GSE167575 Single-cell RNAseq (10x Genomics) analysis of mouse splenic CD4+ T cells in WT and ∆Foxp3 mice and in WT/∆Foxp3 bone marrow chimeras
Contributors : David Zemmour ; Louis Charbonnier ; Juliette Leon ; Tala Chatila ; Diane Mathis ; Christophe BenoistSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSingle-cell RNAseq (10x Genomics) analysis of mouse splenic CD4+ T cells in WT and ∆Foxp3 mice and in WT/∆Foxp3 bone marrow chimeras. Mouse CD4+T cells in 21-day-old male WT and ∆Foxp3 mice were isolated from spleen by flow cytometry as DAPI–TCRβ+CD4+ cells for 10x Genomics Single Cell 3′ Reagent Kit (V2 chemistry, one sample per channel). For bone marrow chimera experi ment: 7 week-old CD45.2-recipien...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE97624 YBX2 and cancer testis antigen 45 contribute to stemness, chemoresistance and a high degree of malignancy in human endometrial cancer
Contributors : Izumi Suzuki ; Sachiko Yoshida ; Kouichi Tabu ; Soshi Kusunoki ; Yumiko Matsumura ; Hiroto Izumi ; Kazuo Asanoma ; Hiroshi Yagi ; Ichiro Onoyama ; Kenzo Sonoda ; Kimitoshi Kohno ; Tetsuya Taga ; Atsuo Itakura ; Satoru Takeda ; Kiyoko KatoSeries Type : Expression profiling by arrayOrganism : Homo sapiensWe aimed to clarify the function of YBX2, a germ cell-specific Y-box-binding protein, in endometrial cancer stem cells. Our data demonstrated that expression of YBX2 was essential for a stem cell-like phenotype of endometrial cancer cells. We analyzed enhanced gene expression of IK cells that overexpressed YBX...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE111330 A host-dependent transcriptional response correlates with Dengue virus infection rate in healthy humans.
We report 190 host-related transcripts in DCs that correlate markedly with infection rates that form an ubiquitin-mediated antiviral network. Furthermore, these transcripts are enriched for glycolysis, which we show is critical for the early phases of infection. Among virus induced transcripts (i.e. significant correlation only after DENV), we identify DUSP10 as the best indicator of the severity of infection. These results indicate the importance of host genetics in shaping the severity of DENV infection rates in DCs and identify novel potential DENV-susceptibility targets. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE126726 RNAseq for MCL cells with ibrutinib treatment
In this study we compared the effects of BTK inhibitor on the gene expression, activation of cell signaling pathways, and functional properties of cells derived from a patient with Anaplastic Mantle Cell Lymphoma. we used RNAseq to map the genome-wide gene expression patterns in MCL cells in response to BTK inhibition (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE143288 A compendium map of Cis-Regulatory Elements in the Pig Genome and epigenetic comparison with the human Genome
Contributors : Yunxia Zhao ; Ye Hou ; Yueyuan Xu ; Shuhong ZhaoSeries Type : Other ; Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Sus scrofaAlthough major advances in genomics have initiated an exciting new era of research, the lack of information about cis-regulatory elements has limited the genetic improvement or manipulation of pig as meat source and biomedical model. Here, we systematically characterize the cis-regulatory elements and their functions in the pig genome in 12 diverse tissues from 4 pig breeds through RNA-Seq, ATAC-Seq, and...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Other Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Sus scrofa Source Type: research

GSE144562 Reorganization of 3D chromatin architecture of rice genomes during heat stress (Bisulfite-seq)
Contributors : Zhe Liang ; Qian Zhang ; Qing Liu ; Changmian Ji ; Pingxian Zhang ; Guihua Hu ; Yifan Wang ; Xiaofeng GuSeries Type : Methylation profiling by high throughput sequencingOrganism : Oryza sativaFunctional changes in spatial genome organization during environmental changes in plant are poorly understood. Here we report a comprehensive profile of nuclear dynamics during heat stress in two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica) by integrating Hi-C, RNA-seq and ATAC-seq. We show that heat stress disrupts different levels of chromosome organization, ranging from A/B compartment changes to inc...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Oryza sativa Source Type: research

GSE144563 Reorganization of 3D chromatin architecture of rice genomes during heat stress (MeDIP-Seq)
Contributors : Zhe Liang ; Qian Zhang ; Qing Liu ; Changmian Ji ; Pingxian Zhang ; Guihua Hu ; Yifan Wang ; Xiaofeng GuSeries Type : Methylation profiling by high throughput sequencingOrganism : Oryza sativaFunctional changes in spatial genome organization during environmental changes in plant are poorly understood. Here we report a comprehensive profile of nuclear dynamics during heat stress in two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica) by integrating Hi-C, RNA-seq and ATAC-seq. We show that heat stress disrupts different levels of chromosome organization, ranging from A/B compartment changes to inc...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Oryza sativa Source Type: research

GSE144564 Reorganization of 3D chromatin architecture of rice genomes during heat stress (ATAC-Seq)
Contributors : Zhe Liang ; Qian Zhang ; Qing Liu ; Changmian Ji ; Pingxian Zhang ; Guihua Hu ; Yifan Wang ; Xiaofeng GuSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Oryza sativaFunctional changes in spatial genome organization during environmental changes in plant are poorly understood. Here we report a comprehensive profile of nuclear dynamics during heat stress in two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica) by integrating Hi-C, RNA-seq and ATAC-seq. We show that heat stress disrupts different levels of chromosome organization, ranging from A/B compartment c...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Oryza sativa Source Type: research

GSE144565 Reorganization of 3D chromatin architecture of rice genomes during heat stress (HiC)
Contributors : Zhe Liang ; Qian Zhang ; Qing Liu ; Changmian Ji ; Pingxian Zhang ; Guihua Hu ; Yifan Wang ; Xiaofeng GuSeries Type : OtherOrganism : Oryza sativaFunctional changes in spatial genome organization during environmental changes in plant are poorly understood. Here we report a comprehensive profile of nuclear dynamics during heat stress in two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica) by integrating Hi-C, RNA-seq and ATAC-seq. We show that heat stress disrupts different levels of chromosome organization, ranging from A/B compartment changes to increase in the size of topologically associating...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Other Oryza sativa Source Type: research

GSE144566 Reorganization of 3D chromatin architecture of rice genomes during heat stress (RNA-Seq)
Contributors : Zhe Liang ; Qian Zhang ; Qing Liu ; Changmian Ji ; Pingxian Zhang ; Guihua Hu ; Yifan Wang ; Xiaofeng GuSeries Type : Expression profiling by high throughput sequencingOrganism : Oryza sativaFunctional changes in spatial genome organization during environmental changes in plant are poorly understood. Here we report a comprehensive profile of nuclear dynamics during heat stress in two rice cultivars, Nipponbare (Nip; Japonica) and 93-11 (Indica) by integrating Hi-C, RNA-seq and ATAC-seq. We show that heat stress disrupts different levels of chromosome organization, ranging from A/B compartment changes to incr...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Oryza sativa Source Type: research

GSE147587 A mechanism for imprinted expression of EIN2 to regulate seed development in Arabidopsis
Contributors : Atsumi Ando ; Qingxin Song ; Hong Qiao ; Z. J ChenSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaSeed size is affected by genetic mutations and imprinting. Imprinting is a widespread epigenetic phenomenon in mammals and flowering plants. In plants the majority of imprinted genes are involved in the development of endosperm, a nutritious tissue that resembles functionally the placenta in mammals. However, there is little overlap among hundreds of imprinted genes identified in different plant species or different ecotypes within the same species. ETHYLENE INSENSI...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE153146 ChIPseq on H4K20me1 on TX1072 cell line at different times of Xist induction through Doxycycline.
Contributors : Sjoerd Tjalsma ; Mayako Hori ; Yuko Sato ; Aurelie Bousard ; Akito Ohi ; Ana C Raposo ; Julia Roensch ; Agnes Le Saux ; Junpei Nogami ; Kazumitsu Maehara ; Tomoya Kujirai ; Yasuyuki Ohkawa ; Hitoshi Kurumizaka ; Sim ão Teixeira da Rocha ; Jan J Żylicz ; Hiroshi Kimura ; Edith HeardSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusDuring X chromosome inactivation (XCI), in female mammals, gene silencing is initiated by a long-noncoding RNA, called Xist. Xist RNA accumulation also allows for the deposition of specific chromatin marks. Among others, PRC...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE153753 Functionally Distinct Pomc-Expressing Neuron Subpopulations in Hypothalamus Revealed by Intersectional Targeting
We report differences in translational profiles between POMCLepr+ and POMCGlp1r+ neurons. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE155679 Repeated stimulation of self-presentation pathway by targeting erythrocytes in vivo drives anergy and profound T cell dysfunction
Contributors : Elyse A Watkins ; Jennifer T Antane ; Andrew C Tremain ; Jaeda L Roberts ; Kristen M Lorentz ; Sarah Zuerndorfer ; Anya C Dunaif ; Luke Bailey ; Mindy Nguyen ; Robert DeLoera ; Stephan Kontos ; Jeffrey A HubbellSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe purpose of this study was to conduct an in-depth analysis of the molecular characteristics of both CD4 and CD8 T cells upon encounter of self-associated antigen bound to erythrocytes, induce therapeutic tolerance in an endogenous repertoire of T cells, and understand the mechanisms involved in uptake and present...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE160934 Nucleo-cytoplasmic RNA distribution responsible for maintaining neuroinflammatory microenvironment.
Contributors : Yuyan Liao ; Chenghao Kuang ; Zheng BaoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCharacteristics of subcellular localization of RNAs are closely associated with their transcriptional outputs and, therefore, involved in the physiological process of many cases of central nervous system diseases, such as hemorrhagic stroke, which threatens millions of people and causes of death and long-term disability world-wide.   Using whole-transcriptome sequencing (RNA-seq), here we report a subcellular gene profiling during hemorrhagic damage. Differentially expressed gene...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE161732 Cellular nucleotide deficiency triggers mitochondrial DNA-dependent innate immunity [A33_OE_RNA-seq]
Contributors : Hans-Georg Sprenger ; Thomas MacVicar ; Janine Altm üllerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCytosolic mitochondrial DNA (mtDNA) elicits a type I interferon response, but signals triggering the release of mtDNA from mitochondria remain enigmatic. We found that mtDNA-dependent immune signalling via the cGAS-STING pathway is under metabolic control and induced by cellular nucleotide deficiency. The mitochondrial protease YME1L preserves nucleotide pools by supporting de novo nucleotide synthesis and by proteolysis of the pyrimidine nucleotide carrier SLC2...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE161733 Cellular nucleotide deficiency triggers mitochondrial DNA-dependent innate immunity [HeLa_CAD_RNA-seq]
Contributors : Amir Bahat ; Hans-Georg Sprenger ; Thomas MacVicar ; Janine Altm üllerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCytosolic mitochondrial DNA (mtDNA) elicits a type I interferon response, but signals triggering the release of mtDNA from mitochondria remain enigmatic. We found that mtDNA-dependent immune signalling via the cGAS-STING pathway is under metabolic control and induced by cellular nucleotide deficiency. The mitochondrial protease YME1L preserves nucleotide pools by supporting de novo nucleotide synthesis and by proteolysis of the pyrimidine nucleotide...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE161734 Cellular nucleotide deficiency triggers mitochondrial DNA-dependent innate immunity [Scr_vs_Yme1l-si_RNA-seq]
Contributors : Hans-Georg Sprenger ; Thomas MacVicar ; Janine Altm üllerSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCytosolic mitochondrial DNA (mtDNA) elicits a type I interferon response, but signals triggering the release of mtDNA from mitochondria remain enigmatic. We found that mtDNA-dependent immune signalling via the cGAS-STING pathway is under metabolic control and induced by cellular nucleotide deficiency. The mitochondrial protease YME1L preserves nucleotide pools by supporting de novo nucleotide synthesis and by proteolysis of the pyrimidine nucleotide carrier SLC2...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE161735 Cellular nucleotide deficiency triggers mitochondrial DNA-dependent innate immunity [WT_vs_Yme1lKO_MEF_RNA-seq]
Contributors : Hans-Georg Sprenger ; Thomas MacVicar ; Janine Altm üllerSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusCytosolic mitochondrial DNA (mtDNA) elicits a type I interferon response, but signals triggering the release of mtDNA from mitochondria remain enigmatic. We found that mtDNA-dependent immune signalling via the cGAS-STING pathway is under metabolic control and induced by cellular nucleotide deficiency. The mitochondrial protease YME1L preserves nucleotide pools by supporting de novo nucleotide synthesis and by proteolysis of the pyrimidine nucleotide carrier SLC2...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE161736 Cellular nucleotide deficiency triggers mitochondrial DNA-dependent innate immunity
Series Type : 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 - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE162245 RNA-seq analysis of Ahr-knockout rats of SuHx model.
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Rattus norvegicusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Rattus norvegicus Source Type: research

GSE165007 Influence of follicular lymphoma B cells on tumor-supportive stromal cells gene expression
Contributors : Karin Tarte ; Erwan Dumontet ; Celine Pangault ; Fabien GuillotonSeries Type : Expression profiling by arrayOrganism : Homo sapiensGEP on Affymetrix U133+2.0 microarrays was performed on in vitro expanded stromal cells with or without B cells priming. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE165165 Mouse PanCancer Immune Panel on WT and SCID mT3-2D KPC Tumors
Contributors : Reham Ajina ; Zoe X Malchiodi ; Allison A Fitzgerald ; Annie Zuo ; Shangzi Wang ; Maha Moussa ; Connor J Cooper ; Yue Shen ; Quentin R Johnson ; Jerry M Parks ; Jeremy C Smith ; Marta Catalfamo ; Elana J Fertig ; Sandra A Jablonski ; Louis M WeinerSeries Type : Expression profiling by arrayOrganism : Mus musculusTo comprehensively assess the immune milieu of WT and SCID mT3-2D tumors, we employed NanoString nCounter immune profiling. The two groups of samples exhibited distinct immune profiles and indicated greater upregulation of immune-related genes in mT3-2D WT tumors than in SCID tumors. (Source: GEO: Ge...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE165166 RNA-seq for WT and SCID mT3-2D KPC Tumors and mT3-2D cell lines
Contributors : Reham Ajina ; Zoe X Malchiodi ; Allison A Fitzgerald ; Annie Zuo ; Shangzi Wang ; Maha Moussa ; Connor J Cooper ; Yue Shen ; Quentin R Johnson ; Jerry M Parks ; Jeremy C Smith ; Marta Catalfamo ; Elana J Fertig ; Sandra A Jablonski ; Louis M WeinerSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTo investigate how pancreatic malignant epithelial cells responded to anti-tumor T-cell immune responses in vivo, RNA-seq was used to examine the gene expression profiles of the mT3-2D-GFP cell line and FACS sorted mT3-2D-GFP cancer cells isolated from WT and SCID tumors. (Source...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE165167 WES for WT and SCID mT3-2D KPC Tumors and mT3-2D cell line
Contributors : Reham Ajina ; Zoe X Malchiodi ; Allison A Fitzgerald ; Annie Zuo ; Shangzi Wang ; Maha Moussa ; Connor J Cooper ; Yue Shen ; Quentin R Johnson ; Jerry M Parks ; Jeremy C Smith ; Marta Catalfamo ; Elana J Fertig ; Sandra A Jablonski ; Louis M WeinerSeries Type : Genome variation profiling by high throughput sequencingOrganism : Mus musculusTo determine the influence of in vivo tumor growth and antitumor immune responses on the generation of tumor neoepitopes, we performed whole exome sequencing (WES) on the mT3-2D cell line, WT tumors and SCID tumors (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Genome variation profiling by high throughput sequencing Mus musculus Source Type: research

GSE165169 SCID mT3-2D KPC Tumors and mT3-2D cell lines
Series Type : Expression profiling by array ; Expression profiling by high throughput sequencing ; Genome variation 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 - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Expression profiling by high throughput sequencing Genome variation profiling by high throughput sequencing Mus musculus Source Type: research

GSE166656 Repetitive in vivo manual loading of the spine elicits cellular responses in porcine annuli fibrosi
Contributors : John R Matyas ; Claudia Klein ; Dragana Ponjevic ; Neil Duncan ; Gre N KawchukSeries Type : Expression profiling by high throughput sequencingOrganism : Sus scrofaBack pain and intervertebral disc degeneration are prevalent, costly, and widely treated by manual therapies, yet the underlying causes of these diseases are indeterminate as are the scientific bases for such treatments. The present studies characterize the effects of repetitive in vivo manual loads on porcine intervertebral disc using RNA deep sequencing. A single session of repetitive manual loading applied to the lumbar spine induced both up- an...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Sus scrofa Source Type: research

GSE166794 FOXO1 mitigates the SMAD3/FOXL2C134W transcriptomic effect in a model of human adult granulosa cell tumor
Contributors : Christian Secchi ; Paola Benaglio ; Francesca Mulas ; Martina Belli ; Dwayne Stupack ; Shunichi ShimasakiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGranulosa cell tumors (GCTs) are a rare form of stromal cell malignant cancer accounting for one in twenty cases of ovarian cancer. More than 400 tumors from aGCT patients of diverse ethnicities showed one single mutation in the Forkhead box L2 transcription factor gene FOXL2: Cys134Trp (c.402C (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE167486 Respiratory syncytial virus induces alternative mRNA processing
Contributors : Allan Brasier ; Xiaofang XuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapienswe examine the effect of RSV infection in human small airway epithelial cells (hSAECs) (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE167489 Swine inflammation and necrosis syndrome is associated with plasma metabolites and liver transcriptome in affected piglets
Contributors : Robert Ringseis ; Denise K Gessner ; Klaus Eder ; Gerald ReinerSeries Type : Expression profiling by arrayOrganism : Sus scrofaSwine Inflammation and Necrosis Syndrome (SINS) can lead to severe clinical signs, especially in tails, ears, teats and claws in pigs. Clinical and histopathological findings in newborn piglets with in-tact epidermis indicate a primarily endogenous etiology, and microbial-associated molecular pat-terns (MAMPs), such as lipopolysaccharide (LPS) are assumed to play a central role in the devel-opment of the syndrome. We hypothesized that swine inflammation and necrosis syndrome (SINS) i...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Sus scrofa Source Type: research

GSE167495 TPX2 Amplification-Driven Aberrant Mitosis in Long-Term Cultured Human Embryonic Stem Cells
Contributor : Hyuk-Jin ChaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAlthough human embryonic stem cells (hESCs) are equipped with highly effective machinery for the maintenance of genome integrity, the frequency of genetic aberrations during long-term in vitro hESC culture has been a serious issue that raises concerns over their safety in future clinical applications.By passaging hESCs over a broad range of timepoints, we found that mitotic aberrations, such as the delay of mitosis, multipolar centrosomes, and chromosome mis-segregation, were increased in the late-passaged hESCs...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE167509 Single cell RNA sequencing in Staphylococcus epidermidis-inoculated nasal epithelial cells
We report the application of single cell RNA sequencing technology for high-throughput profiling of nasal microbiome Staphylococcus epidermidis in human nasal epithelial cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE167514 Transcriptomic analysis of GLUD1-knockdown 786-0 cells under amino acid deprivation
Contributors : Jialiang Shao ; Xiongjun WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensshGLUD1 and shNT 786-0 cells were pretreated by amino acid starvation for 12 hours, then total mRNA were extracted for sequencing. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE167515 Cannibalized Erythroblasts Accelerate Developmental Neurogenesis by Regulating Mitochondrial Dynamics
In this study, we disclose a mechanism triggered during neurulation that programs brain development by donation of sacrificial yolk sac erythroblasts to neuroepithelial cells. At embryonic day (E) 8.5, neuroepithelial cells transiently integrate with the endothelium of yolk sac blood vessels and cannibalize intravascular erythroblasts as transient heme-rich endosymbionts. This cannibalistic behavior instructs precocious neuronal differentiation of neuroepithelial cells in the proximity of blood vessels. By experiments in vitro, we show that access to erythroblastic heme accelerates the pace of neurogenesis by induction of ...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE167526 ARC2 elicits a secondary metabolic response requiring afsR and afsS in Streptomyces coelicolor
Contributors : Vanessa Y Calvelo ; Justin R NodwellSeries Type : Expression profiling by high throughput sequencingOrganism : Streptomyces coelicolorIn this work, we demonstrate that the addition of the small molecule elicitor ARC2 to Streptomyces coelicolor cultures results in global changes in gene expression including many secondary metabolic genes. A profile of the Streptomyces coelicolor transcriptome in the absence and presence of ARC2 was performed by RNA-seq. Total RNA was extracted after 10 hours of treatment with either the DMSO solvent control or the ARC2 small molecule elicitor. A V2 rapid run mode with paired-...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Streptomyces coelicolor Source Type: research

GSE167528 H3K27ac in SARS-CoV-2 infection
Contributors : Jessica S Ho ; Bobo W Mok ; Laura Campisi ; Tristan Jordan ; Soner Yildiz ; Sreeja Parameswaran ; Joseph A Wayman ; Natasha N Gaudreault ; David A Meekins ; Sabarish V Indran ; Igor Morozov ; Jessie D Trujillo ; Yesai S Fstkchyan ; Raveen Rathnasinghe ; Zeyu Zhu ; Simin Zheng ; Nan Zhao ; Kris White ; Helen Ray-Jones ; Valeriya Malysheva ; Michiel J Thiecke ; Siu-Ying Lau ; Honglian Liu ; Anna J Zhang ; Andrew C Lee ; Wen-Chun Liu ; Teresa Aydillo ; Betsaida Salom Melo ; Ernesto Guccione ; Robert Sebra ; Elaine Shum ; Jan Bakker ; David A Kaufman ; Andre L Moreira ; Mariano Carossino ; Udeni R Balasuriya ; M...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE167547 Clinical and molecular differentiation between malignant rhabdoid tumor of normal tissue: A two-case report
Contributors : Chenghao Zhanghuang ; Shuo Chen ; Li Li ; Zhen Yang ; Yucheng Xie ; Jiwei Li ; Haoyu Tang ; Xiaoli He ; Liuyi Dong ; Bing YanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPreoperative B-scan ultrasonography and Computed Tomography (CT) examination in 2 cases suggested that nephroblastoma . Treated with radical nephrectomy after general anesthesia. After operation,MRTK diagnosis by pathological examination. Regular chemotherapy 7 courses(Child 1) and 12 courses(Child 2),followed up for 2 years(Child 1) and 3 years and 1 month(Child 2), without symptoms. RNA-seq results...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE167549 The NK cell stress response status modulates anti-tumor immunity [ATAC-seq]
Contributors : Kathryn Hockemeyer ; Iannis AifantisSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe tumor microenvironment (TME) comprises numerous forms of cellular stress, which can activate Heat Shock Factor 1 (HSF1), the master transcription factor of the proteotoxic stress response. We profiled HSF1 activity across tumor-infiltrating immune populations, revealing the highest activity in CD8+ T cells and the lowest in natural killer (NK) cells. To elucidate the mechanisms through which HSF1 regulates immune surveillance, we generated an in vivo model of augmented ...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE167550 The NK cell stress response status modulates anti-tumor immunity [RNA-seq]
Contributors : Kathryn Hockemeyer ; Iannis AifantisSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe tumor microenvironment (TME) comprises numerous forms of cellular stress, which can activate Heat Shock Factor 1 (HSF1), the master transcription factor of the proteotoxic stress response. We profiled HSF1 activity across tumor-infiltrating immune populations, revealing the highest activity in CD8+ T cells and the lowest in natural killer (NK) cells. To elucidate the mechanisms through which HSF1 regulates immune surveillance, we generated an in vivo model of augmented HSF1 activity....
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE167551 The NK cell stress response status modulates anti-tumor immunity [scRNA-seq]
Contributors : Kathryn Hockemeyer ; Iannis AifantisSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe tumor microenvironment (TME) comprises numerous forms of cellular stress, which can activate Heat Shock Factor 1 (HSF1), the master transcription factor of the proteotoxic stress response. We profiled HSF1 activity across tumor-infiltrating immune populations, revealing the highest activity in CD8+ T cells and the lowest in natural killer (NK) cells. To elucidate the mechanisms through which HSF1 regulates immune surveillance, we generated an in vivo model of augmented HSF1 activity....
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE167552 The NK cell stress response status modulates anti-tumor immunity
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE167553 Effect of DDX3 inhibitors on CD4+ T cells
Contributors : Tokamhe Mahmoudi ; Robert-Jan Palstra ; Wilfred van IJcken ; Shringar RaoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAn innovative approach to eliminate HIV-1-infected cells emerging out of latency, the major hurdle to HIV-1 cure, is to pharmacologically reactivate viral expression and concomitantly trigger intracellular pro-apoptotic pathways in order to selectively induce cell death (ICD) of infected cells, without reliance on the extracellular immune system. In this work we demonstrate the effect of DEAD-box polypeptide 3, X-Linked (DDX3) inhibitors on selectivel...
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE167556 Bovine Sperm-borne miRNAs
Contributors : Yongsheng Wang ; Yue DuSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Bos taurusPurpose: to construct a library of miRNAs in bovine sperm was constructed using Illumina high ‐throughput sequencing technology. Result: Unique sequences that were 18–26 nucleotides in length were mapped to specific precursors in miRBase 20.0 using BLAST. A total of 951 known miRNAs and 8 novel, highly expressed miRNA candidates were identified. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 26, 2021 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Bos taurus Source Type: research

GSE167454 Neural tube closure defect: Single Cell ATAC and single cell mRNA seq
Contributor : Rachel KeulsSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusSingle-cell mRNA sequencing was overlaid with single-cell ATAC sequencing of the mouse E9.5 cranial region for both wildtype and miR-302 knockout embryos, an established example of a neural tube closure defect. The goals of this study were to compare changes in gene expression and chromatin accessibility upon loss of a stem cell miRNA and neural tube closure defect. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 25, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE111425 Gibberellins synthesis is involved in the reduction of cell flux and elemental growth rate in maize leaf under low nitrogen supply
In this study, we investigated cell division and elongation in maize leaf growth in response to LN stress using an integrated approach including kinematic growth analysis, tissue-specific RNA-seq dissection and hormone determination. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Zea mays Source Type: research

GSE111435 Combination Anti-PD-1 and Anti-retroviral Therapy Provides Therapeutic Benefit Against SIV
Contributors : Geetha H Mylvaganam ; Lynette S Chea ; Gregory K Tharp ; Sakeenah Hicks ; Vijayakumar Velu ; Smita Iyer ; Jacob D Estes ; Steven E Bosinger ; Gordon J Freeman ; Rafi Ahmed ; Rama R AmaraSeries Type : Expression profiling by high throughput sequencingOrganism : Macaca mulattaTherapeutic strategies that enhance anti-viral immunity and reduce the viral reservoir are critical to achieving durable remission of HIV. The co-inhibitory receptor programmed death-1 (PD-1) regulates CD8+ T cell dysfunction during chronic HIV and SIV infections 1-4. In addition, PD-1+ CD4+ T cells constitute a significant fraction of th...
Source: GEO: Gene Expression Omnibus - February 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Macaca mulatta Source Type: research

GSE117053 Direct observation of CRISPR/Cas9 guide RNAs in single cell transcriptomes
Contributors : Yeo H Grace ; Juez Oscar ; Chen Qing ; Banerjee Budhaditya ; Chu Lendy ; Logister Ive ; Gifford K David ; Sherwood I RichardSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe introduce poly-adenine CRISPR gRNA-based single cell RNA-sequencing (pAC-Seq), a method enabling simultaneous observation of mutagenic guide RNAs (gRNAs) and their transcriptional consequences in single cell RNA sequencing (scRNA-seq) data. We have made gRNAs robustly visible in scRNA-seq data while maintaining full activity by modifying them with a hardcoded poly-adenine tract. We apply pAC-Seq to...
Source: GEO: Gene Expression Omnibus - February 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE122979 Treatment of MCF-7 cells with TRAIL and Smac mimetic (LCL-161) [seq]
Contributors : Christer Larsson ; Christian Holmgren ; Victoria GranqvistSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe aim was to identify the effect of caspase inhibition on changes in gene expression in MCF-7 cells induced by a combination of TRAIL and LCL-161. Treated samples and control samples were collected after 24 h of treatment. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE122980 Treatment of MCF-7 cells with TRAIL and Smac mimetic (LCL-161)
Series Type : Expression profiling by high throughput sequencing ; Expression profiling by arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Expression profiling by array Homo sapiens Source Type: research

GSE124976 Agaricus bisporus respiratory bursts
Contributors : Aurin M Vos ; Robert-Jan Bleichrodt ; Koen C Herman ; Robin A Ohm ; Heike Schmitt ; Luis G Lugones ; Han A W östenSeries Type : Expression profiling by high throughput sequencingOrganism : Agaricus bisporusRespiratory bursts were observed in A. bisporus. CO2 production and O2 consumption increased up to 3.5 fold during these 3 h bursts while compost temperature increased up to 3 °C. We set out to find which pathways were characteristic for these bursts and the interval between these bursts. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Agaricus bisporus Source Type: research