GSE153670 Bulk RNA sequencing from patient bone marrow samples
Contributors : Nathan Singh ; Elene OrlandoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAnalyzed sequencing data from bone marrow samples taken from patients enrolled on ENSIGN or ELIANA clinical trials prior to infusion of CART19. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 3, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE84017 ABA regulates the circadian clock via RVE3 to gate ABA responses
Contributors : Hongtao Liu ; Xinyi Hu ; Sheen X LuSeries Type : Expression profiling by arrayOrganism : Arabidopsis ; Arabidopsis thalianaABA affected the period length of the circadian clock through ABA signaling pathway, and ABA induced RNA expression were gated by the circadian clock. We next performed microarray to investigate this clock gated ABA sensitivity globally (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by array Arabidopsis Arabidopsis thaliana Source Type: research

GSE128532 Genome wide RNA sequencing to profile response to IL-1 in control and IFT88 depleted cells
Conclusion: Demonstration of the effect of IFT88 depletion on IL-1 response signature over 24h. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE129691 Setd2 deficiency impaired erythroid differentiation and accelerated Myelodysplastic Syndrome(MDS) - associated leukemogenesis through S100A8 and S100A9
Contributors : Bingyi Chen ; Shubei Chen ; Chun-Hui Xu ; Xiao-Jian Sun ; Lan WangSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Mus musculusSetd2, the histone H3 lysine 36 methyltransferase, plays an important role in the pathogenesis of hematologic malignancies. The research on the role of Setd2 in leukemogenesis has made great progress, but its role in MDS is still unknown. Here, we knock out Setd2 in the NUP98-HOXD13 transgenic (NHD13 Tg) mouse, and demonstrate that loss of...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE131743 Comparison of human CD39- and CD39+ thymus-derived regulatory T-cells
Contributors : Klaus Schmetterer ; Marlene GernerSeries Type : Expression profiling by arrayOrganism : Homo sapiensCD39- and CD39+ human thymus-derived regulatory T-cells (tTreg) present as distinct subsets with specific functional and metabolic response patterns. Both cell types express equal levels of the canonical tTreg transcription factors FOXP3 and Helios and overexpression studies have shown that CD39 expression is independent of these two transcription factors. So far, no transcriptomic analyses to adress these differences have been performed.We used microarrays to detail the global programme of gene expression bet...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE132548 HCV infection of adult hepatocytes results in temporally structured transcriptional responses which partially overlap with the IRF1 regulon
We describe the adult hepatocyte response to initial HCV infection and detect temporal perturbations in the transcriptional landscape which correlate with known shifts in replication site location. We also describe an expanded IRF1 regulon and quantify the intrinsic and inducible component in PHHs. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE133296 Matched primary ovarian cancer, omental metastases, and non-omental metastases from 10 patients with high-grade serous ovarian carcinoma
Contributors : Ye Hu ; Barbie Taylor-Harding ; Sandra OrsulicSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMatched high-grade serous ovarian carcinoma samples collected from the ovary (ov), omental metastasis (om-met), and non-omental intraperitoneal metastasis (met) from 10 patients at the time of primary debulking surgery were analyzed for RNA expression by RNA sequencing. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE133843 A novel model for chronic rejection in vascularized composite allotransplantation identifies CXCL9-11 as potential biomarkers
Contributor : Stephan HahnSeries Type : Expression profiling by arrayOrganism : Rattus norvegicusGlobal mRNA expression profiling of transplanted rat hindlimbs (muscle and skin) were collected using Agilent rat whole genome array (Agilent-028282 Whole Rat Genome Microarray 4x44K v3). Hind limb transplantation between Fischer344 (donor) and Lewis (recipient) rats were performed. Isogenic transplantations served as controls. Administration of irregular immunosuppression induced chronic rejection. At the endpoint (post-operativ day 100), hind limbs presented clinicial, histomorphological and genetic changes, known to be highl...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by array Rattus norvegicus Source Type: research

GSE135712 NanoString expression profiling in metastatic ovarian cancer
Contributors : Sandra Orsulic ; Barbie Taylor-HardingSeries Type : OtherOrganism : Homo sapiensPurpose: Most molecular characterizations of high-grade serous ovarian cancer (HGSOC) have been done in primary ovarian tumors. Such data may not be fully representative of HGSOC, which is characterized by widespread peritoneal metastases at the time of diagnosis and upon relapse. The most common site of HGSOC metastasis is the omentum. The omentum is characterized by strong immune and fibrotic activities and is a rich source of mesenchymal stem cells (MSCs), which have the capacity to differentiate into cancer-associated fibrobl...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE135763 Altered 3D chromatin structure permits inversional recombination at the IgH locus
We report that in the absence of intergenic control region 1 (IGCR1), a regulatory sequence that specifies the RAG scanning domain on WT IgH alleles, VH and DH gene segments can recombine with each other by both deletion and inversion of intervening DNA. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research

GSE137138 Transcriptome upon Mof deletion and Etomoxir treatment in ground-state mouse (m) ESCs
This study describes the transcriptome profiling of: 1) Mof fl/fl mESCs cultured in 2i/LIF medium with Ethanol (WT) or 4-OHT (Mof-/-); 2) E14 mESCs cultured in 2i/LIF medium treated with H2O (control) or Etomoxir treatment (ETO, FAO inhibition) and ETO-released (Released). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE137411 Bimodal Adenine and Cytosine CRISPR Base Editing on DNA
Contributors : Julian Grunewald ; Caleb LareauSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAdenine and cytosine base editors (ABEs and CBEs) represent a new genome editing technology that allows the programmable installation of A-to-G or C-to-T alterations on DNA. We engineered Streptococcus pyogenes Cas9-based adenine and cytosine base editor (SpACE) that enables efficient simultaneous introduction of A-to-G and C-to-T substitutions in the same base editing window on DNA. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE137586 Novel fluorescence-based high-throughput method uncovers single-cell DNA supercoiling heterogeneity
Contributors : Alexandre Duprey ; Eduardo A GroismanSeries Type : Expression profiling by high throughput sequencingOrganism : Salmonella enterica subsp. enterica serovar TyphimuriumDNA supercoiling is essential for life because it controls critical processes, including transcription, replication and recombination. Current methods to measure DNA supercoiling in vivo are laborious and unable to examine single cells. Here we report a method for high-throughput measurement of bacterial DNA supercoiling in vivo. Fluorescent Evaluation of DNA Supercoiling (FEDS) utilizes a plasmid harboring the gene for a green fluorescent prot...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Salmonella enterica subsp. enterica serovar Typhimurium Source Type: research

GSE138384 Combined Inhibition of JAK/STAT Pathway and Lysine Demethylase 1 as a Novel Therapeutic Strategy in CSF3R/CEBPA Mutant Acute Myeloid Leukemia [LSD1i RNA-seq]
Contributors : Theodore P Braun ; Julia E MaxsonSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe presence of CSF3R mutations are associated with adverse outcomes in CEBPA mutant AML. Here we report that inhibitors of LSD1 reverse the mutant CEBPA-mediated differentiation blockade and exhibit synergy with JAK/STAT inhibitors. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE138386 Combined Inhibition of JAK/STAT Pathway and Lysine Demethylase 1 as a Novel Therapeutic Strategy in CSF3R/CEBPA Mutant Acute Myeloid Leukemia [RUX_GSK RNA-seq]
Contributors : Theodore P Braun ; Julia E MaxsonSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe presence of CSF3R mutations are associated with adverse outcomes in CEBPA mutant AML. Here we report that inhibitors of LSD1 reverse the mutant CEBPA-mediated differentiation blockade and exhibit synergy with JAK/STAT inhibitors. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE138387 Combined Inhibition of JAK/STAT Pathway and Lysine Demethylase 1 as a Novel Therapeutic Strategy in CSF3R/CEBPA Mutant Acute Myeloid Leukemia [LSD1i ChIP-seq]
Contributors : Theodore P Braun ; Julia E MaxsonSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe presence of CSF3R mutations are associated with adverse outcomes in CEBPA mutant AML. Here we report that inhibitors of LSD1 reverse the mutant CEBPA-mediated differentiation blockade and exhibit synergy with JAK/STAT inhibitors. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE138388 Combined Inhibition of JAK/STAT Pathway and Lysine Demethylase 1 as a Novel Therapeutic Strategy in CSF3R/CEBPA Mutant Acute Myeloid Leukemia
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 - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE139059 TBL1XR1 mutations bias germinal center B-cells towards a pro-tumorigenic memory fate
Contributors : Leandro Venturutti ; Matt Teater ; Ari M MelnickSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDiffuse large B-cell lymphomas (DLBCL) encompass a heterogeneous group of diseases derived from different stages of B-cell differentiation. The most clinically aggressive forms of DLBCL, C5/MCD, carry activating mutations in canonical B-cell signaling pathways, as well as early-occurring hits in the poorly-characterized gene TBL1XR1. Here, we investigated the role of TBL1XR1 mutations in the early steps of malignant transformation. We found that TBL1XR1 mutations disrupt germ...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE139101 Engineering Neuronal Organoids with Network Activity and Plasticity
Contributors : Rashi Halder ; Maria P Zafeiriou ; Andre FischerSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHuman brain organoids are promising tools for disease modelling and drug development. For proper neuronal network formation excitatory and inhibitory neurons as well as glia need to develop concurrently. Here we report a novel method for directed differentiation and self-organization of induced pluripotent stem cells in a collagen hydrogel towards a highly interconnected neuronal network in a macroscale tissue format. Bioengineered Neuronal Organoids (BENOs) comprise of inter...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE139172 ChIRP-seq of Hoxc4-au in epidydimal white adipose tissue (eWAT)-derived preadipocytes.
We report the genome-wide occupancy of Hoxc4-au by using chromatin isolation after RNA purification (CHIRP) in eWAT-derived preadipocytes (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE140703 An Integrative Transcriptome – Proteome Approach Reveals a Robust Expression Pattern of Small Intestinal Epithelial Organoids from Germ-Free and Microbiota Associated Donors
Contributors : Annika Hausmann ; Giancarlo Russo ; Mirjam Zuend ; Miguel Cuenca ; Schinichi Sunagawa ; Mikael Sellin ; Wolf-Dietrich HardtSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe goal of this study is to analyze the influence of different donor microbiota on small intestinal epithelial organoid cultures (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE140800 DNA Methylation in PBMC of chronically HIV infected individuals
Contributors : M Ruiz-Riol ; C BranderSeries Type : Methylation profiling by arrayOrganism : Homo sapiensGenome wide DNA Methylation in PBMC of untreated HIV-chronic individuals with different HIV control. For a total of 70 PBMC samples we determined DNA Methylation levels of more than 450,000 CpG sites with the platform Infinium HumanMethylation450 BeadChip (450K, Illumina). Finally, we compared DNA methylation between HIV-High (>50,000 HIV RNA copies/ml, n=29) and HIV-Low ( (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Methylation profiling by array Homo sapiens Source Type: research

GSE141097 Evolutionarily Conserved Regulation of Immunity by the Splicing Factor RNP-6/PUF60
Contributors : Chun Kew ; Adam AntebiSeries Type : Expression profiling by high throughput sequencingOrganism : Caenorhabditis elegansSplicing is a vital cellular process that modulates important aspects of animal physiology, including metabolism and lifespan. From a cold stress screen, we identified a novel mutant of the splicing factor RNP-6/PUF60, which evokes resistance to various abiotic stresses, yet is highly sensitive to pathogenic bacterial challenge. Molecular and genetic experiments reveal that RNP-6 suppresses immunity, but promotes animal longevity, suggesting a tradeoff between these processes. Pathogen expos...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Caenorhabditis elegans Source Type: research

GSE142012 Dysregulation of MITF in the context of defective MC1R and RB1/p16/CDK4 leads to melanocyte transformation [microarray]
Contributor : Alfonso UrbanucciSeries Type : Expression profiling by arrayOrganism : Homo sapiensExpression analysis of immortalized melanocytes Hermes 3c and Hermes 4c derivative cell lines following lentiviral transduction of a HA-tagged MITF-M construct (pLX3xHAvar4mCherry) or control construct (pLVX IRES mCherry). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE142014 Dysregulation of MITF in the context of defective MC1R and RB1/p16/CDK4 leads to melanocyte transformation [ChIP-Seq]
Contributor : Alfonso UrbanucciSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensChip-seq analysis of immortalized melanocytes Hermes 3c and Hermes 4c derivative cell lines following lentiviral transduction of a HA-tagged MITF-M construct (pLX3xHAvar4mCherry) (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE142017 Dysregulation of MITF in the context of defective MC1R and RB1/p16/CDK4 leads to melanocyte transformation [RNA-Seq]
Contributor : Alfonso UrbanucciSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNAseq Expression analysis of immortalized melanocytes Hermes 3c (3C) and Hermes 4c (4C) cell lines following siRNA transfection with a control scrambled siRNA or an RNA targeting MITF (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE142018 Dysregulation of MITF in the context of defective MC1R and RB1/p16/CDK4 leads to melanocyte transformation
Series Type : Expression profiling by array ; 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 - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by array Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

Gse146760 a multiplex human pluripotent stem cell platform defines molecular and functional subtypes of autism
We report a multiplex human pluripotent stem cell platform to investigate autism associated genetic variation during the development of the prefrontal cortex. This dataset represents the biological replicate datasets of our hPSC-derived prefrontal (PFC) and occipital (OCC) differentiation compared with neural stem cells (NSCs). We find that the top genes associated with PFC identity correlate well with in vivo PFC using the Allen Developmental Transcriptome data. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE147091 Reversal of pre-existing NGFR-driven tumor and immune therapy resistance
Contributors : Julia Boshuizen ; Oscar Krijgsman ; Daniel S PeeperSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensIn spite of the remarkable clinical benefit from immune checkpoint blockade in melanoma, both intrinsic and acquired resistance prevent durable clinical responses in many patients. Whereas melanomas are known to acquire MART-1 T cell resistance by reversible phenotype switching to an NGFRhi state, less is known about mechanisms of intrinsic immune resistance. To mimic recurrent T cell attack, we chronically exposed a panel of (patient-derived) melanoma cell lines to clinic...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE147482 Human neonatal foreskin epidermis
We report transcriptomes of human neonatal foreskin epidermis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE148340 RNA-Sequencing of PEG-stressed Sesame roots in drought sensitive and tolerant genotypes
Series Type : Expression profiling by high throughput sequencingOrganism : Sesamum indicumPurpose: The goals of this study are to understand transcriptional changes in the roots of drought-tolerant and sensitive sesame genotypes using PEG (Polyethylene glycol) induced osmotic stress. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Sesamum indicum Source Type: research

GSE148359 Variability in cerebrospinal fluid microRNAs through life
CONCLUSION: Our results remark the complex differential miRNA expression profile that can be observed through life, which underlines the need for including appropriate age-matched controls when the expression of CSF miRNAs is analyzed in different pathological contexts. Then, to complete a comprehensive miRNA expression map during life, further studies analyzing a more accurate range of ages are needed. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE152766 Single-cell RNA-seq data of Arabidopsis root
We report both raw and processed scRNA-seq data that are used to build transcriptomic atlas of Arabidopsis root. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Third-party reanalysis Arabidopsis thaliana Source Type: research

GSE153434 Exaggerated autophagy as molecular characterization of Stanford type A aortic dissection: A transcriptome analysis of human ascending aortic tissues
Conclusions: We identified exaggerated autophagy as a molecular biomarker for aortic dissection. We also predicted 10 hub genes and an HIF1A-ATG3 axis which could provide new insights in understanding aortic dissection. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE153450 The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos [Hi-C]
Contributors : Feifei Li ; Danyang Wang ; Ruigao Song ; Chunwei Cao ; Zhihua Zhang ; Yu Wang ; Xiaoli Li ; Jiaojiao Huang ; Qiang Liu ; Naipeng Hou ; Bingxiang Xu ; Xiao Li ; Xiaomeng Gao ; Yan Jia ; Jianguo Zhao ; Yanfang WangSeries Type : OtherOrganism : Sus scrofaPigs are important animals for agricultural and biomedical research, and its assisted reproductive technologies are urgently needed to be improved. Determining the underlying mechanism of epigenetic reprogramming in the early stage of preimplantation embryos derived from in vitro fertilization (IVF), parthenogenesis (PA) and androgenesis (AG), will not only con...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Other Sus scrofa Source Type: research

GSE153451 The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos [ChIP-seq]
Contributors : Feifei Li ; Danyang Wang ; Ruigao Song ; Chunwei Cao ; Zhihua Zhang ; Yu Wang ; Xiaoli Li ; Jiaojiao Huang ; Qiang Liu ; Naipeng Hou ; Bingxiang Xu ; Xiao Li ; Xiaomeng Gao ; Yan Jia ; Jianguo Zhao ; Yanfang WangSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Sus scrofaPigs are important animals for agricultural and biomedical research, and its assisted reproductive technologies are urgently needed to be improved. Determining the underlying mechanism of epigenetic reprogramming in the early stage of preimplantation embryos derived from in vitro fertilization (IVF), pa...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Sus scrofa Source Type: research

GSE153452 The asynchronous establishment of chromatin 3D architecture between in vitro fertilized and uniparental preimplantation pig embryos
Series Type : Other ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Sus scrofaThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Other Genome binding/occupancy profiling by high throughput sequencing Sus scrofa Source Type: research

GSE153604 Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes in fetal and 2 weeks old rat islets
Contributors : Yu-Chin Lien ; Rebecca A Simmons ; Kyoung-Jae WonSeries Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusUnlike adult β-cells, fetal and neonatal islets are functional immature and have blunted glucose responsiveness and decreased insulin secretion in response to stimuli. Pancreatic islets are a mixture of different cell types. Study of transcriptomes from intact islets would identify novel molecular mechanisms co ntrolling islet functional development. At e19 and 2 weeks of age, pancreatic islets were isolated and total RNA were extracted for RNA-Seq study. Gene expr...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Rattus norvegicus Source Type: research

GSE153605 Using next-generation sequencing to measure the histone protein H2B and monoubiquitinated H2B (H2Bub) in single yeast cells
Contributors : Yandong Zhang ; Changho Sohn ; Seoyeon Lee ; Long CaiSeries Type : OtherOrganism : Saccharomyces cerevisiaewe report a novel strategy to detect targeted protein and its PTM isoforms in single cells. We barcode the proteins from single cells by tagging them with oligonucleotides, pool barcoded cells together, run bulk gel electrophoresis to separate protein and its PTM isoform and quantify their abundances by sequencing the oligonucleotides associated with each protein species. We used this strategy to measure histone protein H2B and its monoubiquitination isoform, H2Bub, in single yeast cells. Our results re...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Other Saccharomyces cerevisiae Source Type: research

GSE153606 Decidual glycodelin-A polarizes human monocytes into a decidual macrophage-like phenotype through Siglec-7
Contributor : Philip C ChiuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensGdA induces the differentiation of human monocytes into dM-like phenotypes in terms of transcriptome (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE153608 Dog_CGH_Array on 54 breed and village dogs and one wolf
Contributors : Jeff Kidd ; Amanda PendletonSeries Type : Genome variation profiling by arrayOrganism : Canis lupus ; Canis lupus familiarisComprehensive view of structural variation across dog genomes including mobile elements and nuclear mitochondrial insertions (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Genome variation profiling by array Canis lupus Canis lupus familiaris Source Type: research

GSE153617 Expression data from TCQA-treated hAECs
Series Type : Expression profiling by arrayOrganism : Homo sapiensGene expression profiling reveals a potential role of TCQA in neuronal and pigment cell differentiation of hAECs.hAECs were isolated from discarded term placenta and were treated with 20 μM TCQA for seven days. Microarray gene expression profiling was conducted for biological replicates of TCQA-treated (T7) and untreated control cells on day 0 (D0) and day 7 (D7). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE153626 Transcriptomic profiling of normal plasma cells and MM models using bulk RNA-Seq
Contributors : Adhithi Rajagopalan ; Zhi Wen ; Robert Burns ; Jing ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusNRAS Q61 mutations are prevalent in advanced/relapsed multiple myeloma (MM) and correlate with poor patient outcomes. Thus, we generated a novel MM model by conditionally activating expression of endogenous NrasQ61R and a MYC transgene in germinal center B cells (VQ mice). VQ mice developed a highly malignant MM characterized by high proliferation index, hyperactivation of ERK and AKT signaling, impaired hematopoiesis, widespread extramedullary disease, bone lesions,...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE153627 Single-cell RNAseq of VQ myeloma cells reveals unique transcriptional signatures from normal plasma cells
Contributors : Adhithi Rajagopalan ; Zhi Wen ; Robert Burns ; Jing ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusNRAS Q61 mutations are prevalent in advanced/relapsed multiple myeloma (MM) and correlate with poor patient outcomes. Thus, we generated a novel MM model by conditionally activating expression of endogenous NrasQ61R and a MYC transgene in germinal center B cells (VQ mice). VQ mice developed a highly malignant MM characterized by high proliferation index, hyperactivation of ERK and AKT signaling, impaired hematopoiesis, widespread extramedullary disease, bone lesions,...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE153628 Expression of NrasQ61R and MYC transgene in germinal center B cells induces a highly malignant multiple myeloma in mice
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 - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE153636 DNA methylation variations in familial female and male breast cancer
Contributors : Edoardo Abeni ; Ilaria Grossi ; Eleonora Marchina ; Arianna Coniglio ; Fabio Facchetti ; Pietro Cavalli ; Fausto Zorzi ; Pier Luigi Chiodera ; Carlo Terenzio Paties ; Maria Luisa Crosatti ; Giuseppina De Petro ; Alessandro SalviSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensAbout 25% of familial breast cancer (BC) is attributed to germline mutations of BRCA1 and BRCA2 genes while the rest of patients are included in the BRCAX group. BC also affects men with a worldwide incidence of 1%. The epigenetic alterations, including those DNA methylation, have been rarely studied in t...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE153638 RNA-seq analysis of rat neurons treated with shRNA-mediated Trank1 knockdown
In this study, we performed RAN-seq analysis of cultured rat neurons treated with shRNA knockdown of Trank1. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Rattus norvegicus Source Type: research

GSE153652 Antihistamine Drug Ebastine inhibits cancer growth by targeting Polycomb Group Protein EZH2
Contributors : Killia Y Liu ; Guangyu Wang ; Qi Cao ; Kaifu ChenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensAntihistamine Drug Ebastine inhibits cancer growth by targeting Polycomb Group Protein EZH2 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE153662 Next Generation Sequencing of Wild Type and Zeb1-/- CLP
Contributors : Alhomidi Almotiri ; Hamed Alzahrani ; Peter Giles ; Neil RodriguesSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusZeb1, a zinc finger E-box binding homeobox epithelial-mesenchymal (EMT) transcription factor, confers properties of ‘stemness’, such as self-renewal, in cancer. Yet little is known about the function of Zeb1 in adult stem cells. Here, we used the hematopoietic system, as a well-established paradigm of stem cell biology, to evaluate Zeb1 mediated regulation of adult stem cells. We employed a conditional geneti c approach using the Mx1-Cre system t...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE153663 Next Generation Sequencing of Wild Type and Zeb1-/- HSCs
Contributors : Alhomidi Almotiri ; Hamed Alzahrani ; Peter Giles ; Neil RodriguesSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusZeb1, a zinc finger E-box binding homeobox epithelial-mesenchymal (EMT) transcription factor, confers properties of ‘stemness’, such as self-renewal, in cancer. Yet little is known about the function of Zeb1 in adult stem cells. Here, we used the hematopoietic system, as a well-established paradigm of stem cell biology, to evaluate Zeb1 mediated regulation of adult stem cells. We employed a conditional geneti c approach using the Mx1-Cre system t...
Source: GEO: Gene Expression Omnibus - July 2, 2020 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research