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GSE112449 Microarray analysis comparing gene expression of callus tissue extracted from either Cyp24a1-null mice or their control heterozygous littermates
Contributors : Roy P l Naja ; Ren é St-ArnaudSeries Type : Expression profiling by arrayOrganism : Mus musculusThe 24R,25-dihydroxyvitamin D metabolite (24R,25D) has long been suspected of participating to bone fracture repair. We used Cyp24a1-deficient mice, unable to produce 24R25D, to observe gene expression in callus tissue compared to that of control littermates. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE112462 CIRCULATING MICRORNAs PREDICT SURVIVAL OF PATIENTS WITH TUMORS OF GLIAL ORIGIN
Contributors : A Drusco ; C M CroceSeries Type : OtherOrganism : Homo sapiensWe analyzed serum extracellular vescicles (SEV) of 28 patients with glioma tumors and 8 normal samples by Nanostring, and validated a microRNA profile that can differentiate between and among some classes of CNS tumors. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 29, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE112466 Tumor-independent host gene expression changes induced by tyrosine kinase inhibitors
Contributors : Michalis Mastri ; John M EbosSeries Type : Expression profiling by arrayOrganism : Mus musculusTranscriptome analysis was used to identify tumor-independent changes after treatment with different tyrosine kinase inhibitors (TKIs). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE112467 Tumor-independent host gene expression changes induced by VEGFR2 antibody
Contributors : Michalis Mastri ; John M EbosSeries Type : Expression profiling by arrayOrganism : Mus musculusTranscriptome analysis was used to identify tumor-independent changes after treatment with mouse VEGFR2 neutralizing antibody. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE112468 Tumor-independent host gene expression changes induced by PD-1 pathway inhibitors
Contributors : Michalis Mastri ; John M EbosSeries Type : Expression profiling by arrayOrganism : Mus musculusTranscriptome analysis was used to identify tumor-independent changes after treatment with mouse neutralizing PD-1 or PD-L1 antibodies. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 29, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE112354 Transcriptome analysis of gene expression of PAK-AR2 and 1-9
Contributors : Jiajia You ; Hongjiang YangSeries Type : Expression profiling by high throughput sequencingOrganism : Pseudomonas aeruginosaRNAseq analysis was performed to evaluate gene expression differences between strains 1-9 and PAK-AR2.P. aeruginosa PAK-AR2 and 1-9 cells were grown to OD600 of 0.8 before harvesting. The collected cells were treated with RNAprotect Bacteria Reagent (Qiagen) and subjected to snap freezing in liquid nitrogen and delivered to BGI in dry ice for transcriptome resequencing analysis.The differentially expressed genes (DEGs) were determined between PAK-AR2 and 1-9 with the standards of false ...
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Pseudomonas aeruginosa Source Type: research

GSE63217 Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia [RNA-Seq experiments]
Contributor : Tim SomervailleSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo determine whether changes in histone modifications directly correlate with changes in transcription, THP1 AML cells were treated with a potent and selective LSD1 inhibitor (OG86) and then subjected to concomitant RNA sequencing (RNAseq) and ChIP sequencing (ChIPseq) for monomethyl-, dimethyl- and trimethyl histone H3 modifications. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE63218 Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia [ChIP-Seq: histone modifications]
Contributor : Tim SomervailleSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensTo determine whether changes in histone modifications directly correlate with changes in transcription, THP1 AML cells were treated with a potent and selective LSD1 inhibitor (OG86) and then subjected to concomitant RNA sequencing (RNAseq) and ChIP sequencing (ChIPseq) for monomethyl-, dimethyl- and trimethyl histone H3 modifications. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE63222 Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia
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 - March 27, 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

GSE90769 Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia [anti-LSD1, MYB, and GFI1 ChIP-Seq]
Contributor : Tim SomervailleSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensTo identify genomic binding regions, THP1 AML cells were subjected to ChIP sequencing (ChIPseq) using anti-LSD1, MYB or GFI1 antibodies. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE90770 Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia [ATAC-Seq]
Contributor : Tim SomervailleSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensTo identify regions of genome accessibility influenced by LSD1 inhibition, THP1 AML cells were subjected to ATAC sequencing. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE95314 Gene expression profiling in the seminal vesicles (SVs) from neonatal DES-treated mice [array]
The objective of this study is to compare gene expression profiles between the WT-veh and -DES groups or αERKO-veh and -DES from the adult male mice (week 10) of the SV tissues to identify differential genes. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE96923 Expression data from pmel1 CD8+ T cells stimulated with agonist anti-CD27, blockade of PD-1/L1 or both together
Contributor : Sarah L BuchanSeries Type : Expression profiling by arrayOrganism : Mus musculusCD8+ T cells are regulated by inhibitory and activatory receptors. We have investigated the influence of enforced CD27 stimulation compared with blockade of PD-1 and the combination of both agents together.Anti-CD27 and PD-1 blockade combined to enhance CD8+ T-cell accumulation, effector protein expression and tumor therapy. This array was used to further characterize the transcriptional changes in CD8+ T cells that drive this differentiation. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE97073 Impact of conditional uterine deletion of Esr1, Foxa2 or Foxo1 on DES-induced gene expression
Contributors : Wendy N Jefferson ; Tianyuan Wang ; Harriet Kinyamu ; Elizabeth Padilla-Banks ; Alisa Suen ; Carmen J WilliamsSeries Type : Expression profiling by arrayOrganism : Mus musculusNeonatal exposure to diethylstilbestrol (DES) results in abnormal reproductive tract morphology, female infertility and uterine cancer in mice. This exposure also causes altered gene expression in the female reproductive tract that persists into adulthood. To further explore on a genome-wide basis how neonatal estrogen exposure results in permanent epigenetic changes, we performed RNA-seq and ChIP-seq analyses of DES-treated and contro...
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE97698 Epigenetic regulation of in vivo B cell Differentiation
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 - March 27, 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

GSE99655 Host- and stage-dependent secretome of the arbuscular mycorrhizal fungus Rhizophagus irregularis
Contributors : Tian Zeng ; Erik LimpensSeries Type : Expression profiling by high throughput sequencingOrganism : Rhizophagus irregularisArbuscular mycorrhizal fungi arguably form the most successful and wide-spread endosymbiosis with plants. In general terms there is very little host-specificity in this interaction, indicating an extremely broad compatibility. However, host preferences as well as varying symbiotic efficiencies have been observed, the molecular basis of which is still largely unknown. Secreted proteins (SPs) may act as fungal effectors to control symbiotic efficiency in a host-dependent manner. Therefore, ...
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Rhizophagus irregularis Source Type: research

GSE100701 Lifelong calorie restriction and markers of colonic health in aging mice
Contributors : Dieuwertje Kok ; Fenni Rusli ; Benthe van der Lugt ; Carolien Lute ; Luca Laghi ; Stefano Salvioli ; Gianfranco Picone ; Claudio Franceschi ; Hauke Smidt ; Jacques Vervoort ; Ellen Kampman ; Michael M üller ; Wilma SteegengaSeries Type : Expression profiling by arrayOrganism : Mus musculusDiminishment of colonic health is associated with various age-related pathologies. Calorie restriction (CR) is an efficient strategy to increase healthy lifespan, although underlying mechanisms are not fully elucidated. Here we report the effects of lifelong CR on markers of colonic health in aging mice. We show that 3...
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE101622 Genome-wide association study and transcriptome analysis of the white/red earlobe color in Qingyuan Partridge chicken
Contributors : Wei Luo ; Jiguo XuSeries Type : Expression profiling by high throughput sequencingOrganism : Gallus gallusGene expression comparison between red group and white group (Red_vs_White) showed that there were 81 differentially expressed genes (DEGs) (fold changes ≥ 1.5; adjusted P-value
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Gallus gallus Source Type: research

GSE102448 Genome-wide transcriptome in the mouse seminal vesicles (SVs) and uterus (U) following neonatal DES exposure [RNA-seq]
Contributors : Yin Li ; Tianyuan WangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusDES is a synthetic estrogen that is associated with adverse effects on reproductive organs. Our group has employed estrogen receptor (ER) α knockout (αERKO) mice to gain insight into the contribution of ER a in DES-induced toxicity following neonatal exposure. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE102449 DNA methylation profiling by MBD-Seq in the mouse seminal vesicles (SVs) and uterus (U) following neonatal DES exposure
Contributors : Yin Li ; Tianyuan WangSeries Type : Methylation profiling by high throughput sequencingOrganism : Mus musculusDES is a synthetic estrogen that is associated with adverse effects on reproductive organs. Our group has employed estrogen receptor (ER) α knockout (αERKO) mice to gain insight into the contribution of ER α in DES-induced toxicity following neonatal exposure (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE102450 Gene expression and DNA methylation profiling in the seminal vesicles (SVs) from neonatal DES-treated mice
Series Type : Expression profiling by array ; Expression profiling by high throughput sequencing ; Methylation 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 - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Expression profiling by high throughput sequencing Methylation profiling by high throughput sequencing Mus musculus Source Type: research

GSE104400 ER α Dependent Alterations in the Epigenetic Landscape of the Mouse Uterus Following Neonatal Estrogen Exposure [RNA-Seq]
Contributors : Wendy N Jefferson ; H Karimi Kinyamu ; Tianyuan Wang ; Elizabeth Padilla-Banks ; Alisa A Suen ; Carmen J WilliamsSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAbstract. Very little is known regarding how hormonal exposures impact the epigenetic landscape of developing tissues in the context of a whole organism, in contrast to the impact on cultured cells. Here we took a global approach to understanding how neonatal exposure to the xenoestrogen, diethylstilbestrol (DES), alters the uterine epigenome. RNA-seq and ChIP-seq (H3K4me3, H3K27me3, H3K27ac and H3K4me1) were pe...
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE104401 ER α Dependent Alterations in the Epigenetic Landscape of the Mouse Uterus Following Neonatal Estrogen Exposure [ChIP-Seq]
Contributors : Wendy N Jefferson ; H Karimi Kinyamu ; Tianyuan Wang ; Elizabeth Padilla-Banks ; Alisa A Suen ; Carmen J WilliamsSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusAbstract. Very little is known regarding how hormonal exposures impact the epigenetic landscape of developing tissues in the context of a whole organism, in contrast to the impact on cultured cells. Here we took a global approach to understanding how neonatal exposure to the xenoestrogen, diethylstilbestrol (DES), alters the uterine epigenome. RNA-seq and ChIP-seq (H3K4me3, H3K27me3, H3K27ac and H3...
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE104402 ER α Dependent Alterations in the Epigenetic Landscape of the Mouse Uterus Following Neonatal Estrogen Exposure
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by arrayOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Expression profiling by array Mus musculus Source Type: research

GSE104661 NFAT3-regulated genes in human aortic smooth muscle cells (ASMC)
Contributors : Osamu Kaminuma ; Yasumasa Nishito ; Noriko KitamuraSeries Type : Expression profiling by arrayOrganism : Homo sapiensNFAT family transcription factors play crucial roles in immunological and other biological activities. Since we found that NFAT3 was highly expressed in ASMC, the target genes of NFAT3 in ASMC were investigated. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE105060 Total differential RNA-seq in the marine proteobacterium Vibrio harveyi
Contributors : A H Pl ágaro ; V R Kaberdin ; P PeermanSeries Type : Expression profiling by high throughput sequencingOrganism : Vibrio harveyi NBRC 15634 = ATCC 14126Objectives: determination of transcription start sites in Vibrio harveyi genome and discovery of new transcriptsMethods: we performed differential seqencing of total RNA isolated from o.n. control Vibrio harveyi cultures. Sample treatment with Terminator EXonuclease (TEX) allowed differenciation of primary and secondary transcripts, helping in the definition of transcription start sites (TSS)Results: by data-mining RNA-seq data and performing some Nort...
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Vibrio harveyi NBRC 15634 = ATCC 14126 Source Type: research

GSE107870 Expression data from human macrophages treate with miR-1246 mimic/inhibitor
Contributor : Tomer CooksSeries Type : Expression profiling by arrayOrganism : Homo sapiensMiR-1246 was found to promote tumorigenesis and metastasis in sevearl cancer types. In the context of tumor microenvironment, tumor-associated macrophages are a central part typically correlated with poor prognosis.We used microarray data to determine the gene expression profile in M2-like macrophages when treated with an overexpression of miR-1246 (conducted by miR-1246 mimic). As controls, we used either scambaled mimic control sequence, or a miR-1246 inhibitor. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE110158 Genome-wide identification of ParB binding sites in Pseudomonas aeruginosa
Contributors : Aneta A Bartosik ; Adam Kawalek ; Krzysztof Glabski ; Grazyna Jagura-BurdzySeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Pseudomonas aeruginosaParA and ParB homologs are involved in accurate chromosome segregation in bacteria. ParBs participate in proper folding and initial separation of ori domains by binding to specific parS sites (palindromic centromere-like sequences), mainly localized close to oriC. Bioinformatic analyses identified 10 parS sequences in the Pseudomonas aeruginosa PAO1 genome. One parS from the parS1-parS4 cluster is required for ParB mediated c...
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Pseudomonas aeruginosa Source Type: research

GSE110597 Placental miR-340 mediates vulnerability to activity based anorexia in mice
Contributors : Mariana Schroeder ; Alon ChenSeries Type : Non-coding RNA profiling by arrayOrganism : Mus musculusAnorexia nervosa (AN) is a devastating eating disorder characterized by self-starvation that mainly affects women. Its etiology is unknown, which impedes successful treatment options leading to a limited chance of full recovery. Here, we show that gestation is a vulnerable window that can influence the predisposition to AN. By screening placental microRNA expression of naive and prenatally stressed (PNS) fetuses and assessing vulnerability to activity-based anorexia (ABA) in early adulthood, we identify miR-340...
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Mus musculus Source Type: research

GSE112068 Study of dynamic transcriptome profiling in DNA damage-induced cellular senescence and transient cell-cycle arrest
Contributors : Zhen Zhao ; Xiaowo WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensFor studing dynamic transcriptome profiling in DNA damage-induced cellular senescence and transient cell-cycle arrest, samples were treated with the DNA-damaging agent bleomycin at 0 ug/ml, 2 ug/ml and 40 ug/ml for 2 h. High-resolution time course analysis of gene expression in DNA damage-induced cellular senescence and transient cell-cycle arrest was used to explore the transcriptomic differences between different cell fates after DNA damage response. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE112074 Inhibitors of LSD1 target demethylase-independent activity to induce differentiation in acute myeloid leukemia [anti-H3K9 ac, anti-H3K27, RCOR1, SPI1, and MLL4 ChIP-Seq]
Contributor : Tim SomervailleSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensTo determine whether changes in histone modifications directly correlate with changes in transcription, THP1 AML cells were treated with a potent and selective LSD1 inhibitor (OG86, 250nM) and then subjected to concomitant RNA sequencing (RNAseq) and ChIP sequencing (ChIPseq) for histone acetylation modifications, RCOR1, SPI1 and MLL4. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE112307 Microarray analysis of subcutaneous adipose tissue obtained in 27 moderate obese women
Contributors : Maria C Pelloux ; Karine ClementSeries Type : Expression profiling by arrayOrganism : Homo sapiensThe mechanisms responsible for weight loss-induced improvement in insulin sensitivity are partially understood. Greater insight can now be achieved through deep phenotyping and data integration. Here, we used an integrative approach to investigate associations between changes in insulin sensitivity and variations in lifestyle factors (diet and physical activity), subcutaneous adipose tissue (sAT) gene expression, metabolomics in serum, urine and feces, and gut microbiota composition after a 6-week calorie restri...
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE112326 Genome-wide maps of SMAD2-chromatin binding state in TGFbeta-treated vascular smooth muscle cells
Contributors : Pei-Yu Chen ; Lingfeng Qin ; Sharvari Gujja ; Zehua ChenSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensTo further explore the role of these two factors in SMC reprogramming, we treated human aortic smooth muscle (HASMCs) in vitro with TGF β and mapped binding of Smad2/3, which reflects TGFβ activity, and Pol2-Ser2p, which reflects transcriptional activity, by ChIP-seq analysis. Smad2/3 bound to numerous regulatory regions in the genome differentially regulating expression of numerous genes as demonstrate by alterations in Pol2-Serp 2 binding pro...
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE112343 Large differences in small RNA composition between human biofluids - 10 biofluids
This study contains samples associated with 10 different biofluids, and all data (sequencing data, full alignments, etc.) is openly available. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE112349 Expression data from heat-damaged MHCC97H treated by HGF
Contributors : Rui Zhang ; Min Ma ; Xia-Hui Lin ; Hua-Hua Liu ; Jie Chen ; Jun Chen ; Dong-Mei Gao ; Jie-Feng Cui ; Zheng-Gang Ren ; Rong-Xin ChenSeries Type : Expression profiling by arrayOrganism : Homo sapiensIncomplete heat-damaged MHCC97H ususlly recurred. The mechanism of how residual HCC cells survive sublethal heat stress and develop rapid outgrowth remains poorly understood.We used microarrays to detail the gene expression and identified distinct classes of up-regulated and downregulated genes under the treatment of HGF at different dosages. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 27, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE112292 Transcriptome profiling reveals cleft palate-related genes in Chinese sturgeon (Acipenser sinensis)
In this study, we reported cleft-palate Chinese sturgeons in artificial population for the first time. In order to explore the genetic basis of palate malformation in A. sinensis, Illumina RNA-seq technology was used to analyze the transcriptome data of normal and cleft-palate individuals in farmed Chinese sturgeons. Raw reads were obtained and assembled into 808,612 unigenes, with an average length of 509.33 bp and an N50 of 574 bp. Sequence similarity analyses against four public databases (Nr, Uniprot, KEGG and COGs) found 158,642 unigenes that can be annotated. GABAergic synapse and TGF- β signal pathway were the ...
Source: GEO: Gene Expression Omnibus - March 24, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Acipenser sinensis Source Type: research

GSE67274 Impact of Vitamine D depletion and repletion on rat skeletal muscle
Contributors : Jerome Salles ; Sandra Pesenti ; Emmanuelle MeugnierSeries Type : Expression profiling by arrayOrganism : Rattus norvegicus15 months Old Wistar Rat were submitted to 3 differents diets: control, without vitamin D and without vitamin D followed by a supplementation in vitamin D. At sacrifice, skeletal muscle were recovered, quickly frozen in liquid nitrogen. RNA profiling by microarrays was performed. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 24, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Rattus norvegicus Source Type: research

GSE96969 Genome-wide analysis identifies Nr4a1 as a key mediator of T cell tolerance
This study thus identifies Nr4a1 as a key regulator in T cell tolerance, which may be targeted in tumor immunotherapy. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 24, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE112248 AKBA regulates mRNA expression of mouse epidermis.
Contributors : Honglin Wang ; Jing BaiSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe goal of this study was to determine the effects of AKBA on mRNA expression of mouse epidermis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 24, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE112272 Development of gene expression signatures during fasting and refeeding (compensatory growth) for zebrafish liver
Contributors : Wensheng Li ; Caiyun Sun ; Jirong JiaSeries Type : Expression profiling by arrayOrganism : Danio rerioHere, we certified zebrafish to be a suitable model for the compensatory growth study. After a 3-weeks fasting, recovered for 3 days, 10 days and 15 days were chose as the initial, middle and late sampling sites for compensatory growth analysis, and liver samples of each time point were chose for the microarray analysis.At the same time, zebrafish fed ad libitum, as well as fasting for 3 weeks were also added to the microarray research. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 24, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Danio rerio Source Type: research

GSE112290 In Vitro Culture of the Insect Endosymbiont Spiroplasma poulsonii Highlights Bacterial Genes Involved in Host-Symbiont Interaction
Contributors : Florent Masson ; Sandra Calderon Copete ; Fanny Sch üpfer ; Gonzalo Garcia-Arraez ; Bruno LemaitreSeries Type : Expression profiling by high throughput sequencingOrganism : Spiroplasma poulsoniiEndosymbiotic bacteria associated with eukaryotic hosts are omnipresent in nature, particularly in insects. Studying the bacterial side of host-symbiont interactions is, however, often limited by the unculturability and genetic intractability of the symbionts. Spiroplasma poulsonii is a maternally transmitted bacterial endosymbiont that is naturally associated with several Drosophila species. S. poulsonii strongl...
Source: GEO: Gene Expression Omnibus - March 24, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Spiroplasma poulsonii Source Type: research

GSE112239 Molecular profiling of SV-BR-1-GM, a clinically effective GM-CSF-secreting human breast cancer cell line
Contributor : Markus D LacherSeries Type : Expression profiling by arrayOrganism : Homo sapiensThe SV-BR-1 cell line was derived from a chest wall lesion of a breast cancer patient. SV-BR-1 cells were stably transfected with CSF2 (encoding GM-CSF), resulting in the SV-BR-1-GM cell line. Following irradiation to prevent cell replication, both SV-BR-1 (Wiseman and Kharazi, The Open Breast Cancer Journal, 2010, 2, 4-11) and SV-BR-1-GM (Wiseman and Kharazi, Breast J. 2006 Sep-Oct;12(5):475-80) cells have been applied as whole-cell therapeutics in clinical trial settings for advanced breast cancer. Molecular profiles of non-irr...
Source: GEO: Gene Expression Omnibus - March 23, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE67199 Gene expression in beta-cells in mice submitted to a high-fat diet
Contributors : Sophie Rome ; Sandra Pesenti ; Emmanuelle MeugnierSeries Type : Expression profiling by arrayOrganism : Mus musculusGene expression in beta pancreatic cells of mice submitted to a high-fat diet. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 23, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE67504 Glycyrrhizin, silymarin, and ursodeoxycholic acid regulate a common hepatoprotective pathway in HepG2 cells
Conclusion: Our data suggested that glycyrrhizin, silymarin, and ursodeoxycholic acid protected livers from damage by regulating the genes involved in apoptosis and oxidative stress. Moreover, the regulation of genes by hepatoprotectants might be through the suppression of NF- κB activities. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - March 23, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE79538 Rheb1-mTORC1 maintains macrophage differentiation and phagocytosis in mice
Contributors : Xiaomin Wang ; Minghao Li ; Yanan Gao ; Juan Gao ; Wanzhu Yang ; Honghai Liang ; Qing Ji ; Yanxin Li ; Hanzhi Liu ; Tao Cheng ; Weiping Yuan ; Jian HuangSeries Type : Expression profiling by arrayOrganism : Mus musculusRas homolog enriched in brain (Rheb1) is a small GTPase and is known to be a direct activator of mTORC1. Dysregulation of Rheb1 has been shown to impair the cellular-energetic state and cell homeostasis. However, the role of Rheb1 in monocytes/macrophages differentiation and maturation is not clear. Here, we investigate the role of Rheb1 in mouse myelopoiesis using a Rheb1 conditional deletion...
Source: GEO: Gene Expression Omnibus - March 23, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE102002 c-kitCre Knock-ins Fail to Identify, Effectively Recombine and Fate-Map Cardiac Stem Cells
Contributors : Carla Vicinanza ; Iolanda Aquila ; Eleonora Cianflone ; Mariangela Scalise ; Fabiola Marino ; Teresa Mancuso ; Francesca Fumagalli ; Emilia Dora Giovannone ; Francesca Cristiano ; Enrico Iaccino ; Pina Marotta ; Annalaura Torella ; Roberto Latini ; Valter Agosti ; Pierangelo Veltri ; Konrad Urbanek ; Andrea M Isidori ; Dieter Saur ; Ciro Indolfi ; Bernardo Nadal-Ginard ; Daniele TorellaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusA recent cell-fate mapping study by Van Berlo et al. using a Cre knock-in (KI) into the c-kit locus, and two other studies using a similar ...
Source: GEO: Gene Expression Omnibus - March 23, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE106400 Gene expression profile of Ba/F3 variant (#BEB1) cells that have binding ability to Ecrg4
Contributors : Kei Enomoto ; Tetsuo MoriguchiSeries Type : Expression profiling by arrayOrganism : Mus musculusEsophageal cancer-related gene 4 (Ecrg4) encodes a hormone-like peptide, and is thought to be involved in a variety of physiological phenomena including tumor suppressor function. Recent progress of Ecrg4 reveals that Ecrg4 peptides are pro-inflammatory and induce the expression of several cytokines and chemokines. However, detailed molecular mechanisms of Ecrg4 signaling, especially the receptors for Ecrg4 peptides, remain poorly understood. Here, using retrovirus-mediated expression cloning, we identified lectin...
Source: GEO: Gene Expression Omnibus - March 23, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE110335 Glycyrrhetinic acid antagonizes pressure-induced venous remodeling in mice
Contributors : Thomas Korff ; Carsten StichtSeries Type : Expression profiling by arrayOrganism : Homo sapiensDevelopment of spider veins is caused by the remodeling of veins located in the upper dermis and promoted by risk factors such as obesity or pregnancy that chronically increase venous pressure. We have repeatedly shown that the pressure-induced increase in biomechanical wall stress is sufficient to evoke the formation of enlarged corkscrew-like superficial veins in mice. Subsequent experimental approaches revealed that interference with endothelial- and/or smooth muscle cell activation counteracts this remodeling p...
Source: GEO: Gene Expression Omnibus - March 23, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE111508 Multi-environment fitness landscapes of a tRNA gene
Contributors : Chuan Li ; Jianzhi ZhangSeries Type : Genome variation profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeA fitness landscape (FL) describes the genotype-fitness relationship in a given environment. To explain and predict evolution, it is imperative to measure the FL in multiple environments because the natural environment changes frequently. Using a high-throughput method that combines precise gene replacement with next-generation sequencing, we determine the in vivo FL of a yeast tRNA gene comprising over 23,000 genotypes in four environments. Although genotype-by-environment interac...
Source: GEO: Gene Expression Omnibus - March 23, 2018 Category: Genetics & Stem Cells Tags: Genome variation profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE112007 Next Generation Sequencing Facilitates Quantitative of Transcriptomes in Various Cells Treated with or without LD100 and siRNA of SOD1
Conclusions: The global transcriptomic data on HeLa, DU145 and RWPE-1 after SOD1 inhibition using its specific inhibitor-LD100 indicated that the most changed expression upon this interruption of ROS homeostasis is the key genes in plenty of signaling pathways inside cancer cells, not inside normal cells, although mRNA levels of numerous genes are altered in three lines of cells. The modulation of gene expression leads to repression of multiple signaling pathways including ERK, PI3K and NF-KB and their crosstalk to promote cell growth and activation of the signaling pathways to cause both cell cycle arrest and apoptosis. T...
Source: GEO: Gene Expression Omnibus - March 23, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research