GSE125763 Differential expression of miRNAs inEGF treated SWAN-71 versus untreated control by next generation sequencing
Contributors : Satish K Gupta ; Ankita MalikSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensThe goal of this study is to compare miRNAs expressed by EGF treated SWAN-71 cells to miRNAs expressed in untreated control SWAN-71 cells to identify micro RNAs which play a role during EGF-mediated SWAN-71 cell invasion (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE125765 RNA-sequencing of NALT from mouse after intranasal immunization with B. abortus rMDH loaded chitosan nanoparticles (CNs)
Contributors : Soojin Shim ; HanSang YooSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusBrucellosis is a serious zoonotic disease caused by the genus Brucella, a group of Gram-negative and facultative intracellular bacteria. At present, although live attenuated vaccine such as Rev.1, S19 and RB51 have been widely used for bovine brucellosis, these vaccines have some drawbacks, and safe and effective alternatives have been demanded. Previously, our group showed that several Brucella proteins malate dehydrogenase (rMDH) are effective in eliciting IgG responses in murine model following ...
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE125767 Differential expression of miRNAs in HGF treated HTR-8/SVneo versus untreated control by next generation sequencing
Contributors : Satish K Gupta ; Piyush ChaudharySeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensThe goal of this study is to compare miRNAs expressed by HGF treated HTR-8/SVneo cells to miRNAs expressed in untreated control HTR-8/SVneo cells to identify micro RNAs which play a role during HGF-mediated HTR-8/SVneo cells invasion (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE125774 Differential expression of miRNAs in IFN-gamma treated HTR-8/SVneo versus untreated control by next generation sequencing
Contributors : Satish K Gupta ; Sonam VermaSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensThe goal of this study is to compare miRNAs expressed by IFN-gamma treated HTR-8/SVneo cells to miRNAs expressed in untreated control HTR-8/SVneo cells to identify micro RNAs which play a role during IFN-gamma-mediated HTR-8/SVneo cells invasion (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE125776 Analysing the gene expression between wildtype and Nxt1 trans-heterozygotes in larval carcasses
Contributors : Kevin van der Graaf ; Helen White-CooperSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterWe used larval carcasses of both wildtype and Nxt1 trans-heterozygotes for RNA paired-end sequencing and obtained a read depth between 21M to 32M reads across all samples. A total of 1821 genes were down-regulated and 1339 genes were up-regulated. A python script extracting intron data of genes from the FlyMine database identified a trend where down-regulated genes had a higher total intron length and had more introns. Up-regulated genes had a lower total intron length and...
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Drosophila melanogaster Source Type: research

GSE125777 Study on Cyanidin Metabolism in Flower colors of Pink-flowered Strawberry Based on Transcriptome Sequencing and Metabolite Analysis
Contributors : Li Xue ; Jiajun LeiSeries Type : Expression profiling by high throughput sequencingOrganism : Fragaria x ananassaPink-flowered strawberry is a new promising ornamental flower derived from intergeneric hybridization (Fragaria × Potentilla) with bright color, prolonged flowering period and edible fruits. However, the transcriptional events underlying anthocyanins biosynthesis pathway have not been fully characterized in its petal coloration. The pigment compounds accumulated in its fruits were the same as cultivated stra wberry, but different from in its flowers. To gain insights into the regulatory netw...
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Fragaria x ananassa Source Type: research

GSE125778 Differential expression of mRNAs in IFN-gamma treated HTR-8/SVneo versus untreated control by next generation sequencing
Contributors : Satish K Gupta ; Sonam VermaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe goal of this study is to compare genes expressed by IFN-gamma treated HTR-8/SVneo cells to genes expressed in untreated control HTR-8/SVneo cells to identify genes which play a role during IFN-gamma-mediated HTR-8/SVneo cells invasion (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE125779 Transcriptome analysis of tubulointerstitial tissues of patients with focal segmental glomerulosclerosis
Contributors : Hao Bao ; Zhihong LiuSeries Type : Expression profiling by arrayOrganism : Homo sapiensTranscriptome comparison of tubulointerstitial tissues from kidneys with focal segmental glomerulosclerosis (FSGS) and tubulointerstitial tissues from the unaffected portion of surgical nephrectomies.High-density Affymetrix Human Transcriptome Arrays (HTA) 2.0 were used for the gene expression analysis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE125781 Analysing the gene expression between wildtype and Nxt1 trans-heterozygotes in whole larvae
Contributors : Kevin van der Graaf ; Helen White-CooperSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterWe used whole larvae of both wildtype and Nxt1 trans-heterozygotes for RNA paired-end sequencing and obtained a read depth between 6.4M to 11.1M reads across all samples. In wandering larvae, stationary larvae and white prepupae, a total of 435, 855, and 611 genes were differentially expressed. A high percentage of down-regulated genes were highly expressed/testis-specific in the Drosophila testis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Drosophila melanogaster Source Type: research

GSE125783 Defining genes in the Caulobacter crescentus SpdR regulon
Contributors : Leila Reyes-Ruiz ; Aretha Fiebig ; Sean CrossonSeries Type : Expression profiling by high throughput sequencingOrganism : Caulobacter vibrioidesWe measured steady-state transcript levels in 1) wild-type C. crescentus, 2) an spdR response regulator deletion strain ( ΔspdR), and an spdR phosphomimic strain (SpdR(D64E)) (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Caulobacter vibrioides Source Type: research

GSE125784 CRAC channel-mediated gene expression in Treg cells
Contributors : Stefan Feske ; Martin VaethSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusT regulatory (Treg) cells maintain immunological tolerance and their depletion in humans and mice results in autoimmune disease. The development of Treg cells in the thymus, their differentiation into effector T cells and their activation depends on Ca2+ release-activated Ca2+ (CRAC) channels formed by STIM and ORAI proteins. Gene expression analysis of murine Treg cells with genetic deletion of Stim1 and Stim2 genes after their development in the thymus shows an important role of CRAC channel-me...
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE125787 Identification of p53-regulated genes in wild-type p53 or p53-null HCT116 cells
Contributors : Yu-Yu Liu ; Chizu Tanikawa ; Takafumi Miyamoto ; H Lo ; Makoto Hirata ; Koichi MatsudaSeries Type : Expression profiling by arrayOrganism : Homo sapiensMicroarray-based gene expression analysis of HCT116 p53+/+ and HCT116 p53 −/− treated with doxorubicin to activate p53 in time-dependent manner. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE125789 Differential expression of miRNAs in IFN-gamma treated SWAN-71 versus untreated control by next generation sequencing
Contributors : Satish Kumar Gupta ; Sonam VermaSeries Type : Non-coding RNA profiling by high throughput sequencingOrganism : Homo sapiensThe goal of this study is to compare miRNAs expressed by IFN-gamma treated SWAN-71 cells to miRNAs expressed in untreated control SWAN-71 cells to identify micro RNAs which play a role during IFN-gamma-mediated SWAN-71 cells invasion (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE125790 Differential expression of miRNAs in HGF treated SWAN-71 versus untreated control by next generation sequencing
Contributors : Satish K Gupta ; Piyush ChaudharySeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe goal of this study is to compare miRNAs expressed by HGF treated SWAN-71 cells to miRNAs expressed in untreated control SWAN-71 cells to identify micro RNAs which play a role during HGF-mediated SWAN-71 cell invasion (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE125793 RNA sequencing of whole Dorsal Root Ganglia (DRG) and laser captured large diameter DRG neurons upon Environmental Enrichment (EE) compared to Standard Housing (SH)
Contributors : Thomas Hutson ; Ilaria Palmisano ; Matt C Danzi ; Simone Di Giovanni ; Dejan LazarevicSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose: A) compare the gene expression in whole DRG and in large diameter DRG neurons of mice exposed to EE compared to SHResults: we found that EE induces transcriptional changes promoting axon regeneration (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE125798 Identification of drought resistance related factors in Quercus liaotungensis leaf via transcriptome sequencing
Conclusions:RNA-Seq was applied to polyadenylate-enriched mRNAs from leaves of Q. liaotungensis to obtain the transcriptome. De novo assembly was then applied followed by gene annotation and functional classification. The SSRs and SNPs were also obtained using assembled transcripts as reference sequences. The results of this study lay the foundation for further research on genetic diversity of Quercus. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Quercus wutaishanica Source Type: research

GSE125799 Transcriptomic analysis of Quercus mongolica leaves: de novo assembly, functional annotation and molecular markers mining
Conclusions:RNA-Seq was applied to polyadenylate-enriched mRNAs from leaves of Q. mongolica to obtain the transcriptome. De novo assembly was then applied followed by gene annotation and functional classification. The SSRs and SNPs were also obtained using assembled transcripts as reference sequences. The results of this study lay the foundation for further research on genetic diversity of Quercus. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Quercus mongolica Source Type: research

GSE125800 Unravelling the cellular and humoral immune responses of Antheraea pernyi hemolymph to Antheraea pernyi nucleopolyhedrovirus infection
Conclusions: The transcriptome sequences were de novo assembled. The differentially expressed genes (DEGs) including both up- and down-regulated genes were obtained. We focused on the innate immunity related DEGs, and screened numerous of DEGs involved in cellular and humoral immune related pathways via bioinformatic analysis. The results of this study lay the foundation for a better understanding of the molecular mechanisms of cellular and humoral immunity of A. pernyi. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 29, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Antheraea pernyi Source Type: research

GSE122385 Epigenome regulation during epidermal lineage commitment
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 - January 28, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE108248 Epigenome regulation during epidermal lineage commitment [ATAC-seq]
Contributors : Lingjie Li ; Gautam ShankarSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiensRecent advances in human pluripotent stem cell (hPSC) technology provide a unique resource for skin tissue replacement, but the detailed understanding of regulatory mechanisms limits standardization and broad clinical application. Here, we interrogate chromatin accessibility and transcriptome dynamics during hPSC-derived epidermal differentiation, and discover two critical transition periods: surface ectoderm initiation and kerati...
Source: GEO: Gene Expression Omnibus - January 28, 2019 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE122383 Epigenome regulation during epidermal lineage commitment [RNA-seq]
Contributors : Lingjie Li ; Gautam ShankarSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRecent advances in human pluripotent stem cell (hPSC) technology provide a unique resource for skin tissue replacement, but the detailed understanding of regulatory mechanisms limits standardization and broad clinical application. Here, we interrogate chromatin accessibility and transcriptome dynamics during hPSC-derived epidermal differentiation, and discover two critical transition periods: surface ectoderm initiation and keratinocyte maturation. Using inference network modeling, we develop a c...
Source: GEO: Gene Expression Omnibus - January 28, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE125699 Oocyte-specific deletion of Mitofusin1 causes female infertility and accelerated follicular depletion
Contributors : Man Zhang ; Zongliang Jiang ; Muhammed B Bener ; Emre SeliSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe performed RNAseq analysis to determine the effect of MFN1 deletion on oocyte global gene expression profile. RNAseq revealed a total of 982 genes were significantly differentially expressed (p (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE100672 Combined chemosensitivity and chromatin profiling prioritizes drug combinations in CLL
Contributors : Christian Schmidl ; Gregory I Vladimer ; Andr é F Rendeiro ; Thomas Krausgruber ; Tea Pemovska ; Nikolaus Krall ; Berend Snijder ; Oscar Lopez de la Fuente ; Anna Ringler ; Stefan Kubicek ; Cathrin Skrabs ; Edit Porpaczy ; Michaela Gruber ; Gregor Hörmann ; Philipp B Staber ; Medhat Shehata ; Giulio Superti-Furga ; Ulrich Jäger ; Christoph BockSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThe Bruton Tyrosine Kinase inhibitor ibrutinib has substantially improved the treatment of chronic lymphocytic leukemia (CLL). However, drug responses ...
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE110278 Induction of human regulatory innate lymphoid cells from group 2 innate lymphoid cells by retinoic acid
Contributors : Hideaki Morita ; Cezmi A AkdisSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe aimed to determine the characteristic of IL-10-producing ILCs induced from ILC2s by RA. We found that IL-10-producing ILCs has distinct characteristic compared to IL-10 negative ILCs. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE120725 Mycobacterium tuberculosis response to environmental potassium
Contributors : Nathan J MacGilvary ; Shumin TanSeries Type : Expression profiling by high throughput sequencingOrganism : Mycobacterium tuberculosisThe purpose of this study was to identify genes that are differentially expressed under conditions of potassium limitation, to elucidate how Mycobacterium tuberculosis (Mtb) senses and responds to ionic changes, and the role of these responses in host colonization. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mycobacterium tuberculosis Source Type: research

GSE125636 Transcriptional profiling of CAI4 (Wild-type), cpp1 Δ/Δ, cek1Δ/Δ, cek2Δ/Δ, cpp1Δ/Δ cek1Δ/Δ, cpp1Δ/Δ cek2Δ/Δ and cek1Δ/Δ cek2Δ/Δ strains in the absence or presence of alpha pheromone in Candida albicans
Contributors : Raha Parvizi Omran ; Debra FultonSeries Type : Expression profiling by high throughput sequencingOrganism : Candida albicansTwenty-one pheromone-induced genes were selected from the literature (Zhao, Daniels et al. 2005 was the major source) as the reference set for assessing the pheromone response of CAI4 (Wild-type), cpp1 Δ/Δ, cek1Δ/Δ, cek2Δ/Δ, cpp1Δ/Δ cek1Δ/Δ, cpp1Δ/Δ cek2Δ/Δ and cek1Δ/Δ cek2Δ/Δ strains.Our aim was to check whether or not these 21 pheromone-induced genes are up-regulated in response...
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Candida albicans Source Type: research

GSE125642 RNA-sequencing of human mammary epithelial cells (HMLEs) engineered to express either ER or ER-SOX4 with and without 4-OHT to induce nuclear translocation
Contributors : S Vervoort ; A R Louren ço ; P J CofferSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThrough RNA-sequencing we analysed the differentially expressed genes upon inducible activation of SOX4. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE125643 The effects of SOX4 on the global epigenetic landscape in Mammary Epithelial Cells
Contributors : S Vervoort ; A R Louren ço ; P J CofferSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensBy chromatine-immunoprecipitating (ChIP) using the mammary epithelial cell line HMLE with a Doxycyclin-inducible overexpression of SOX4 we determined various histone modifications and presence of the POL2 polymerase in presence and absence of overexpressed SOX4. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE125667 Two distinct interstitial macrophage populations coexist across tissues in unique subtissular niches [FACs sorted]
Contributors : Svetoslav Chakarov ; Hwee Y Lim ; Leonard Tan ; Sheau Y Lim ; Peter See ; Josephine Lum ; Xiaomeng Zhang ; Shihui Foo ; Satoshi Nakamizo ; Duan Kaibo ; Wan T Kong ; Rebecca Gentek ; Akhila Balachander ; Daniel Carbajo ; Camille Bleriot ; Benoit Malleret ; John K Tam ; Sonia Baig ; Muhammad Shabeer ; Sue-Anne E Toh ; Andreas Schlitzer ; Anis Larbi ; Thomas Marichal ; Bernard Malissen ; Jinmiao Chen ; Michael Poidinger ; Kenji Kabashima ; Marc Bajenoff ; Lai G Ng ; Veronique Angeli ; Florent GinhouxSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMacrophages are a heteroge...
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE125675 Deficiency in the Phosphorylated Pathway of Serine Biosynthesis perturbs sulfur assimilation in Arabidopsis
Contributors : Armand D Anoman ; Mar ía Flores-Tornero ; Ruben M Benstein ; Samira Blau ; Sara Rosa-Téllez ; Andrea Bräutigam ; Alisdair R Fernie ; Jesús Muñoz-Bertomeu ; Sören Schilasky ; Andreas J Meyer ; Stanislav Kopriva ; Juan Segura ; Stephan Krueger ; Roc RosSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaAlthough the plant Phosphorylated Pathway of L-serine Biosynthesis (PPSB) is essential for embryo and pollen development, and for root growth, its metabolic implications have not yet been investigated in depth. A transcriptomics an...
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE125676 Two distinct interstitial macrophage populations coexist across tissues in unique subtissular niches [lung interstitial]
Contributors : Svetoslav Chakarov ; Hwee Y Lim ; Leonard Tan ; Sheau Y Lim ; Peter See ; Josephine Lum ; Xiaomeng Zhang ; Shihui Foo ; Satoshi Nakamizo ; Duan Kaibo ; Wan T Kong ; Rebecca Gentek ; Akhila Balachander ; Daniel Carbajo ; Camille Bleriot ; Benoit Malleret ; John K Tam ; Sonia Baig ; Muhammad Shabeer ; Sue-Anne E Toh ; Andreas Schlitzer ; Anis Larbi ; Thomas Marichal ; Bernard Malissen ; Jinmiao Chen ; Michael Poidinger ; Kenji Kabashima ; Marc Bajenoff ; Lai G Ng ; Veronique Angeli ; Florent GinhouxSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMacrophages are a heteroge...
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE125677 All the regulated lncRNAs and mRNAs in breast cancer tissues compared to adjacent normal breast tissues
Contributor : Liang JinSeries Type : Expression profiling by arrayOrganism : Homo sapiensCirculating transcriptional landscapes between breast cancer tissues and adjacent normal tissues were compared using the Affymetrix Human OE LncRNA Microarray with probes for profiling of 63542 human lncRNAs and 27134mRNAs. Goal was to investigate potential lncRNAs involved in breast cancer progression. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE125678 All the regulated lncRNAs in breast cancer stem cells (BCSCs, CD44+CD24- sorted)MCF-7 cells compared to non-BCSCs (non-CD44+CD24- sorted) MCF-7 cells
Contributor : Liang JinSeries Type : Expression profiling by arrayOrganism : Homo sapiensCirculating transcriptional landscapes between BCSCs and non-BCSCs were compared using the Affymetrix Human OE LncRNA Microarray with probes for profiling of 63542 human lncRNAs and 27134mRNAs. Goal was to investigate potential lncRNAs involved in BCSCs progression. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE125685 RNA-seq analysis of FACS-sorted control and Tsc2 cKO nociceptors with and without sciatic nerve crush
Contributors : Dan Carlin ; Alexandra Halevi ; Eric E Ewan ; Amy Moore ; Valeria CavalliSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe goals of this study are to compare the transcriptomes of control heterozygous and Tuberous sclerosis 2 (Tsc2) homozygous nociceptors 3 days after sciatic nerve injury that have been enriched by fluorescence-associated cell sorting (FACS) with the aim of identifying differences in genes associated with axon regeneration. Nav1.8-Cre transgenic mice were used to delete Tsc2 as well as express Green fluorescent protein from the Rosa26 locus. Tsc2 dele...
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE125686 Transcriptomic profiling of peripheral blood NK cells of chronic HBV, HCV and HIV patients
Conclusion: We compare, for the first time, NK cell transcripts of viremic HIV, HCV and HBV patients. We clearly demonstrate distinctive NK cell gene signatures in 3 different populations, suggestive for a different degree of functional alterations of the NK cell compartment as compared to healthy individuals. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE125689 Two distinct interstitial macrophage populations coexist across tissues in unique subtissular niches [lung monocytes]
Contributors : Svetoslav Chakarov ; Hwee Y Lim ; Leonard Tan ; Sheau Y Lim ; Peter See ; Josephine Lum ; Xiaomeng Zhang ; Shihui Foo ; Satoshi Nakamizo ; Duan Kaibo ; Wan T Kong ; Rebecca Gentek ; Akhila Balachander ; Daniel Carbajo ; Camille Bleriot ; Benoit Malleret ; John K Tam ; Sonia Baig ; Muhammad Shabeer ; Sue-Anne E Toh ; Andreas Schlitzer ; Anis Larbi ; Thomas Marichal ; Bernard Malissen ; Jinmiao Chen ; Michael Poidinger ; Kenji Kabashima ; Marc Bajenoff ; Lai G Ng ; Veronique Angeli ; Florent GinhouxSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusMacrophages are a heteroge...
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE125691 Two distinct interstitial macrophage populations coexist across tissues in unique subtissular niches
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 - January 26, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE125694 A Myt1 family transcription factor defines neuronal fate by repressing non-neuronal genes
Contributors : Joo Lee ; Emerson V Stewart ; Caitlin A Taylor ; Kristopher M Barnes ; Allison Chen ; Zhirong Bao ; Ao Shen ; Kang ShenSeries Type : Expression profiling by high throughput sequencingOrganism : Caenorhabditis elegansCellular differentiation requires both activation of target cell programs and repression of non-target cell programs. Transcriptional repressors such as RE1-silencing transcription factor (REST) and Hairy/Enhancer of Split (Hes) repress neuronal genes in non-neuronal cells. However, it is unknown whether transcriptional repressors of non-neuronal genes in neuronal precursors are required to speci...
Source: GEO: Gene Expression Omnibus - January 26, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Caenorhabditis elegans Source Type: research

GSE125629 A HOTAIR regulatory element modulates glioma cell sensitivity to temozolomide through long-range regulation of multiple target genes
Contributors : Lei Zhang ; Wange LuSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensTemozolomide (TMZ) is a frequently used chemotherapy for glioma; however, chemoresistance is a major problem limiting its effectiveness. Thus knowledge of mechanisms underlying this outcome could improve patient prognosis. Here, we report that deletion of a regulatory element in the HOTAIR locus increases glioma cell sensitivity to TMZ and alters transcription of multiple genes. Analysis of a combination of RNA-seq, Capture HiC and patient survival data suggests that CALCOCO1 and ZC3H10 are targ...
Source: GEO: Gene Expression Omnibus - January 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Homo sapiens Source Type: research

GSE65830 En bloc and segmental deletions of human XIST reveal X chromosome inactivation-involving RNA elements
Contributors : Hyeon J Lee ; Ramu Gopalappa ; Hongjae Sunwoo ; Seo-Won Choi ; Suresh Ramakrishna ; Jeannie T Lee ; Hyongbum Kim ; Jin-Wu NamSeries Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensRNA-seqs followed by whole and segmental deletions of XIST genes in human K562 cells.The XIST RNA is a non-coding RNA that induces X chromosome inactivation (XCI). Unlike the mouse Xist RNA, how the human XIST RNA controls XCI in female cells is less well characterized, and the XCI-involving RNA elements remain unclear. To systematically decipher the XCI-involving elements of XIST RNA, ten sm...
Source: GEO: Gene Expression Omnibus - January 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Homo sapiens Source Type: research

GSE77268 DNA Hypermethylation at Loci Associated with Diabetes, Obesity and Cardiac Abnormalities in CD3+ Lymphocytes of Intrauterine Growth Restricted Newbors
Contributors : Maureen J Charron ; Yoshinori Seki ; Lyda WilliamsSeries Type : Methylation profiling by high throughput sequencingOrganism : Homo sapiensIntrauterine growth restriction (IUGR) is associated with increased susceptibility to obesity, metabolic syndrome and type 2 diabetes. Although the mechanisms underlying the fetal origin of metabolic disease are poorly understood, evidence suggests epigenomic alterations play a critical role. We sought to identify changes in DNA methylation patterns that define IUGR in CD3+ T-cells purified from umbilical cord blood obtained from appropriate for gestational age (Control) a...
Source: GEO: Gene Expression Omnibus - January 25, 2019 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Homo sapiens Source Type: research

GSE94078 Gene expression profiling of LSKSLAM cells in mice deficient for cholinergic fibers
Contributors : Sim ón Méndez-Ferrer ; Claudia Korn ; Winnie Lau ; Andrés García-GarcíaSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRNASeq of LSKSLAM cells from Gfra2 WT vs KO mice (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE109620 Gene Expression Profiling of Cutaneous CD30+ Lymphoproliferative Disorders by RNA-seq
Contributors : Jingru Sun ; Yang WangSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCutaneous CD30+ lymphoproliferative disorder (CD30+LPDs), including lymphomatoid papulosis (LyP) and primary cutaneous anaplastic large-cell lymphoma (PCALCL), comprises the second most common group of cutaneous T cell lymphoma. Previously, we reported that special AT-rich sequence-binding protein1 (SATB1), a thymocyte specific chromatin organizer, was over-expressed and promoted malignant T-cell proliferation in a portion of CD30+LPDs, whereas other CD30+LPDs didn't express SATB1 at all. To elucidate...
Source: GEO: Gene Expression Omnibus - January 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE109673 Dual inhibition of EZH1/2 depletes stem cells and over-activates WNT signaling in multiple myeloma [RNA-seq]
Contributors : Makoto Nakagawa ; Issay KitabayashiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMultiple myeloma (MM) is a hematological malignancy caused by accumulation of abnormal clonal plasma cells. Despite the recent development of novel therapies, relapse of MM eventually occurs due to a remaining population of drug-resistant myeloma stem cells. Side population (SP) cells exhibit cancer stem cell-like characteristics in MM; thus targeting these cells is a promising strategy to completely cure this malignancy. Here, we showed that SP cells expressed higher levels of enhancer o...
Source: GEO: Gene Expression Omnibus - January 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE109674 Dual inhibition of EZH1/2 depletes stem cells and over-activates WNT signaling in multiple myeloma [ChIP-seq]
Contributors : Makoto Nakagawa ; Issay KitabayashiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensMultiple myeloma (MM) is a hematological malignancy caused by accumulation of abnormal clonal plasma cells. Despite the recent development of novel therapies, relapse of MM eventually occurs due to a remaining population of drug-resistant myeloma stem cells. Side population (SP) cells exhibit cancer stem cell-like characteristics in MM; thus targeting these cells is a promising strategy to completely cure this malignancy. Here, we showed that SP cells expressed higher levels...
Source: GEO: Gene Expression Omnibus - January 25, 2019 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE109675 Dual inhibition of EZH1/2 depletes stem cells and over-activates WNT signaling in multiple myeloma
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 - January 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE109702 RNA-seq analysis on high altitude exposure
Contributors : Chang Liu ; Bao Liu ; Binda Sun ; Er-long Zhang ; Jian Chen ; Yuqi GaoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiens30 samples were collected from 15 subjects at two time points (at plain and at high altitude). Significance was determined by comparing the expression profiling at high altitude with that of plain. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE113118 Expression data from Saccharomyces cerevisiae strains deleted for the nucleoporin Nup84
Contributors : Jos é M Santos-Pereira ; Hélène Gaillard ; Andrés AguileraSeries Type : Expression profiling by arrayOrganism : Saccharomyces cerevisiae ; Schizosaccharomyces pombethe nuclear pore complex (NPC) is emerging as an important mediator of cellular processes beyond molecule transport, including control of gene expression, replication and DNA repair.We used microarrays to study the global impact of Nup84 in gene expression, in particular expression of DNA repair genes. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - January 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Saccharomyces cerevisiae Schizosaccharomyces pombe Source Type: research

GSE113185 IL-6 trans-signaling induced gene expression in airway epithelial cells
Contributors : Zala Jevnikar Rojnik ; Elisabeth Ax ; Kristofer Th örn ; Elisabeth Israelsson ; Lisa Öberg ; Henric K OlssonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensBackground: Although several studies link high levels of IL-6 and soluble IL-6 receptor (sIL-6R) with asthma severity and decreased lung function, the role of IL-6 trans-signaling (IL-6TS) in asthma is unclear.Objective: To explore the association between epithelial IL-6TS pathway activation and molecular and clinical phenotypes in asthma.Methods: Primary human bronchial epithelial cell (HBEC) air-liquid in...
Source: GEO: Gene Expression Omnibus - January 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE118472 Transcriptome analysis of the oriental fruit fly Bactrocera dorsalis early embryos
Contributors : Wei Peng ; Hongyu ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Bactrocera dorsalisWe constructed three RNA libraries from embryos at 0-1, 2-4 and 5-8 post-oviposition (hpo) of Bactrocera dorsalis for deep sequencing. Using an Illumina HiSeq 2500 platform, we mapped more than 83, 85 and 98 million sequence reads from 0-1, 2-4 and 5-8 hour embryos respectively, and identified a total of 13,489 unigenes. 1683, 3201 and 3134 unigenes showed differential expression between the 0-1 and 2-4 hour embryos, the 0-1 and 5-8 hour embryos, and the 2-4 and 5-8 hour embryos respectively. ...
Source: GEO: Gene Expression Omnibus - January 25, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Bactrocera dorsalis Source Type: research