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA-seq was done on eight different lymphoblastoid cell lines for vehicle control, 3-MC agonist treatment and GNF-351 antagonist treatment for AHR to look at AHR regulated genes with different genetic backgrounds. We identified 69 genes that were highly differentially expressed after 3-MC or GNF-351 antagonist treatment with variation in the degree fo differential expression between the eight cell lines. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE116638 Role of AHR in lymphoblastoid cell lines
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; 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 - July 6, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE116640 Segregation of the mammalian germline and soma is policed by Otx2
Contributors : Jingchao Zhang ; Man ZhangSeries Type : Expression profiling by arrayOrganism : Mus musculusThe successful segregation of germ cells from somatic lineages is vital for sexual reproduction and species survival. In the mouse, primordial germ cells (PGCs), precursors of all germ cells, are induced from the post-implantation epiblast. Induction requires BMP4 signalling to prospective PGCs and the intrinsic action of PGC transcription factors (TFs). However, the molecular mechanisms connecting BMP4 action to induction of PGC TFs that are responsible for segregation of PGCs from somatic lineages are unknown. Here ...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE116676 Microarray expression data from iSOD2 adapted livers
Contributors : Carly S Cox ; Gerald S ShadelSeries Type : Expression profiling by arrayOrganism : Mus musculusTransient mitochondrial stress can promote beneficial physiological responses and longevity, termed "mitohormesis." To interrogate mitohormetic pathways in mammals, we generated mice in which mitochondrial superoxide dismutase 2 (SOD2) can be knocked-down in an inducible and reversible manner (iSOD2-KD). Depleting SOD2 only during embryonic development did not cause post-natal lethality, allowing us to probe adaptive responses to mitochondrial oxidant stress in adult mice. Liver from adapted mice had incr...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE116679 Desmoplasia is associated with carcinoma associated fibroblasts ’ heterogeneity in non-small cell lung cancer patients
Contributors : Ming S Tsao ; C Q Zhu ; Quan LiSeries Type : Expression profiling by arrayOrganism : Homo sapiensCancer associated fibroblasts (CAFs) are well known to strongly influence tumor development, progression, and metastasis. Their characteristics and prognostic gene signature in non-small cell lung cancer (NSCLC) patients have been recognized. Heterogeneity of CAFs has long been observed, however, the functional heterogeneity of CAFs between patients and their genetic basis are far less known. Here, we report the distinction of two CAF subtypes obtained from primary cultures of CAFs and matched normal fibroblasts ...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE116686 Diurnal oscillations in human salivary microRNA and microbial transcription
Contributor : Frank A MiddletonSeries Type : Other ; Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensWe investigated daily oscillations in salivary miRNA and microbial RNA to explore relationships between these components of the gut-brain-axis and their implications in human health. Nine subjects provided 120 saliva samples at designated times, on repeated days. Samples were divided into three sets for exploration and cross-validation. Identification and quantification of host miRNA and microbial RNA was performed using next generation sequencing. Eleven miRNAs and 11 microbial RNAs demonstrate...
Source: GEO: Gene Expression Omnibus - July 6, 2018 Category: Genetics & Stem Cells Tags: Other Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research