GSE106979 Histone H3-G34V and H3-G34R mutant fission yeast exhibit distinct chromatin changes and different DNA damage sensitivities.
Contributors : Brandon R Lowe ; Rajesh K Yadav ; Atsushi Matsuda ; Ryan A Henry ; Alfonso G Fernandez ; Joshua J Hamey ; David Finkelstein ; Satish Kallappagoudar ; Carolyn M Jablonowski ; Marc W Wilkins ; Andrew J Andrews ; Yasushi Hiraoka ; Janet F PartridgeSeries Type : Expression profiling by high throughput sequencingOrganism : Schizosaccharomyces pombeRecurrent somatic mutations of H3F3A in aggressive pediatric high-grade gliomas generate K27M or G34R mutant histone H3.3. H3.3-G34R mutants are common in tumors additionally mutant for p53 and ATRX, an H3.3-specific chromatin remodeler. To gain insight into the role of...
Source: GEO: Gene Expression Omnibus - November 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Schizosaccharomyces pombe Source Type: research

GSE119685 Microarray expression data from the dissected MNTBs of FVB wild-type mice at P0, P1, P2, P3, P4, P6 and P14
Contributors : Douglas R Kolson ; Jun Wan ; Peter H Mathers ; George A SpirouSeries Type : Expression profiling by arrayOrganism : Mus musculusThe medial nucleus of the trapezoid body (MNTB) contains a nearly homogeneous population of neurons, which are innervated by large glutamatergic nerve terminals called calyces of Held (CH). Key steps in maturation of CHs and MNTB neurons, including CH growth and competition, occur very quickly for most cells between postnatal days (P)2 and P6. Therefore, we characterized genome-wide changes in this system, with dense temporal sampling during the first postnatal week.We identified 54...
Source: GEO: Gene Expression Omnibus - November 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE120293 Comparative RNA-Seq in mouse prelimbic cortex (PL)
Contributors : Yongqing Liu ; Zhuo HuangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMajor depressive disorder (MDD) is a prevalent and life-threatening illness in modern society. The susceptibility to MDD is profoundly influenced by environmental factors, such as stressful lifestyle or traumatic events, which could impose maladaptive transcriptional program through epigenetic regulation. However, the underlying molecular mechanisms remain elusive. Here we report that stress-susceptible rodents exhibit lower levels of histone crotonylation in the medial prefrontal cortex (mPFC), co...
Source: GEO: Gene Expression Omnibus - November 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE120371 Deregulated expression of mammalian lncRNA through loss of SPT6 induces R-loop formation, replication stress and cellular senescence
Contributors : S Tan-Wong ; Somdutta Dhir ; Nick J ProudfootSeries Type : OtherOrganism : Homo sapiensExtensive tracts of the mammalian genome that lack protein-coding function are still transcribed into long noncoding RNA. While these lncRNA are generally short-lived, length-restricted and non-polyadenylated, how their expression is distinguished from protein-coding genes remains enigmatic. Surprisingly depletion of the ubiquitous Pol II associated transcription elongation factor SPT6, promotes a redistribution of H3K36me3 histone marks from active protein coding to lncRNA genes which correlates with increased lncRNA tran...
Source: GEO: Gene Expression Omnibus - November 15, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE121224 An enhancer in the middle of the Ig κ locus orchestrates nuclear architecture to generate a diverse antigen receptor repertoire
Contributors : Edgar M Barajas-Mora ; Ann J FeeneySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose:The goal of this study is to assess transcriptome profile in the absence of a potent enhancer located in the V gene region of the Ig κ locus in cell lines and miceMethods: RNAseq from CD19+ cells from B6.RAG1-/- and E88-/-.RAG1-/- mice. RNAseq from 445.3, wild-type (WT) and E88-/-, pro-B cell lines (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE122141 Avermectin treatment for Lepeophtheirus salmonis: Impacts on host (Salmo salar) and parasite immunophysiology
This study investigates the transcriptomic responses of salmon lice (L. salmonis) infecting salmon treated with emamectin benzoate (either 1x or 3x), ivermectin, or commercial feed controls (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Lepeophtheirus salmonis Source Type: research

GSE122498 Gene expression data of glioblastoma patients from GAPVAC trial (Glioma Actively Personalized Vaccine Consortium)
Contributor : J FritscheSeries Type : Expression profiling by arrayOrganism : Homo sapiensPatients with glioblastoma (GB) so far do not sufficiently benefit from recent breakthroughs with checkpoint inhibitors (CPI), for which high mutational load and responses to neo-epitopes are regarded essential. GB tumours show limited intra-tumoral immune cell infiltration and carry 30-50 non-synonymous mutations only. Exploitation of the full repertoire of tumour antigens - non-mutated and neo-epitopes – may offer more effective immunotherapies, especially for tumours with low mutational load. In the first-in-human trial GAPVA...
Source: GEO: Gene Expression Omnibus - November 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE122504 Nrf2 ChIP-seq data of Nrf2KO, wild-type and Keap1KO esophagus
Contributors : Xiong Zhaohui ; Chen XiaoxinSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusTo understand how hyperactive NRF2 causes the esophageal phenotype in mice. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 15, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE122512 Gene expression analysis of head and neck squamous cell carcinoma (HNSCC) cell lines.
Contributors : Curtis R Pickering ; Faye M Johnson ; Jeffrey N MyersSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHuman cancer cell lines are the most frequently used preclinical models in the study of cancer biology and the development of therapeutics. Although anatomically diverse, human papillomavirus (HPV)-driven cancers have a common etiology and similar mutations that overlap with but are distinct from those found in HPV-negative cancers. Building on prior studies that have characterized subsets of head and neck squamous cell carcinoma (HNSCC) and cervical squamous cell carcin...
Source: GEO: Gene Expression Omnibus - November 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE122519 Transcriptional profiling in the anterior pituitary gland of juvenile broiler chickens genetically selected for high or low body weight
Contributors : Laura E Ellestad ; Tom E PorterSeries Type : Expression profiling by arrayOrganism : Gallus gallusSeveral processes governing growth and metabolism are regulated by the neuroendocrine system, particularly the trophic hormones produced in the anterior pituitary gland. However, many of the differences that exist in pituitary gene expression and functional gene networks associated with divergent growth characteristics are still largely unknown. Using the Del-Mar 14K Chicken Integrated Systems microarray, this experiment evaluated global gene expression in the anterior pituitary gland during the first 7 weeks of...
Source: GEO: Gene Expression Omnibus - November 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Gallus gallus Source Type: research

GSE122530 LncRNA expression profiling in advanced resected gastric adenocarcinoma tissues
Contributor : Dang YuanSeries Type : Expression profiling by array ; Non-coding RNA profiling by arrayOrganism : Homo sapiensWe studied the lncRNA and mRNA expression in 6 advanced resected GA (ARGA) tissues using a lncRNA microarray chip. Among 22,870 lncRNAs expressed in ARGA and paired non-neoplastic tissues (non-GA), 1,769 and 1,710 were up- or down- regulated, respectively in all 6 ARGA tissues ( ≥2.0-fold, p (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE122531 T cell receptor-triggered nuclear actin network formation drives CD4 T cell effector functions
Contributors : Nikolaos Tsopoulidis ; Oliver FacklerSeries Type : Expression profiling by arrayOrganism : Homo sapiensT cell antigen receptor (TCR) signaling triggers selective cytokine expression to drive T cell proliferation and differentiation required for immune defense and surveillance. The nuclear signaling events responsible for specificity in cytokine gene expression upon T cell activation are largely unknown. Here, we uncover formation of a dynamic actin filament network in the nucleus that regulates cytokine expression for effector functions of CD4 T lymphocytes. TCR engagement triggers the rapid and transient fo...
Source: GEO: Gene Expression Omnibus - November 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE122535 Transcriptomic analysis to functionally map the intrinsically disordered domain of EWS/FLI [Experiment 1]
This study reports the first genome-wide transcriptomic description of a partially-functional EWS/FLI mutant . We report new structure-function dependencies across different classes of response element and tie these dependencies to the ability of EWS/FLI to transform cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE122536 Transcriptomic analysis to functionally map the intrinsically disordered domain of EWS/FLI [Experiment 2]
This study reports the first genome-wide transcriptomic description of a partially-functional EWS/FLI mutant . We report new structure-function dependencies across different classes of response element and tie these dependencies to the ability of EWS/FLI to transform cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE122537 Transcriptomic analysis to functionally map the intrinsically disordered domain of EWS/FLI
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 - November 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE122543 Bud13 Promotes a Type I Interferon Response by Countering Intron Retention in Irf7
Contributor : Luke FrankiwSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIntron retention (IR) has emerged as an important mechanism of gene expression control. Despite this, the factors that control IR events remain poorly understood. We observed consistent IR in one intron of the Irf7 gene and identified Bud13 as an RNA-binding protein that acts at this intron to increase the amount of successful splicing. Deficiency in Bud13 led to increased IR, decreased mature Irf7 transcript and protein levels, and consequently to a dampened type I interferon response. This impairment of Irf7 p...
Source: GEO: Gene Expression Omnibus - November 15, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE122453 ChIP-seq and DNase-seq profiling in eWAT, iWAT, and BAT-derived adipocytes
Series Type : 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 - November 13, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE99885 Chromatin opening alters the mutational context and promotes tumour progression through selection of genomically-unstable p53-mutant cells [ATAC-seq]
Contributors : Alexandra Avgustinova ; Aikaterini Symeonidi ; Lloren ç Solé ; Mercé Martín ; Andrés Castellanos ; Neus Prats ; Fran Supek ; Ben Lehner ; Salvador B AznarSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusMutations and expression changes of epigenetic modifiers are pervasive in human tumours, making epigenetic factors attractive as antitumour targets. However, the mutational landscape of tumours correlates with the chromatin state of their cell-of-origin, raising the concern that targeting epigenetic factors might alter the ...
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE99930 Chromatin opening alters the mutational context and promotes tumour progression through selection of genomically-unstable p53-mutant cells (bulge cells)
Contributors : Alexandra Avgustinova ; Aikaterini Symeonidi ; Lloren ç Solé ; Mercé Martín ; Andrés Castellanos ; Neus Prats ; Fran Supek ; Ben Lehner ; Salvador Aznar BenitahSeries Type : Expression profiling by arrayOrganism : Mus musculusMutations and expression changes of epigenetic modifiers are pervasive in human tumours, making epigenetic factors attractive as antitumour targets. However, the mutational landscape of tumours correlates with the chromatin state of their cell-of-origin, raising the concern that targeting epigenetic factors might alter the mutational burden and possibl...
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE99931 Chromatin opening alters the mutational context and promotes tumour progression through selection of genomically-unstable p53-mutant cells (interfollicular epidermis cells)
Contributors : Alexandra Avgustinova ; Aikaterini Symeonidi ; Lloren ç Solé ; Mercé Martín ; Andrés Castellanos ; Neus Prats ; Fran Supek ; Ben Lehner ; Salvador Aznar BenitahSeries Type : Expression profiling by arrayOrganism : Mus musculusMutations and expression changes of epigenetic modifiers are pervasive in human tumours, making epigenetic factors attractive as antitumour targets. However, the mutational landscape of tumours correlates with the chromatin state of their cell-of-origin, raising the concern that targeting epigenetic factors might alter the mutational burden and possibl...
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE99932 Chromatin opening alters the mutational context and promotes tumour progression through selection of genomically-unstable p53-mutant cells (induced SCC tumor)
Contributors : Alexandra Avgustinova ; Aikaterini Symeonidi ; Lloren ç Solé ; Mercé Martín ; Andrés Castellanos ; Neus Prats ; Fran Supek ; Ben Lehner ; Salvador Aznar BenitahSeries Type : Expression profiling by arrayOrganism : Mus musculusMutations and expression changes of epigenetic modifiers are pervasive in human tumours, making epigenetic factors attractive as antitumour targets. However, the mutational landscape of tumours correlates with the chromatin state of their cell-of-origin, raising the concern that targeting epigenetic factors might alter the mutational burden and possibl...
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE99934 Chromatin opening alters the mutational context and promotes tumour progression through selection of genomically-unstable p53-mutant cells (homeostatic skin)
Contributors : Alexandra Avgustinova ; Aikaterini Symeonidi ; Lloren ç Solé ; Mercé Martín ; Andrés Castellanos ; Neus Prats ; Fran Supek ; Ben Lehner ; Salvador Aznar BenitahSeries Type : Expression profiling by arrayOrganism : Mus musculusMutations and expression changes of epigenetic modifiers are pervasive in human tumours, making epigenetic factors attractive as antitumour targets. However, the mutational landscape of tumours correlates with the chromatin state of their cell-of-origin, raising the concern that targeting epigenetic factors might alter the mutational burden and possibl...
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE99945 Chromatin opening alters the mutational context and promotes tumour progression through selection of genomically-unstable p53-mutant cells [Exome-seq]
Contributors : Alexandra Avgustinova ; Aikaterini Symeonidi ; Lloren ç Solé ; Mercé Martín ; Andrés Castellanos ; Neus Prats ; Fran Supek ; Ben Lehner ; Salvador Aznar BenitahSeries Type : OtherOrganism : Mus musculusMutations and expression changes of epigenetic modifiers are pervasive in human tumours, making epigenetic factors attractive as antitumour targets. However, the mutational landscape of tumours correlates with the chromatin state of their cell-of-origin, raising the concern that targeting epigenetic factors might alter the mutational burden and possibly aggravate disease prog...
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research

GSE99956 Chromatin opening alters the mutational context and promotes tumour progression through selection of genomically-unstable p53-mutant cells
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Other ; Expression profiling by arrayOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Other Expression profiling by array Mus musculus Source Type: research

GSE110079 Comparative analysis of transcriptome profiles between wild-type Arabidopsis and two ABA deficit mutants aba3-1 and aba2-2 in osmotic stress conditions
Contributors : Shunsuke Watanabe ; Mitsunori SeoSeries Type : Expression profiling by arrayOrganism : Arabidopsis thalianaCompared transcriptome profiles between 2-week old seedlings of wild-type Col-0, aba3-1 and aba2-2 after two differential osmoic stress (acute and prolonged stress) (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Arabidopsis thaliana Source Type: research

GSE111389 Gene expression profiles of PD1-high, PD1-intermediate, and PD1-negative tumor-infiltrating CD8 T cells in hepatocellular carcinoma
We report the gene expression profiles of FACS-sorted PD1-high, PD1-intermediate, and PD1-negative tumor-infiltrating CD8 T cells in hepatocellular carcinoma. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE112374 miRNA expression profiling of gamma-irradiated A549 cells at 4 h after irradiation
Contributors : Celeste Piotto ; Alberto Biscontin ; Caterina Millino ; Maddalena MognatoSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensWe analyzed the combination of ionizing radiation (IR, 2.0 Gy) along with microRNA-mediated targeting of genes involved in DSB repair to sensitize human non-small cell lung cancer (NSCLC) cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE112375 miRNA expression profiling of gamma-irradiated A549 cells at 24 h after irradiation.
Contributors : Celeste Piotto ; Alberto Biscontin ; Caterina Millino ; Maddalena MognatoSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensWe analyzed the combination of ionizing radiation (IR, 2.0 Gy) along with microRNA-mediated targeting of genes involved in DSB repair to sensitize human non-small cell lung cancer (NSCLC) cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE112376 Functional validation of microRNAs targeting genes of DNA double-strand break repair to radiosensitize non-small lung cancer cells
In this study, we analyzed the combination of ionizing radiation (IR) along with microRNA-mediated targeting of genes involved in DSB repair to sensitize human non-small cell lung cancer (NSCLC) cells. MicroRNAs are natural occurring modulators of gene expression and therefore represent an attractive strategy to affect the expression of DSB repair genes. As possible IR-sensitizing targets genes we selected genes of homologous recombination (HR) and non-homologous end joining (NHEJ) pathway (i.e. RAD51, BRCA2, PRKDC, XRCC5, LIG1). We examined these genes to determine whether they may be real targets of selected miRNAs by fu...
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE114130 Transcriptional response of Acinetobacter baumannii to hydrogen peroxide and role of mumR and oxyR in regulating this response
In this study, we determined the transcriptional response of A. baumannii to hydrogen peroxide stress using RNASequencing. Upon exposure to hydrogen peroxide, A. baumannii differentially transcribes several hundred genes. In this study, we also determined the transcriptional profile of A. baumannii strains with the transcriptional regulators mumR or oxyR genetically inactivated and identified transcriptional differences between these strains and wild-type A. baumannii in response to hydrogen peroxide stress. In doing this, the function of A. baumannii OxyR in hydrogen peroxide stress resistance and regulation of genes requ...
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Acinetobacter baumannii Source Type: research

GSE114980 Genome-wide maps of ParBVc1 binding on V .cholerae genome
We report the genome-wide analysis from chromatin immunoprecipitated DNA (ChIP-sequencing) at very high resolution of the DNA binding pattern of ParBVc1 on the chromosome of Vibrio cholerae. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Vibrio cholerae Source Type: research

GSE115440 Maresin 1 attenuates neuroinflammation in a mouse model of perioperative neurocognitive disorders
Contributors : Souren Mkrtchian ; Niccolo TerrandoSeries Type : Expression profiling by arrayOrganism : Mus musculusMaresin 1 administered to mice prior to orthopedic surgery exerts distinct anti-inflammatory and pro-resolving effects through regulation of M Φ infiltration, NF-κB signaling, and cytokine release.We used microarrays to detail the global programme of gene expression underlying Maresin 1 effect on mouse hippocampus and identified distinct classes of dysregulated genes during this process. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE115461 TP63-mediated enhancer reprogramming drives the squamous subtype of pancreatic ductal adenocarcinoma (ChIP-seq)
Contributors : Tim D Somerville ; Christopher R VakocSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThe aberrant expression of squamous lineage markers in pancreatic ductal adenocarcinoma (PDA) has been correlated with poor clinical outcomes. However, the functional role of this putative trans-differentiation event in PDA pathogenesis remains unclear. Here, we show that expression of the transcription factor TP63 ( ΔN isoform) is sufficient to install and sustain the enhancer landscape and transcriptional signature of the squamous lineage in human PDA cells. In ad...
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE115462 TP63-mediated enhancer reprogramming drives the squamous subtype of pancreatic ductal adenocarcinoma (RNA-seq)
Contributors : Tim D Somerville ; Christopher R VakocSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusThe aberrant expression of squamous lineage markers in pancreatic ductal adenocarcinoma (PDA) has been correlated with poor clinical outcomes. However, the functional role of this putative trans-differentiation event in PDA pathogenesis remains unclear. Here, we show that expression of the transcription factor TP63 ( ΔN isoform) is sufficient to install and sustain the enhancer landscape and transcriptional signature of the squamous lineage in human PDA cells. In a...
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE115463 TP63-mediated enhancer reprogramming drives the squamous subtype of pancreatic ductal adenocarcinoma
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusThe aberrant expression of squamous lineage markers in pancreatic ductal adenocarcinoma (PDA) has been correlated with poor clinical outcomes. However, the functional role of this putative trans-differentiation event in PDA pathogenesis remains unclear. Here, we show that expression of the transcription factor TP63 ( ΔN isoform) is sufficient to install and sustain the enhancer landscape and transcriptional signature of the squamous lineage in human P...
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE118587 Expression data for participants in iWITH study at screening visit
Contributors : Alberto Sanchez-Fueyo ; Sandy FengSeries Type : Expression profiling by arrayOrganism : Homo sapiensA cross sectional study using data collected at the time of liver biopsy, the final eligibility assessment for participation in iWITH (NCT01638559), an immunosuppression withdrawal trial.Microarrays were used to understand the gene expression profile differences among the three histological clusters (Cluster 1, Cluster 2 and Cluster 3) (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE119267 MicroRNA and mRNA regulatory network in EGFR-mutated lung adenocarcinoma [mRNA]
Contributors : Sophia Subat ; Kentato Inamura ; Hiroko Nagano ; Yuichi IshikawaSeries Type : Expression profiling by arrayOrganism : Homo sapiensWe have examined the both miRNA and mRNA expression profiles in 155 lung adenocarcinoma samples with known EGFR mutation status (52 mutated and 103 wild-type cases).An integrative analysis was performed to identify the unique miRNA-mRNA regulatory network in EGFR-mutated lung adenocarcinoma. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE119268 MicroRNA and mRNA regulatory network in EGFR-mutated lung adenocarcinoma [miRNA]
Contributors : Sophia Subat ; Kentato Inamura ; Hiroko Nagano ; Yuichi IshikawaSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensWe have examined the both miRNA and mRNA expression profiles in 155 lung adenocarcinoma samples with known EGFR mutation status (52 mutated and 103 wild-type cases).An integrative analysis was performed to identify the unique miRNA-mRNA regulatory network in EGFR-mutated lung adenocarcinoma. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE119269 MicroRNA and mRNA regulatory network in EGFR-mutated lung adenocarcinoma
Series Type : Expression profiling by array ; Non-coding RNA profiling by arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE119461 Gut Adaptation of Ahr Expression Cell-intrinsically Restricts Group 2 Innate Lymphoid Cell Function
Contributors : Liang Zhou ; Shiyang Li ; John W Bostick ; Jian Ye ; Ju Qiu ; Bin Zhang ; Joseph F Urban ; Dorina AvramSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusInnate lymphoid cells (ILCs) are important for mucosal immunity. The intestine harbors all ILC subsets; however, how these cells orchestrate each other to achieve immune homeostasis and mount appropriate immunity during infection remains elusive. Here, we show that the adaptation of the aryl hydrocarbon receptor (Ahr) expression in the gut is a key regulat...
Source: GEO: Gene Expression Omnibus - November 13, 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

GSE120332 PPARg-K107 SUMOylation regulates insulin sensitivity but not adiposity in mice
Contributors : Takeshi Katafuchi ; Rahul K Kollipara ; Ralf Kittler ; David Mangelsdorf ; Steven KliewerSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHomozygous K107R mutation of PPARg in mice alters the expression of its downstream target genes and increases insulin sensitivity but not adiposity. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE121062 Trisomy of a ‘Down syndrome critical region’ globally amplifies transcription via HMGN1 overexpression [ChIP-Seq]
Contributors : Cody T Mowery ; Andrew A LaneSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensDown syndrome (DS, trisomy 21) is associated with developmental abnormalities and increased leukemia risk. To reconcile chromatin alterations with transcriptome changes in cells with trisomy 21, we performed paired exogenous spike-in normalized RNA and chromatin immunoprecipitation sequencing in DS models. Absolute per cell normalization unmasked global amplification of gene expression associated with trisomy 21. Overexpression of the nucleosome binding protein HMGN1 (encoded on c...
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE121065 Trisomy of a ‘Down syndrome critical region’ globally amplifies transcription via HMGN1 overexpression [NALM6 RNA-Seq]
Contributors : Cody T Mowery ; Andrew A LaneSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDown syndrome (DS, trisomy 21) is associated with developmental abnormalities and increased leukemia risk. To reconcile chromatin alterations with transcriptome changes in cells with trisomy 21, we performed paired exogenous spike-in normalized RNA and chromatin immunoprecipitation sequencing in DS models. Absolute per cell normalization unmasked global amplification of gene expression associated with trisomy 21. Overexpression of the nucleosome binding protein HMGN1 (encoded on chr21q22) recap...
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE121066 Trisomy of a ‘Down syndrome critical region’ globally amplifies transcription via HMGN1 overexpression [proB RNA-Seq]
Contributors : Cody T Mowery ; Andrew A LaneSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDown syndrome (DS, trisomy 21) is associated with developmental abnormalities and increased leukemia risk. To reconcile chromatin alterations with transcriptome changes in cells with trisomy 21, we performed paired exogenous spike-in normalized RNA and chromatin immunoprecipitation sequencing in DS models. Absolute per cell normalization unmasked global amplification of gene expression associated with trisomy 21. Overexpression of the nucleosome binding protein HMGN1 (encoded on chr21q22) recap...
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE121070 Trisomy of a ‘Down syndrome critical region’ globally amplifies transcription via HMGN1 overexpression [SLAM-Seq]
Contributors : Andrew A Lane ; Charles Y Lin ; Jarey H Wang ; Kristen L Karlin ; Thomas F WestbrookSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDown syndrome (DS, trisomy 21) is associated with developmental abnormalities and increased leukemia risk. To reconcile chromatin alterations with transcriptome changes in cells with trisomy 21, we performed paired exogenous spike-in normalized RNA and chromatin immunoprecipitation sequencing in DS models. Absolute per cell normalization unmasked global amplification of gene expression associated with trisomy 21. Overexpression of the nucle...
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE121071 Trisomy of a ‘Down syndrome critical region’ globally amplifies transcription via HMGN1 overexpression
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy 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 - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE122417 DNase-seq profiling in eWAT, iWAT, and BAT-derived adipocytes.
Contributors : Anne Loft ; Majken Siersb æk ; Ronni Nielsen ; Susanne MandrupSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusHere we have employed DNase-seq combined with deep sequencing to map and compare DNase hypersensitive sites in in vitro differentiated primary mouse adipocytes isolated from epididymal and inguinal white adipose tissus as well as brown adipose tissue. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE122418 Transcriptome of undifferentiated bovine trophoblast cells
Contributors : Viju V Pillai ; Vimal SelvarajSeries Type : Expression profiling by high throughput sequencingOrganism : Bos taurusQuantitative examination of transcripts expressed in bovine blastocyst derived trophoblasts. These data showcase the fundamental physiology of bovine trophectoderm and indicate hallmarks of the self-renewing undifferentiated state akin to trophoblast stem cells described in other species. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 13, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Bos taurus Source Type: research

GSE122349 Identification of genes related with carcass fatness in pigs based on RNA-seq results
Conclusions: The presented results allowed to pinpointed the interesting, candidate genes related with fat content in carcasses in pigs, which can be analyzed in future in the term of using in breeding practice as genetic markers. The study was financed from funds of the project -BIOSTRATEG, the decision number BIOSTRATEG2/297267/14/NCBR/2016. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 12, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Sus scrofa Source Type: research

GSE107224 The splicing factor SRSF1 regulates the radio-resistance of cancer cells through modulating the alternative splicing of PTPMT1
Contributors : Wang Yang ; Sun BingSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA-seq was performed on H1299 cells that stably knocking down SRSF1 or control, as well as these cells that were treated with ionizing radiation, in order to profile the alternative splicing events that were regulated by SRSF1 upon ionizing radiation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - November 12, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research