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GSE110993 RNA-seq identifies circulating miR-125a-5p, miR-125b-5p and miR-143-3p as potential biomarkers for acute ischemic stroke
Conclusions: A set of circulating miRNAs (miR-125a-5p, miR-125b-5p, miR-143-3p) associates with acute IS and might have clinical utility as an early diagnostic marker. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE54916 Cell resilience to folate deprivation boosts aberration tolerance [Illumina]
Contributors : Inmaculada Rapado ; Santiago Barrio ; Ana Rivero ; Florinda Gilsanz ; Joaquin Martinez-LopezSeries Type : SNP genotyping by SNP array ; Genome variation profiling by SNP arrayOrganism : Homo sapiensWe detected numerous copy number aberrations in SNP arrays from follicular lymphoma patients. Additionally, we found an outstanding homozygous state involving folic acid-related genes. To study a hypothetical association between both traits, we cultured folate-depleted cell lines. After restoring normal medium to the cultures, we performed CGH arrays to examine the induced copy number aberrations. (Source: GEO: Ge...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: SNP genotyping by SNP array Genome variation profiling by SNP array Homo sapiens Source Type: research

GSE54919 Cell resilience to folate deprivation boosts aberration tolerance [Agilent]
Contributors : Inmaculada Rapado ; Santiago Barrio ; Ana Rivero ; Florinda Gilsanz ; Joaquin Martinez-LopezSeries Type : Genome variation profiling by genome tiling arrayOrganism : Homo sapiensWe detected numerous copy number aberrations in SNP arrays from follicular lymphoma patients. Additionally, we found an outstanding homozygous state involving folic acid-related genes. To study a hypothetical association between both traits, we cultured folate-depleted cell lines. After restoring normal medium to the cultures, we performed CGH arrays to examine the induced copy number aberrations. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by genome tiling array Homo sapiens Source Type: research

GSE54920 Cell resilience to folate deprivation boosts aberration tolerance
Series Type : SNP genotyping by SNP array ; Genome variation profiling by SNP array ; Genome variation profiling by genome tiling arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: SNP genotyping by SNP array Genome variation profiling by SNP array Genome variation profiling by genome tiling array Homo sapiens Source Type: research

GSE66467 Genome-wide transcriptome analysis during dehydration and recovery in gametophores of Physcomitrella patens
Contributor : Lihong XiaoSeries Type : Expression profiling by high throughput sequencingOrganism : Physcomitrella patensGene transcript abundances were analyzed with samples taken from hydrated (HD), moderate dehydration (MDH), desiccated (SDH), partially recovered (PRE) and fully recovered (FRE) gametophores of P. patens by using RNA-Seq. Totally, 14686 transcripts were identified as differentially expressed transcripts.The results provided insight for exploring the mechanisms of desiccation tolerance and their evolution. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Physcomitrella patens Source Type: research

GSE66474 Genome-wide transcriptome analysis during dehydration in leaf tissues of Boea hygrometrica (10%, 50% and 100%)
Contributor : Lihong XiaoSeries Type : Expression profiling by high throughput sequencingOrganism : Dorcoceras hygrometricumGene transcript abundances were analyzed with samples taken from desiccated (10% RWC), rehydrated to 50% RWC (RE50% RWC) and rehydrated to 100% RWC (RE100% RWC) leaf tissues of resurrection plant species B. hygrometrica by using RNA-Seq. Totally, 10207 genes were identified as differentially expressed genes.The results provided insight for exploring the mechanisms of desiccation tolerance. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Dorcoceras hygrometricum Source Type: research

GSE66485 Genome-wide DNA methylation maps during rehydration in gametophores of Physcomitrella patens.
Contributor : Lihong XiaoSeries Type : Methylation profiling by high throughput sequencingOrganism : Physcomitrella patensTo examine the P. patens genome-wide methylation landscape and assess its functional significance during dehydration, we generated the first single-base resolution genome methylation maps for P. patens gametophores of hydrated (HD), moderate dehydrated (MDH), severe dehydrated (SDH), partially recovered (PRE) and fully recovered (FRE). The overall density of methyl-cytosine was not broadly altered by dehydration and recovery. There is, however, a small increase in intensity both for the whole genome and...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Physcomitrella patens Source Type: research

GSE66589 Genome-wide small RNAtranscriptome analysis during dehydration and recovery in gametophores of Physcomitrella patens
Contributor : Lihong XiaoSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Physcomitrella patensSmall RNA transcript abundances were analyzed with samples taken from hydrated (HD), moderate dehydration (MDH), desiccated (SDH), partially recovered (PRE) and fully recovered (FRE) gametophores of P. patens by using next generation sequencing. Totally, 147 microRNAs were identified as differentially expressed miRNAs.The results provided insight for exploring the mechanisms of desiccation tolerance and their evolution. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Physcomitrella patens Source Type: research

GSE67170 The signature of liver cancer in host peripheral blood mononuclear cells and T cells DNA methylation
Contributors : Yonghong Zhang ; Sophie Petropoulos ; Liu Jinhua ; Sergiy Dymov ; Ning Li ; Moshe SzyfSeries Type : Methylation profiling by arrayOrganism : Homo sapiensWe demonstrate the feasibility of developing noninvasive DNA methylation biomarkers of early stages of HCC in the host T cells. These data are consistent with involvement of epigenetic modulation of the immune system in HCC. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by array Homo sapiens Source Type: research

GSE74205 microRNA data in cardiomyocytes isolated from rat at 1 versus 10 day of age
This study was to identify microRNAs responsible for postnatal cardiomyocyte proliferation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Rattus norvegicus Source Type: research

GSE77096 Genome wide DNA methylation analysis of C3(1) SV40TAg mouse model of breast cancer
Contributors : Katharina Heilmann ; Clarissa Gerh äuser ; Christoph PlassSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusGenome-wide screen for aberrant DNA methylation in mammary gland tumors of the C3(1) Sv40Tag mouse model of breast cancer in comparison with wildtype mammary glands. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE77143 Foxc1 ablated mice are anhidrotic and recapitulate features of human miliaria sweat retention disorder
Contributors : Changyi Cui ; Piao YulanSeries Type : Expression profiling by arrayOrganism : Mus musculusSweat glands are critical for thermoregulation. The single tubular structure of sweat glands has a lower secretory portion and an upper reabsorptive duct leading to the secretory pore in the skin. Genes that determine sweat gland structure and function are largely unidentified. Here we report that a Fox family transcription factor, Foxc1, is obligate for appreciable sweat duct activity in mice. When Foxc1 was specifically ablated in skin, sweat glands appeared mature, but the mice were severely hypohidrotic. Morphologic...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE77355 mRNA expression profile in Al2O3 nanoparticle treated A549 cells
Contributors : Xiaobo Li ; Rui ChenSeries Type : Expression profiling by arrayOrganism : Homo sapiensWe evaluated the profile of mRNA expression in control and 100 μg/ml Al2O3 nanoparticle treated A549 cells using the Arraystar Human LncRNA Array v3.0 array,7th generation. Our findings implicates that dysregulation of cell death and cell cycle invovled mRNAs may play important role in cytotoxicity of Al2O3 nanoparticles. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE78050 ESRRG gene expression profile in gastric cancer cells
Contributors : Myoung-Hee Kang ; Yun-Yong ParkSeries Type : Expression profiling by arrayOrganism : Homo sapiensESRRG is one of nuclear receptor super family. ESRRG contributes to many physiological pathway. Especially, ESRRG is clearly involved in various cancers. To identify the downstream target of ESRRG in gastric cancer, we carried out microarray. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE78789 Human NPY/AgRP hypothalamic cell lines for study of obesity susceptibility
Contributors : Li Yao ; Yuanhang Liu ; Iriscilla Ayala ; Zhifang Qiu ; Sateesh Kumar ; Joanne E Curran ; Yidong Chen ; Donna M LehmanSeries Type : Expression profiling by arrayOrganism : Homo sapiensRecent data suggests that common genetic risk for metabolic disorders such as obesity may be human-specific and exert effects through the central nervous system. To overcome the limitation of human tissue access for study, we have generated induced human pluripotent stem cell (hiPSC)- derived neuronal cultures which recapture many features of hypothalamic neurons within the arcuate nucleus. Here we have comprehensively characte...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE78812 Human NPY/AgRP hypothalamic cell lines for study of obesity susceptibility (miRNA-Seq)
Contributors : Li Yao ; Yuanhang Liu ; Iriscilla Ayala ; Zhifang Qiu ; Sateesh Kumar ; Joanne E Curran ; Yidong Chen ; Donna M LehmanSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensRecent data suggests that common genetic risk for metabolic disorders such as obesity may be human-specific and exert effects through the central nervous system. To overcome the limitation of human tissue access for study, we have generated induced human pluripotent stem cell (hiPSC)- derived neuronal cultures which recapture many features of hypothalamic neurons within the arcuate nucleus. Here we have...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE80033 Somatic PRDM2 c.4459delA mutations in colorectal cancers control histone methylation and tumor growth
Contributors : Tatjana Pandzic ; Tobias Sj öblomSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPurpose: To identify the contribution of PRDM2 c.4459delA mutation to colorectal tumorigenesisMethods: We employed rAAV-mediated genome editing to correct somatic PRDM2 c.4459delA mutation in homozygously mutated cell line. Using next-generation sequencing we have compared transcriptional profile of parental and PRDM2-corrected cells.Results: RNA-seq profiling revealed that several hallmark cancer gene sets are affected by PRDM2 c.4459delA (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE85213 Astrocyte-specific deletion of SOX2 promotes recovery after traumatic brain injury
Contributors : Smith Derek K. ; Chen Chunhai ; Yang Jianjing ; Zhang Chun-LiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusInjury to the adult brain induces activation of resident astrocytes, which serves as a compensatory response modulating tissue damage and recovery. However, the mechanism governing astrocyte activation and the role of reactive astrocytes remain largely unknown. Here we show that SOX2, a transcription factor critical for stem cells and brain development, is also required for injury-induced activation of adult cortical astrocytes. Genome-wide ChIP-seq...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE85221 Developmental Exposure to 2,2 ’,4, 4’ –Tetrabromodiphenyl Ether Induces Long-Lasting Changes in Liver Metabolism in Male Mice
In this study pregnant CD-1 mice were exposed to 0.2 mg/kg 2,2 ’,4,4’-tetrabromodiphenyl ether (BDE-47) from gestation day 8 till postnatal day 21 and liver RNA-seq was performed on the last day of dam exposure and on postnatal week 20 in male offspring. Several groups of metabolic genes, including ribosomal and mitochondrial genes were significantly upreg ulated at both time-points. Genes regulated via mechanistic target of rapamycin (mTOR pathway), the gatekeeper of metabolic homeostasis, were whether up- or down- regulated at both time-points. Thus, perinatal exposure to environmentally relevant doses of BDE...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE87643 O antigen acts as a shield to delay early plant immune recognition of the pathogenic bacterium, Xylella fastidiosa
In this study, we demonstrate that the xylem-limited bacterium, Xylella fastidiosa, which lacks a T3SS, utilizes an alternative strategy to delay elicitation of innate immune responses. By decorating its LPS PAMP molecule with a high molecular weight O antigen, this bacterium physically masks itself from early recognition by the grapevine innate immune system. We have elucidated the chemical structure of the O antigen and found that it is primarily an α1,2-linked rhamnan polymer. X. fastidiosa cells lacking O antigen elicited hallmarks of PTI such as ROS production, specifically in the plant xylem tissue compartment,...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Vitis vinifera Source Type: research

GSE93229 RET Ligands Mediate Endocrine Sensitivity via a Bi-stable Feedback Loop with ER α
Contributor : Charles G DankoSeries Type : OtherOrganism : Homo sapiensThe molecular mechanisms of endocrine resistance in breast cancer remain poorly understood. Here we used PRO-seq to map the location of hundreds of genes and thousands of distal enhancers whose activities differ between endocrine sensitive and resistant MCF-7 cells. Our genome-wide screen identified a 16-fold transcriptional increase in glial-cell line derived neurotrophic factor (GDNF), a RET tyrosine kinase receptor ligand, which is both necessary and sufficient for resistance in MCF-7 cells. GDNF causes endocrine resistance by switching the active st...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE94958 Identification of the RB loss-induced E2F1 cistrome in prostate cancer [ChIP-seq]
Contributors : Karen E Knudsen ; Christopher McNairSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThe retinoblastoma protein (RB) is preferentially lost in the progression to castrate resistant prostate cancer (CRPC). However, the alterations associated with such loss have been scantly described. The current study aims to provide molecular mechanisms underlying Rb loss-driven CRPC phenotypes. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE94959 Identification of the RB loss-induced transcriptome and E2F1 cistrome in prostate cancer
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 - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE95243 Transcriptomes of iPSC-derived and post-mortum Hypothalamus Neurons from obese and control donors
Contributors : Dhruv Sareen ; Uthra RajamaniSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe sequenced the transcriptomes of seven samples of hypothalamic neurons dervied from pluripotent stem cells taken from healthy patients; five samples of hypothalamic neurons derived from pluripotent stem cells of constitutionally obese donors; five samples of sectioned hypothalami from post-mortem dissection of brains, and two samples for motor neurons derived from pluripotent stem cells of healthy donors in order to assess the similarity of our iPSC-derived cells against those of sectioned br...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE95369 RNA sequencing of prostate cancers reveal insights on the prognostic significance of visibility on multi-parametric MRI
Contributors : Hyung L Kim ; Sungyong YouSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensNot all prostate cancers are visible on multiparametric MRI. The biologic basis and clinical implication of MRI visibility are unknown. We sought to identify genes associated with prognosis and MRI visibility. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE95460 DNA methylation signature defines genes modulated by stromal cell contents of human breast tumors [MethylationEPIC]
Contributors : Pauline Mathot ; M élodie Grandin ; Guillaume Devailly ; Frédérique Souaze ; Vincent Cahais ; Sebastian Moran ; Mario Campone ; Zdenko Herceg ; Manel Esteller ; Philippe Juin ; Patrick Mehlen ; Robert DanteSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensUsing genome-wide approaches we have identified groups of genes modulated by CAF-secreted factors from human breast cancer cell lines grown in different CAF-conditioned medium. The genes modulated by CAF secreted factors were characterized by a specific DNA methylation pattern: hypermethylation at transcri...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE95461 DNA methylation signature defines genes modulated by stromal cell contents of human breast tumors [RNA-seq]
Contributors : Pauline Mathot ; M élodie Grandin ; Guillaume Devailly ; Frédérique Souaze ; Vincent Cahais ; Sebastian Moran ; Mario Campone ; Zdenko Herceg ; Manel Esteller ; Philippe Juin ; Patrick Mehlen ; Robert DanteSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensUsing genome-wide approaches, we have identified groups of genes modulated by CAF-secreted factors from human breast cancer cell lines grown in different CAF-conditioned medium. The genes modulated by CAF secreted factors were characterized by a specific DNA methylation pattern: hypermethylation at t...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE95462 DNA methylation signature defines genes modulated by stromal cell contents of human breast tumors
Series Type : Methylation profiling by genome tiling array ; 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 - February 22, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE95771 AG221 and Ruxolitinib Treatment Effects on LSKs in IDH2-R140Q JAK2-V617F Transplant Recipients
Contributors : Anna S McKenney ; Barbara Spitzer ; Ross L LevineSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTransplant recipients of IDH2-R140Q JAK2-V617F expressing bone marrow were treated with AG221 and ruxolitinib monotherapy, combined therapy, or vehicle. LSKs were sorted from terminal samples and sequenced with three WT controls. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE96641 Genome-wide Screen for Differentially Methylated Long Noncoding RNAs identifies Esrp2 and lncRNA Esrp2-as Regulated by Enhancer DNA Methylation with Prognostic Relevance for Human Breast Cancer
Contributors : Katharina Heilmann ; Reka Toth ; Caroline Bossmann ; Karin Klimo ; Christoph Plass ; Clarissa Gerh äuserSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe majority of long noncoding RNAs (lncRNAs) is still poorly characterized with respect to function, interactions with protein-coding genes, and mechanisms that regulate their expression. As for protein-coding RNAs, epigenetic deregulation of lncRNA expression by alterations in DNA methylation might contribute to carcinogenesis. To provide genome-wide information on lncRNAs aberrantly methylated in breast cancer we...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE97015 The Evolutionarily Conserved AU-Dinucleotide at the 5 ’ End of U1 snRNA is Critical for the Biogenesis and Functionality of U1 snRNP
Contributor : Jeffrey A PleissSeries Type : Expression profiling by arrayOrganism : Saccharomyces cerevisiaeSplicing is initiated by a productive interaction of pre-mRNA and the U1 snRNP, which dictates the formation a short RNA duplex between the 5 ’ splice site of a pre-mRNA and the 5’ end of the U1 snRNA. A long-standing puzzle has been why the AU dincucleotide at the 5’-end of the U1 snRNA shows strict conservation, despite the absence of an apparent role in duplex formation. To explore this conundrum, we varied this AU dinucleotide into to all possible permutations and analyzed the resulting molecula...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Saccharomyces cerevisiae Source Type: research

GSE97767 Transcriptome analysis of secreted proteins responding to nutrient-selection pressure
Contributors : Runmao Lin ; Baoming Shen ; Feifei Qin ; Xinyue Cheng ; Bingyan XieSeries Type : Expression profiling by high throughput sequencingOrganism : Pochonia chlamydosporiaTo determine secreted proteins that involved in adaptation of nutrient sources and response to nutrient stresses, we analyzed transcriptomes of Pochonia chlamydosporia strain 170 under three different nutrient conditions, CD (nutrient rich medium) that was predicted to repress parasitism, MM (nutrient-poor liquid minimal medium) that was predicted de-repress genes associated with parasitism, and MM-eggs(minimal medium with root-knot nematode eggs...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Pochonia chlamydosporia Source Type: research

GSE98230 RNA-Seq of treatment response of platinum sensitive and platinum resistant ovarian cancer cells
Contributors : Sarah Schott ; Pauline Wimberger ; Barbara Klink ; Konrad Gr ützmann ; Julian Puppe ; Ulrike S Wauer ; Daniel Klotz ; Evelin Schröck ; Jan D KuhlmannSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensResistance to platinum-based chemotherapy is a clinical challenge in the treatment of ovarian cancer (OC) and limits survival. Therefore, innovative drugs against platinum-resistance are urgently needed. Our therapeutic concept is based on the conjugation of two chemotherapeutic compounds to a monotherapeutic pro-drug, which is taken up by cancer cells and cleaved in...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE98266 TFEB target in epithelial cells during DSS colitis
Contributors : Tatsuro Murano ; Kara Lassen ; Ramnik J Xavier ; Javier IrazoquiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTFEB in IEC has a protective role in DSS colitis. The goal is to examine what genes/pathways are TFEB target during DSS colitis (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE98427 STAT3-initiated epigenetic activation during T helper 17 (Th17) cell differentiation is mediated by Tripartite motif containing 28
Contributors : Yu Jiang ; Huiping Lu ; Ying Liu ; Shao-cong Sun ; Wei Jin ; Xiaohu Wang ; Chen DongSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusEpigenetic regulation is important for T cell fate decision. Although STAT3 is known to initiate Th17 differentiation program, the downstream mechanism is unclear. Here we show that tripartite motif containing 28 (TRIM28) expression in Th17 cells was required for cytokine production and autoimmune diseases. Genome-wide occupancy analysis revealed that TRIM28-bound regions co...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE98639 CD300E is activated by Helicobacter pylori macrophages infection
Contributors : Matteo Pagliari ; Fabio Munari ; Silvia Lonardi ; Francesco Chemello ; Gaia Codolo ; Caterina Millino ; Beniamina Pacchioni ; William Vermi ; Matteo Fassan ; Marina de Bernard ; Stefano CagninSeries Type : Expression profiling by arrayOrganism : Homo sapiensMacrophages are important cells involved in infections responses. They are mediators of gastritis in acute Helicobacter pylori (Hp) infection. After macrophages infection with Hp one of the most up-regulated protein is CD300E. To identify effects of CD300E activation in macrophages an agonistic antibody was used to activate CD300E and effects on gene expr...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE98641 The expression of miRNAs is influenced by the infection of Helicobacter Pylori
Contributors : Matteo Pagliari ; Fabio Munari ; Silvia Lonardi ; Francesco Chemello ; Gaia Codolo ; Caterina Millino ; Beniamina Pacchioni ; William Vermi ; Matteo Fassan ; Marina de Bernard ; Stefano CagninSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensMacrophages are important cells involved in infections responses. They are mediators of gastritis in acute Helicobacter pylori (Hp) Infection and to identify how Hp affects macrophages response to infection we measured miRNA expression after macrophages Hp infection. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE98888 Underestimation of inadvertent morpholino RNA targets: evidence from the study of Danio rerio Ser/Arg-rich splicing factors using gene editing tools
Contributors : Marine Joris ; Patrick Motte ; Marc MullerSeries Type : Expression profiling by high throughput sequencingOrganism : Danio rerioWe used morpholinos and gene editing tools to inactivate the srsf5a gene. In contrast to srsf5a homozygous mutants that did not display any phenotypic traits, microinjection of sMOsrsf5a led to developmental defects. By using RNA sequencing on morphants and control embryos we were able to identify a plethora of morpholino inadvertant target. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Danio rerio Source Type: research

GSE99422 KH-type splicing regulatory protein (KHSRP) is involved in esophageal squamous cell carcinoma progression through regulating a subset of microRNAs [mRNA]
Contributors : Yuji Fujita ; Kiyoshi Masuda ; Issei ImotoSeries Type : Expression profiling by arrayOrganism : Homo sapiensKH-type splicing regulatory protein (KHSRP) is a multifunctional RNA-binding protein (RBP), which is involved in many post-transcriptional aspects of RNA metabolism including microRNA (miRNA) biogenesis, affects distinct cell functions in different tissues and can impact on various pathological conditions. However, the function and underlying mechanisms of KHSRP in esophageal squamous cell carcinoma (ESCC) remain largely unknown. In the present study, we uncover a novel oncogenic function of KHSRP in e...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE99423 KH-type splicing regulatory protein (KHSRP) is involved in esophageal squamous cell carcinoma progression through regulating a subset of microRNAs [miRNA]
Contributors : Yuji Fujita ; Kiyoshi Masuda ; Issei ImotoSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensKH-type splicing regulatory protein (KHSRP) is a multifunctional RNA-binding protein (RBP), which is involved in many post-transcriptional aspects of RNA metabolism including microRNA (miRNA) biogenesis, affects distinct cell functions in different tissues and can impact on various pathological conditions. However, the function and underlying mechanisms of KHSRP in esophageal squamous cell carcinoma (ESCC) remain largely unknown. In the present study, we uncover a novel oncogenic function of KHSRP ...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE99424 KH-type splicing regulatory protein (KHSRP) is involved in esophageal squamous cell carcinoma progression through regulating a subset of microRNAs
Series Type : Expression profiling by array ; Non-coding RNA profiling by arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE99985 RNA-seq reveals abundant circRNA, lncRNA and mRNA in blood exosomes of patients with coronary heart disease
Contributor : Yuan TangSeries Type : Non-coding RNA profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiensExosomes are small membrane vesicles of endocytic origin secreted by most cells, and contain a wealthy cargo of protein and RNA species that can modulate recipient cells ’ behaviors and may be used as biomarkers for diagnosis of human diseases. They have been found in blood and are valuable sources for biomarkers due to selective cargo loading and resemblance to their parental cells. The goal of this study is to identify circRNA, lncRNA and mRNA profile...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE100063 RNA-seq reveals abundant circRNA, lncRNA and mRNA in blood exosomes of patients with colorectal carcinoma
Contributors : Jiang Zhao ; Ye XuSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensExosomes are small membrane vesicles of endocytic origin secreted by most cells, and contain a wealthy cargo of protein and RNA species that can modulate recipient cells ’ behaviors and may be used as biomarkers for diagnosis of human diseases. They have been found in blood and are valuable sources for biomarkers due to selective cargo loading and resemblance to their parental cells. The goal of this study is to identify circRNA, lncRNA and mR...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE100207 RNA-seq reveals abundant circRNA, lncRNA and mRNA in blood exosomes of patients with hepatocellular carcinoma
Contributor : Lu WangSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensExosomes are small membrane vesicles of endocytic origin secreted by most cells, and contain a wealthy cargo of protein and RNA species that can modulate recipient cells ’ behaviors and may be used as biomarkers for diagnosis of human diseases. They have been found in blood and are valuable sources for biomarkers due to selective cargo loading and resemblance to their parental cells. The goal of this study is to identify circRNA, lncRNA and mRNA profiles ...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE100232 RNA-seq reveals abundant circRNA, lncRNA and mRNA in blood exosomes of patients with pancreatic carcinoma
Contributors : Shulin Yu ; Peng WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensExosomes are small membrane vesicles of endocytic origin secreted by most cells, and contain a wealthy cargo of protein and RNA species that can modulate recipient cells ’ behaviors and may be used as biomarkers for diagnosis of human diseases. They have been found in blood and are valuable sources for biomarkers due to selective cargo loading and resemblance to their parental cells. The goal of this study is to identify circRNA, lncRNA and mRNA profiles in human blood by high-throughput RNA sequ...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE100882 SAMHD1 is recurrently mutated in T-cell prolymphocytic leukemia [RNA-seq]
Contributors : Ludger Klein-Hitpass ; Patricia JohanssonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe identified novel recurrent genetic lesions in T-PLL affecting genes involved in JAK/STAT signaling (PTPRC), epigenetic regulation (PRDM2), or DNA damage repair (SAMHD1, PARP10, HERC1, HERC2). Mutations of the tumor suppressor gene SAMHD1 causing amino-acid exchanges or protein truncations as well as copy number variations in SAMHD1 were seen in 20% of cases. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE102264 Electrochemically active bacteria sense electrode potentials for regulating catabolic pathways
Contributors : Atsushi Kouzuma ; Atsumi Hirose ; Kazuya WatanabeSeries Type : Expression profiling by arrayOrganism : Shewanella oneidensis ; Shewanella oneidensis MR-1Electrochemically active bacteria (EAB) receive considerable attention for their utility in bioelectrochemical processes. Although electrode potentials are known to affect the metabolic activity of EAB, it is unclear whether EAB are able to sense and respond to electrode potentials. Here, we show that, in the presence of a high-potential electrode, a model EAB Shewanella oneidensis MR-1 can utilize NADH-dependent catabolic pathways and a background formate-d...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Shewanella oneidensis Shewanella oneidensis MR-1 Source Type: research

GSE102873 Genome-wide transcriptome analysis of NIPBL iPSC and commited cardiomyoctes
Conclusion: Our data is the represents the first human developmental model for studying CdLS through pluripotent stem cells and lineage commited subtypes (cardiomyocytes). This data highlights NIPBLs role in regulating transcriptional regulation and has significant consequences on DNA nucleosome involvement as it relates to global gene expression. This work provides preliminary evidence that NIPBL is required for normal epigenetic and DNA landscape establishment during embryonic cardiomyocyte generation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE102895 Modulation of human dendritic cell (DC) activity by Ascaris suum
Contributor : Andrew R WilliamsSeries Type : Expression profiling by arrayOrganism : Homo sapiensThe hypothesis was that A. suum downregulates LPS-induced inflammatory pathways in human DCs (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE103666 Human primary macrophages derived in vitro from circulating monocytes comprise adherent and non-adherent subsets with differential expression of Siglec-1 and CD4 and permissiveness to HIV-1 infection
This study highlights the interplay of macrophage heterogeneity in HIV-1 pathogenesis. We show that monocyte-derived macrophages (MDM) could be divided into two distinct subsets: CD14+Siglec-1hiCD4+ (non-adherent MDM), and CD14+Siglec-1LoCD4- (adherent MDM). The CD14+Siglec-1hiCD4+MDM subset represented the smaller proportion in the macrophage pool, and varied among different donors. Fractionation and subsequent exposure of the two MDM subsets to HIV-1 revealed opposite outcomes in terms of HIV-1 capture and infection. Although the CD14+Siglec-1hiCD4+MDM captured significantly more HIV-1, infection was significantly higher...
Source: GEO: Gene Expression Omnibus - February 22, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research