GSE173885 Transcriptome of the audiogenic rat strain and identification of possible audiogenic epilepsy-associated genes
Contributor : Sergei FunikovSeries Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusAudiogenic epilepsy (AE), developing in rodent strains in response to loud sound, is widely used as the model of generalized convulsive epilepsy. The molecular and genetic mechanisms that determine the expression of AE are currently non well understood. In the present work we compared transcriptomes from the inferior and superior colliculi (corpora quadrigemina), the crucial epileptogenic midbrain zone for AE in order to identify genes associated to the AE phenotype. Transcriptomes of rats from three stra...
Source: GEO: Gene Expression Omnibus - May 6, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Rattus norvegicus Source Type: research

Cortical responsive neurostimulation in a baboon with genetic generalized epilepsy
Publication date: July 2021Source: Epilepsy & Behavior, Volume 120Author(s): C. Ákos Szabó, Melissa De La Garza, Robert Shade, Alexander M. Papanastassiou, Peter Nathanielsz (Source: Epilepsy and Behavior)
Source: Epilepsy and Behavior - May 5, 2021 Category: Neurology Source Type: research

Analysis of overlapping genetic association in type 1 and type 2 diabetes
AbstractAims/hypothesisGiven the potential shared aetiology between type 1 and type 2 diabetes, we aimed to identify any genetic regions associated with both diseases. For associations where there is a shared signal and the allele that increases risk to one disease also increases risk to the other, inference about shared aetiology could be made, with the potential to develop therapeutic strategies to treat or prevent both diseases simultaneously. Alternatively, if a genetic signal co-localises with divergent effect directions, it could provide valuable biological insight into how the association affects the two diseases di...
Source: Diabetologia - May 5, 2021 Category: Endocrinology Source Type: research

Multi-omic analysis elucidates the genetic basis of hydrocephalus
Publication date: 4 May 2021Source: Cell Reports, Volume 35, Issue 5Author(s): Andrew T. Hale, Lisa Bastarache, Diego M. Morales, John C. Wellons, David D. Limbrick, Eric R. Gamazon (Source: Cell Reports)
Source: Cell Reports - May 5, 2021 Category: Cytology Source Type: research

Genetics, odor perception and food liking: the intriguing role of cinnamon
Publication date: Available online 5 May 2021Source: Food Quality and PreferenceAuthor(s): Maria Pina Concas, Anna Morgan, Giulia Pelliccione, Paolo Gasparini, Giorgia Girotto (Source: Food Quality and Preference)
Source: Food Quality and Preference - May 5, 2021 Category: Food Science Source Type: research

Modification of COL1A1 in autologous adipose tissue ‐derived progenitor cells rescues the bone phenotype in a mouse model of osteogenesis imperfecta
AbstractOsteogenesis imperfecta (OI) is a congenital genetic disorder mainly manifested as bone fragility and recurrent fracture. Mutation ofCOL1A1/COL1A2 genes encoding the type I collagen are most responsible for the clinical patients. Allogenic mesenchymal stem cells (MSCs) provide the potential to treat OI through differentiation into osteoblasts. Autologous defective MSCs have not been utilized in OI treatment mainly because of their impaired osteogenesis, but the latent mechanism has not been well understood. Here, the relative signaling abnormality of adipose ‐derived mesenchymal stem cells (ADSCs) isolated from O...
Source: Journal of Bone and Mineral Research - May 5, 2021 Category: Orthopaedics Authors: Yi Liu, Zihan Wang, Mingyan Ju, Yuxia Zhao, Yaqing Jing, Jiaci Li, Chenyi Shao, Ting Fu, Zhe Lv, Guang Li Tags: Original Article Source Type: research

Leu72Met polymorphism of GHRL gene increase the risk factor of obesity in a Javanese ethnic group from Indonesia
Publication date: Available online 5 May 2021Source: Meta GeneAuthor(s): Demes Chornelia Martantiningtyas, Pramudji Hastuti, Ahmad Hamim Sadewa (Source: Meta Gene)
Source: Meta Gene - May 5, 2021 Category: Genetics & Stem Cells Source Type: research

Severe clinical outcomes of infection with babA2-positive Helicobacter pylori strains in the Iranian population: A systematic review and meta-analysis
Publication date: Available online 5 May 2021Source: Meta GeneAuthor(s): Parvin Askari, Mohsen Karbalaei, Kiarash Ghazvini, Masoud Keikha (Source: Meta Gene)
Source: Meta Gene - May 5, 2021 Category: Genetics & Stem Cells Source Type: research

< b > < i > Mus musculus < /i > < /b > Barrier-To-Autointegration Factor 2 ( < b > < i > Banf2 < /i > < /b > ) is Not Essential for Spermatogenesis or Fertility
The barrier-to-autointegration factor (BAF) is widely expressed in most human tissues and plays a critical role in chromatin organization, nuclear envelope assembly, gonadal development, and embryonic stem cell self-renewal. Complete loss ofBAF has been shown to lead to embryonic lethality and gonadal defects. TheBAF paralog, namely, barrier-to-autointegration factor 2 (BANF2), exhibits a testis-predominant expression pattern in both humans and mice. UnlikeBAF, it may cause isolated male infertility. Therefore, we used the CRISPR/Cas9 system to generateBanf2-knockout mice to further study its function in spermatogenesis. U...
Source: Cytogenetic and Genome Research - May 5, 2021 Category: Genetics & Stem Cells Source Type: research

Longitudinal phenotypic study of late-onset retinal degeneration due to a founder variant c.562C & gt;A p.(Pro188Thr) in the < em > C1QTNF5 < /em > gene
Conclusions: Phenotypic analysis showed three distinct presenting phenotypes with a considerable intrafamilial variability both in age of onset of clinical signs and in disease progression, with a fair visual potential (>20/40) until the seventh decade.Abbreviations: L-ORD: Late-onset retinal degeneration; C1QTNF5: complement 1Q tumor necrosis factor 5; OCT: Ocular coherence tomography; BCVA: Best-corrected visual acuity; RPE: Retinal pigment epithelium; ffERG: Full-field electroretinography; IRD: Inherited retinal dystrophy; CNV: Choroidal neovascularization; LAZ: Long anteriorly inserted zonules; AMPK: AMP-activated p...
Source: Ophthalmic Genetics - May 5, 2021 Category: Opthalmology Authors: Julie De Zaeytijd Frauke Coppieters Marieke De Bruyne Jasper Van Royen Dimitri Roels Rani Six Caroline Van Cauwenbergh Elfride De Baere Bart P Leroy Source Type: research

A 7-year old female with arthrogryposis multiplex congenita, Duane retraction syndrome, and Marcus Gunn phenomenon due to a ZC4H2 gene mutation: a clinical presentation of the Wieacker-Wolff syndrome
Conclusion: This case confirms ZC4H2 as a cause of syndromic DRS and extends the ZC4H2 phenotype to include Marcus Gunn jaw winking.PMID:33949289 | DOI:10.1080/13816810.2021.1923040 (Source: Ophthalmic Genetics)
Source: Ophthalmic Genetics - May 5, 2021 Category: Opthalmology Authors: Deena Godfrey Alcy Torres Gena Heidary Hovra Zahoor Arthur Lee Gerard Berry Elizabeth Engle Source Type: research

Characterization of effects of genetic variants via genome-scale metabolic modelling
Cell Mol Life Sci. 2021 May 5. doi: 10.1007/s00018-021-03844-4. Online ahead of print.ABSTRACTGenome-scale metabolic networks for model plants and crops in combination with approaches from the constraint-based modelling framework have been used to predict metabolic traits and design metabolic engineering strategies for their manipulation. With the advances in technologies to generate large-scale genotyping data from natural diversity panels and other populations, genome-wide association and genomic selection have emerged as statistical approaches to determine genetic variants associated with and predictive of traits. Here,...
Source: Cellular and Molecular Life Sciences : CMLS - May 5, 2021 Category: Cytology Authors: Hao Tong Anika K üken Zahra Razaghi-Moghadam Zoran Nikoloski Source Type: research

Patient personalized translational tools in Cystic fibrosis to transform data from bench to bed-side and back
Am J Physiol Gastrointest Liver Physiol. 2021 May 5. doi: 10.1152/ajpgi.00095.2021. Online ahead of print.ABSTRACTCystic fibrosis is a deadly multi-organ disorder caused by loss of function mutations in the gene that encodes for the cystic fibrosis transmembrane conductance regulator (CFTR) chloride/bicarbonate ion channel. More than 1700 CFTR genetic variants exist that can cause CF, and, majority of these are extremely rare. Due to genetic and environmental influences, CF patients exhibit large phenotypic variation. These factors make clinical trials difficult and largely impractical due to limited and heterogenous patie...
Source: American Journal of Physiology. Gastrointestinal and Liver Physiology - May 5, 2021 Category: Physiology Authors: Kavisha Arora Fanmuyi Yang John J Brewington Gary McPhail Alexander R Cortez Nambirajan Sundaram Yashaswini Ramananda Herbert Ogden Michael Anthony Helmrath John Paul Clancy Anjaparavanda P Naren Source Type: research

Obesity Cardiomyopathy: Evidence, Mechanisms and Therapeutic Implications
Physiol Rev. 2021 May 5. doi: 10.1152/physrev.00030.2020. Online ahead of print.ABSTRACTThe prevalence of heart failure is on the rise and imposes a major health threat, in part, due to the rapidly increased prevalence of overweight and obesity. To this point, epidemiological, clinical and experimental evidence supports the existence of a unique disease entity termed "obesity cardiomyopathy", which develops independent of hypertension, coronary heart disease and other heart diseases. Our contemporary review evaluates the evidence for this pathological condition, examines putative responsible mechanisms, and discu...
Source: Physiological Reviews - May 5, 2021 Category: Physiology Authors: Jun Ren Ne N Wu Shuyi Wang James R Sowers Yingmei Zhang Source Type: research

Genetic Differentiation in Anthocyanin Content among Berry Fruits
Curr Issues Mol Biol. 2021 Apr 29;43(1):36-51. doi: 10.3390/cimb43010004.ABSTRACTAnthocyanins are widely distributed secondary metabolites that play an essential role in skin pigmentation of many plant organs and microorganisms. Anthocyanins have been associated with a wide range of biological and pharmacological properties. They are also effective agents in the prevention and treatment of many chronic diseases. Berries are particularly abundant in these compounds; therefore, their dietary intake has health-promoting effects. The aim of this study was to identify and determine the anthocyanin content in selected species an...
Source: Current Issues in Molecular Biology - May 5, 2021 Category: Molecular Biology Authors: Alicja Ponder Ewelina Hallmann Martyna Kwolek Dominika Średnicka-Tober Renata Kazimierczak Source Type: research

Wal Mutant Mice Have a Mutation Associated with Autism Spectrum Disorders
We examined the wal locus by sequencing the exons of candidate genes in which the mutation was expected, and performed genome-wide sequencing to identify the cause of the wal mutation. The sequences of exons of candidate genes located in this region did not carry changes that could lead to a change in the structure of the protein. However, outside the wal zone, a mutation in the Slc9a9 gene was found that is probably not associated with the wal phenotype. According to the literature, a mutation in the Slc9a9 gene leads to autism spectrum disorders. This is the first discovered spontaneous mutation in the Slc9a9 gene in mic...
Source: Doklady Biological Sciences - May 5, 2021 Category: Biology Authors: E S Chermnykh D M Schepetov E A Vorotelyak Source Type: research

Variability in porcine microRNA genes and its association with mRNA expression and lipid phenotypes
CONCLUSIONS: Our findings show a reduced variability of porcine miRNA genes, which is consistent with strong purifying selection, particularly in the seed region that plays a critical role in miRNA binding. Although it is generally assumed that SNPs mapping to the seed region are those with the most pronounced consequences on mRNA expression, we show that a SNP mapping to the apical region of ssc-miR-326 is significantly associated with hepatic mRNA levels of the PPP1CC gene, one of its predicted targets. Although experimental confirmation of such an interaction is reported in humans but not in pigs, this result highlights...
Source: Genet Sel Evol - May 5, 2021 Category: Genetics & Stem Cells Authors: Emilio M ármol-Sánchez Mar ía Gracia Luigi-Sierra Anna Castell ó Dailu Guan Raquel Quintanilla Raul Tonda Marcel Amills Source Type: research

Current clinical and research fluid biomarkers to aid risk stratification of pancreatic cystic lesions
Rev Esp Enferm Dig. 2021 May 5. doi: 10.17235/reed.2021.7948/2021. Online ahead of print.ABSTRACTPancreatic cystic lesions (PCL) are composed of a heterogeneous group of entities that are increasingly diagnosed, generally as incidental findings in asymptomatic patients. In conjunction with this growing incidence, the potential for malignant transformation of mucin-producing cysts makes PCL a challenging clinical conundrum for the clinician, patient, and healthcare system. Cyst characterization based on morphology is often difficult and inaccurate, therefore several intracystic fluid biomarkers have been evaluated as ancill...
Source: Revista Espanola de Enfermedades Digestivas - May 5, 2021 Category: Gastroenterology Authors: Ana Garcia Garcia de Paredes Ferga Claudine Gleeson Elizabeth Rajan Enrique Vazquez-Sequeiros Source Type: research

Where the Ends Meet: An Overview of Sex Determination in Atheriniform Fishes
Atheriniform fishes have recently emerged as attractive models for evolutionary, ecological, and molecular/physiological studies on sex determination. Many species in this group have marked temperature-dependent sex determination (TSD) and yet many species also have a sex determinant gene that provides a strong drive for male differentiation. Thus, in these species the 2 forms of sex determination that were once considered to be mutually exclusive, environmental (ESD) and genotypic (GSD) sex determination, can coexist at environmentally relevant conditions. Here, we review the current knowledge on sex determination in athe...
Source: Sexual Development - May 5, 2021 Category: Biology Source Type: research

The Belgian DNA Debate: An Online Deliberative Platform on the Ethical, Legal, and Social Issues of Genomics
Conclusion: The attitude of contributors towards the societal use of genomic information and its ELSI aligns with a soft precautionary approach, in which prudence and the weighing of different values should result in protective measures against potential risks and harms. Further societal implementation of genomics should include these values and concerns.Public Health Genomics (Source: Public Health Genomics)
Source: Public Health Genomics - May 5, 2021 Category: Genetics & Stem Cells Source Type: research

[ASAP] Biochemical Activity Architectures Visualized –Using Genetically Encoded Fluorescent Biosensors to Map the Spatial Boundaries of Signaling Compartments
Accounts of Chemical ResearchDOI: 10.1021/acs.accounts.1c00056 (Source: Accounts of Chemical Research)
Source: Accounts of Chemical Research - May 5, 2021 Category: Chemistry Authors: Sohum Mehta and Jin Zhang Source Type: research

[ASAP] Sequence-Engineering Polyethylene –Polypropylene Copolymers with High Thermal Conductivity Using a Molecular-Dynamics-Based Genetic Algorithm
Journal of Chemical Theory and ComputationDOI: 10.1021/acs.jctc.1c00134 (Source: Journal of Chemical Theory and Computation)
Source: Journal of Chemical Theory and Computation - May 5, 2021 Category: Chemistry Authors: Tianhang Zhou, Zhenghao Wu, Hari Krishna Chilukoti, and Florian Mu ̈ller-Plathe Source Type: research

GSE173840 TP53-mediated therapy-related clonal hematopoiesis contributes to doxorubicin-induced cardiomyopathy by augmenting a neutrophil-mediated cytotoxic response in a murine model
Contributors : Soichi Sano ; Ying Wang ; Hayato Ogawa ; Keita Horitani ; Miho Sano ; Ariel H Polizio ; Anupreet Kour ; Yoshimitsu Yura ; Heather Doviak ; Kenneth WalshSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTherapy-related clonal hematopoiesis (t-CH) is often observed in cancer survivors. This form of clonal hematopoiesis typically involves somatic mutations in driver genes that encode components of the DNA damage response (DDR) and confer hematopoietic stem and progenitor cells (HSPC) with resistance to the genotoxic stress of the cancer therapy. A model of TP53-mediated t-CH...
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE173838 DDX17 is involved in DNA damage repair and modifies FUS toxicity in an RGG-domain dependent manner
Contributors : Tyler R Fortuna ; Udai B Pandey ; Dhivyaa RajasundaramSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterMutations in the RNA binding protein, Fused in Sarcoma (FUS), lead to amyotrophic lateral sclerosis (ALS), the most frequent form of motor neuron disease. Cytoplasmic aggregation and defective DNA repair machinery are etiologically linked to mutant FUS-associated ALS. Although FUS is involved in numerous aspects of RNA processing, little is understood about the pathophysiological mechanisms of mutant FUS. Here, we employed RNA-sequencing technology in Drosoph...
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Drosophila melanogaster Source Type: research

GSE173829 Oncogene-induced maladaptive activation of Trained Immunity in the pathogenesis of human inflammatory myeloid neoplasm [BRAF]
Contributors : Giulio Cavalli ; Ivan MerelliSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTrained immunity (TI) is a pro-inflammatory program induced in monocyte/macrophages upon sensing of specific pathogens and characterized by immunometabolic and epigenetic changes enhancing cytokine production. Maladaptive activation of TI (i.e., in the absence of infection) might result in detrimental inflammation and disease development; however, the exact role and extent of inappropriate activation of TI in the pathogenesis of human diseases is undetermined. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE173830 Oncogene-induced maladaptive activation of Trained Immunity in the pathogenesis of human inflammatory myeloid neoplasm
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 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE173832 Transcriptional organization and regulation of the Pseudomonas putida flagellar system
Contributors : Fernando Govantes ; Marta Pulido-S ánchez ; Aroa López-SánchezSeries Type : Expression profiling by high throughput sequencingOrganism : Pseudomonas putida KT2440The entire set of flagellar structural components and flagellar-specific transcriptional regulators, as well as much of the core chemotaxis machinery, is encoded into a>70 kbp cluster in Pseudomonas putida KT2440 genome. We have performed RNA-seq of the wild-type strain in order to identify operon boundaries and promoters location in this cluster. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Pseudomonas putida KT2440 Source Type: research

GSE173834 The regulatory landscape of Arabidopsis thaliana roots at single-cell resolution
Contributors : M W Dorrity ; C Queitsch ; J CuperusSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Arabidopsis thalianaRoot cells from Arabidopsis seedlings profiled with single-cell ATAC-seq. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE173826 A novel vitronectin peptide facilitates differentiation of oligodendrocytes from human embryonic stem cells (Synthetic ECM for oligodendrocyte differentiation)
Contributors : Won Park ; Gyu-Bum Yeon ; Dae-Sung KimSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensDifferentiation of oligodendrocytes (ODs) presents a challenge in regenerative medicine due to their role in various neurological diseases associated with dysmyelination and demyelination. Here, we designed a peptide derived from vitronectin (VN) using in silico docking simulation and examined its use as a synthetic substrate to support the differentiation of ODs derived from human embryonic stem cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE173828 Oncogene-induced maladaptive activation of Trained Immunity in the pathogenesis of human inflammatory myeloid neoplasm [ECD]
Contributors : Giulio Cavalli ; Ivan MerelliSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTrained immunity (TI) is a pro-inflammatory program induced in monocyte/macrophages upon sensing of specific pathogens and characterized by immunometabolic and epigenetic changes enhancing cytokine production. Maladaptive activation of TI (i.e., in the absence of infection) might result in detrimental inflammation and disease development; however, the exact role and extent of inappropriate activation of TI in the pathogenesis of human diseases is undetermined. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE173816 MicroRNA-200c/141 confines ER α  activity and expression pattern by targeting Ccnd1 [single-cell RNA-seq]
Contributor : Ting WuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusER α is one of the most important transcription factors and therapeutic targets in breast cancer. The patterns of ERα expression in normal breast tissue and cancerous lesions are strikingly different. What drives the change of ERα pattern during lesions formation remains unclear. Here, we describe a novel regulatory mechanism through which miR-200c/141 regulates the level as well as the distribution of ERα in the mammary gland. miR-200c/141 is specifically expressed in luminal cells....
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE173817 MicroRNA-200c/141 confines ER α  activity and expression pattern by targeting Ccnd1
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE173813 c-Myc targeted genes validated by PCR array in STEAP1-silenced HepG2 cells.
Contributor : Hajime NakamuraSeries Type : Expression profiling by RT-PCROrganism : Homo sapiensTo confirm the relationship between STEAP1 and c-Myc in liver cancer, we analyzed components of c-Myc-related genes after STEAP1 knockdown in HepG2 cells by PCR array. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by RT-PCR Homo sapiens Source Type: research

GSE173807 Transcriptome sequencing of human neutrophil
Contributors : Qian Ou ; Jia-qi Fang ; Jian-ping PanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTcpC is a multifunctional virulence factor of uropathogenic E. coli (UPEC). Neutrophil extracellular trap formation (NETosis) is a crucial anti-infection mechanism of neutrophils. Here we show the influence of TcpC on NETosis and related mechanisms. In situ NETosis of kidneys from pyelonephritis mouse model induced by TcpC-secreting wild-type CFT073 (CFT073wt) and LPS-induced in vitro NETosis in CFT073wt- or recombinant TcpC (rTcpC)-treated neutrophils are inhibited. rTcpC enters neutro...
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE173808 The transcriptome of paired major and minor salivary gland tissue in patients with primary Sj ögren's syndrome
Contributors : Gwenny M Verstappen ; Lu Gao ; Sarah Pringle ; Erlin A Haacke ; Bert van der Vegt ; Silvia C Liefers ; Vishal Patel ; Yanhua Hu ; Sumanta Mukherjee ; Julie Carman ; Laurence Menard ; Frederik K Spijkervet ; Arjan Vissink ; Hendrika Bootsma ; Frans G KroeseSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWhile all salivary glands (SGs) can be involved in primary Sj ögren’s syndrome (pSS), their respective role in pathogenesis remains unclear. To assess immunopathway activation in paired parotid and labial gland tissue from biopsy-positive and biopsy-negative pS...
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE173799 High throughput RNA sequencing to identify genes up regulated by the transcription factor ATF-4
We report RNA sequencing (RNA-seq) data WT, atf-4 loss-of-function mutants, and ATF-4 OE worms under non-stressed conditions. Three independent biological replicates were prepared for each sample, and worms were harvested at L4 stage. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Caenorhabditis elegans Source Type: research

GSE173778 Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE173776 Multi-resolution deconvolution of spatial transcriptomics data reveals continuous patterns of inflammation (Spatial scRNA-Seq)
Contributors : Romain Lopez ; Hadas Keren-Shaul ; Baoguo Li ; Pierre Boyeau ; Michael I Jordan ; Merav Kedmi ; David Pilzer ; Allon Wagner ; Yoseph Addad ; Nir Yosef ; Ido AmitSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe function of mammalian cells is largely influenced by their tissue microenvironment and by inter- celllular interactions. Advances in spatial transcriptomics open the way for studying these important determinants of cellular function, by enabling a transcriptome wide evaluation of gene expression in-situ. A critical limitation of the current technologies, howeve...
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE173849 LCDR maintains the integrity of lysosomal membrane by hnRNP K-stabilized LAPTM5 transcript and promotes cell survival
Contributors : Shan Gao ; Xiwang Yang ; Ya Wen ; Shaomin Liu ; Liqiang Duan ; Tongfeng Liu ; Zhuo Wang ; Yinmin Gu ; Yibo Xi ; Xiaodong Wang ; Dingshan Luo ; Ruobing Zhang ; Yajuan Liu ; Yang Wang ; Tianyou Cheng ; Siyuan Jiang ; Xiaofeng Zhu ; Xiaohui Yang ; Yongbo Pan ; Shuwen Chen ; Jinfei Chen ; Xiaoding XuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensLysosome plays important roles in cellular homeostasis and its dysregulation is associated with cancer. However, the regulation and underlying mechanism of lysosome in cancer survival remain incompletely understood. Here, we reveal...
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE173853 Characterization of the chromatin accessibility profile of Plagl1+/-pat retina
Contributors : Yacine Touahri ; Yaroslav Ilnytskyy ; Igor Kovalchuk ; Carol SchuurmansSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusRetinal damage triggers reactive gliosis in M üller glia across vertebrate species, but only in regenerative animals, such as teleost fish, do Müller glia initiate repair; proliferating and undergoing neurogenesis to replace lost cells. We found that Plagl1, a maternally imprinted gene, is dynamically regulated in reactive Müller glia post-i nsult, with transcript levels transiently increasing before stably declining. To stu...
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE173854 Levels and Characteristics of mRNAs in Dormant Spores of Firmicute Species
Contributors : Peter Setlow ; Melissa Caimano ; Wendy W MokSeries Type : Expression profiling by high throughput sequencingOrganism : Bacillus atrophaeus ATCC 9372 ; Bacillus megaterium QM B1551 ; Bacillus subtilis ; Bacillus thuringiensis str. Al Hakam ; Clostridioides difficile 630 ; Geobacillus stearothermophilus ATCC 12980Spores of Bacillales and Clostridiales species contain 100s of different mRNAs, and their major function in Bacillus subtilis is to provide ribonucleotides for new RNA synthesis when spores germinate. In new work, RNA was isolated from spores of five Bacillales and one Clostridioides species and relat...
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Bacillus atrophaeus ATCC 9372 Bacillus megaterium QM B1551 Bacillus subtilis Bacillus thuringiensis str. Al Hakam Clostridioides difficile 630 Geobacillus stearothermophilus ATCC 12980 Source Type: research

GSE173858 HP1 γ/CBX3 Promotes Lung Adenocarcinoma by Activating Rho GTPases Signaling Pathway
Contributors : H Yu ; X JinSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe performed CBX3 knockdown in lung adenocarcinoma cells along with RNA sequencing. The expression profiling showed Rho GTPases signaling as a potential CBX3 target and the conclusions were also verified in clinical samples. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE173873 Roles of Stra8 and Tcerg1l in retinoic acid induced spermatogonial differentiation in mouse.
Contributors : Nilam Sinha ; Eoin C Whelan ; John W Tobias ; Mary Avarbock ; Darko Stefanovski ; Ralph L BrinsterSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRetinoic acid (RA) induces spermatogonial differentiation, but the mechanism by which it operates remains largely unknown. We developed a germ cell culture assay system to study genes involved in spermatogonial differentiation triggered by RA. Stimulated by Retinoic Acid 8 (Stra8), an RA-inducible gene, is indispensable for meiosis initiation, and its deletion results in a complete block of spermatogenesis at the pre-leptotene...
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE172476 Epigenetic Plasticity Enables CNS-Trafficking of EBV-infected B Lymphocytes [ATAC-Seq]
Contributors : Paul Lieberman ; Samantha SoldanSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensSubpopulations of B-lymphocytes traffic to different sites and organs to provide diverse and tissue-specific functions. Here, we provide evidence that epigenetic differences confer a neuroinvasive phenotype. An EBV+ B cell lymphoma cell line (M14) with low frequency trafficking to the CNS was neuroadapted to generate a highly neuroinvasive B-cell population (MUN14). MUN14 B cells efficiently infiltrated the CNS within one week and produced neurological pathologies. We compared ...
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE172477 Epigenetic Plasticity Enables CNS-Trafficking of EBV-infected B Lymphocytes
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE172475 Epigenetic Plasticity Enables CNS-Trafficking of EBV-infected B Lymphocytes [RNA-Seq]
Contributors : Paul Lieberman ; Samantha SoldanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensSubpopulations of B-lymphocytes traffic to different sites and organs to provide diverse and tissue-specific functions. Here, we provide evidence that epigenetic differences confer a neuroinvasive phenotype. An EBV+ B cell lymphoma cell line (M14) with low frequency trafficking to the CNS was neuroadapted to generate a highly neuroinvasive B-cell population (MUN14). MUN14 B cells efficiently infiltrated the CNS within one week and produced neurological pathologies. We compared the gene expre...
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE171820 Human blastocyst model by self-organization of na ïve pluripotent stem cells
Contributors : Daniel Spindlow ; Ayaka YanagidaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHuman na ïve pluripotent cells can differentiate to extraembryonic trophoblast and hypoblast cells. Here we report formation of human blastocyst models by self-organization solely of naïve pluripotent stem cells. The embryo models comprise the three founding lineages, epiblast, trophoblast and hypoblast, a rranged to mimic the natural blastocyst. Single-cell RNA sequencing validated the identity of each cell type. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE171836 Expression data from ferulic acid treated C. elegans
Contributors : Hui Li ; Xiaoxuan Yu ; Fanwei Meng ; Liping WangSeries Type : Expression profiling by high throughput sequencingOrganism : Caenorhabditis elegansGene expression in N2 worms treated with 500 μM or 0 μM ferulic acid, at days 5. Effects of ferulic acid in C. elegans gene expression is studied, as our results indicate a lifespan extension effect produced by this molecule. RNA-seq were used to detail the global programme of gene expression underlying the lifespan extension and identifi ed distinct classes of up/down-regulated genes in animals treated with ferulic acid. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Caenorhabditis elegans Source Type: research

GSE171099 Impaired inhibitory GABAergic synaptic transmission and transcription studied in single neurons by Patch-seq in Huntington ’s disease
Contributors : Foteini Paraskevopoulou ; Poorya Parvizi ; G ökçe Senger ; Nurcan Tuncbag ; Christian Rosenmund ; Ferah YildirimSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTranscriptional dysregulation in Huntington ’s disease (HD) causes functional deficits in striatal neurons. Here, we performed Patch-seq in an in vitro HD model to investigate the effects of mutant huntingtin (Htt) on synaptic transmission and gene transcription in single striatal neurons. We found that expression of mutant Htt decreased th e synaptic output of striatal neurons in a cell autonom...
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE169045 iPSC-endothelial cell phenotypic drug screening and in silico analyses identify tyrphostin AG1296 for pulmonary arterial hypertension
Contributors : Mingxia Gu ; Michele Donato ; Minzhe GuoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPulmonary arterial hypertension (PAH) is a progressive disorder leading to occlusive vascular remodeling. Current PAH therapies improve quality of life but do not reverse structural abnormalities in the pulmonary vasculature. Here, we used a high-throughput drug screen combined with in silico analyses of existing transcriptomic datasets to identify a promising lead compound to reverse PAH. Induced pluripotent stem cell-derived endothelial cells (iPSC-EC) generated from six patients w...
Source: GEO: Gene Expression Omnibus - May 5, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research