GSE138808 Transcriptomic analysis of transformed murine hepatic progenitors depleted or not for CDK8 or CDK19 kinases
We report transcriptomes of hepatic progenitors cells (BMEL) wild-type or transformed by the expression of H-RasG12V, depleted of CDK8 or CDK19 kinases by crispr/Cas9 mediated editing. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 14, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE88737 The profile of long non-coding RNAs in mouse testis and sperm after exposure to cadmium
Contributors : Xiaoning Zhang ; Fengxin GaoSeries Type : Non-coding RNA profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Mus musculusIncreasing evidences have shown that cadmium could caused male infertility. However, the exhaustive mechanisms have not been elucidated in mammals. Here, the mice testes and sperm RNA were used to investigate lncRNA expression profiles by stranded-specific RNA-seq on the transcriptome levels after exposure to cadmium. More LncRNA expression have been changed than mRNA genes by cadmium. Furthermore, many novel LncRNA were inducible expressi...
Source: GEO: Gene Expression Omnibus - October 14, 2019 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE88912 Lung collapse and respiratory distress in neonatal cloned cows is caused by surfactant homeostasis disorders
Contributors : Xiaojing Jiang ; Huabin Zhu ; Yifan Rao ; Linhua Huang ; Weihua Du ; Haisheng Hao ; Xueming Zhao ; Dong Wang ; Qiuling Jiang ; Yunwei Pang ; Xiuzhu Sun ; Yan LiuSeries Type : Expression profiling by arrayOrganism : Bos taurusRespiratory distress is one of the major causes of the high mortality rate in neonatal cloned animals. Although some therapeutic methods have been used to improve the survival of cloned neonatal animals, the mechanisms of their neonatal respiratory distress lacked thorough investigation. Pathological analyses including necropsy and histology were implemented to determine the precise dise...
Source: GEO: Gene Expression Omnibus - October 14, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Bos taurus Source Type: research

GSE120750 Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [ChIP-seq]
Contributors : Gina Renschler ; Gautier Richard ; Claudia I Valsecchi ; Sarah Toscano ; Laura Arrigoni ; Fidel Ramirez ; Asifa AkhtarSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Drosophila busckii ; Drosophila virilisWe used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi...
Source: GEO: Gene Expression Omnibus - October 14, 2019 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Drosophila busckii Drosophila virilis Source Type: research

GSE120751 Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling [HiC]
Contributors : Gina Renschler ; Gautier Richard ; Claudia I Valsecchi ; Sarah Toscano ; Laura Arrigoni ; Fidel Ramirez ; Asifa AkhtarSeries Type : Other ; Third-party reanalysisOrganism : Drosophila busckii ; Drosophila melanogaster ; Drosophila virilisWe used an approach combining PacBio data and published Illumina reads to de novo assemble D. busckii contigs. We generated Hi-C data from D. busckii embryos to order these contigs into chromosome-length scaffolds. For D. virilis we generated Hi-C data to order and orient the published Dvir_caf1 scaffolds into chromosome-length assemblies. Furthermore, we compared Hi-C matri...
Source: GEO: Gene Expression Omnibus - October 14, 2019 Category: Genetics & Stem Cells Tags: Other Third-party reanalysis Drosophila busckii Drosophila melanogaster Drosophila virilis Source Type: research

GSE120752 Hi-C guided assemblies reveal conserved regulatory topologies on X and autosomes despite extensive genome shuffling
Series Type : Genome binding/occupancy profiling by high throughput sequencing ; OtherOrganism : Drosophila busckii ; Drosophila melanogaster ; Drosophila virilisThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 14, 2019 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Other Drosophila busckii Drosophila melanogaster Drosophila virilis Source Type: research

GSE126842 Transcriptomic changes during cell wall biogenesis and modifications during xylogenesis in stems and pioneer roots of Populus trichocarpa
Contributors : Katarzyna Marzec-Schmidt ; Agnieszka Bagniewska-ZadwornaSeries Type : Expression profiling by arrayOrganism : Populus sp. ; Populus trichocarpaWe studied the changes that occur in gene transcription and the biosynthesis of cell-wall-related compounds during xylogenesis in Populus trichocarpa pioneer roots and stems. Transcriptional profiling was conducted with the use of microarrays to identify genes involved in xylem formation. Pioneer roots were examined in segments corresponding to their developmental stage: apical meristem (PR1), primary development (PR2), and secondary development (PR3). Comparative seg...
Source: GEO: Gene Expression Omnibus - October 14, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Populus sp. Populus trichocarpa Source Type: research

GSE128136 Full-length transcriptome reconstruction reveals large diversity of RNA isoforms and open reading frames in rat hippocampus
Contributors : Xi Wang ; Jingyi Hou ; Claudia Quedenau ; Wei ChenSeries Type : Expression profiling by high throughput sequencingOrganism : Rattus norvegicusWe developed a hybrid-sequencing workflow, combining next-generation and third-generation sequencing, to reconstruct full-length transcriptomes. Integrating with polysome profiling and ribosome footprinting data, we predicted isoform –specific translational status and reconstructed ORFeome. Moreover, we identified isoforms with specific subcellular localization pattern in neurons. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 14, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Rattus norvegicus Source Type: research

GSE138297 The host response of IBS patients to allogenic and autologous faecal microbiota transfer
Contributors : Savanne Holster ; Guido J Hooiveld ; Robert J Brummer ; Julia K önigSeries Type : Expression profiling by arrayOrganism : Homo sapiensIn this randomised placebo-controlled trial, irritable bowel syndrome (IBS) patients were treated with faecal material from a healthy donor (n=8, allogenic FMT) or with their own faecal microbiota (n=8, autologous FMT). The faecal transplant was administered by whole colonoscopy into the caecum (30 g of stool in 150 ml sterile saline). Two weeks before the FMT (baseline) as well as two and eight weeks after the FMT, the participants underwent a sigmoidoscopy, and biopsies...
Source: GEO: Gene Expression Omnibus - October 14, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE138728 Transcriptome analysis of marigold color
Contributors : Huali Zhang ; Shiya Zhang ; Hua Zhang ; Fang Liang ; Helan Qin ; Yue Zhang ; Richen Cong ; Haibo Xin ; Zhao ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Tagetes erectaMarigold (Tagetes erecta L.) is an important ornamental plant with a wide variety of colors. Despite its economic value, there are few biochemical and molecular basic studies of flower color in marigold. To study the mechanism behind its color formation, metabolomics analysis and de novo cDNA sequencing was performed on marigold inbred line ‘V-01’ and its petal color mutant ‘V-01M’, in ...
Source: GEO: Gene Expression Omnibus - October 14, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Tagetes erecta Source Type: research

GSE138806 Oncogenic changes and EMT in normal human bile duct epithelial cells are caused by parasite-derived materials and N-nitrosodimethylamine
Contributors : Kim Eun-Min ; Yong Tai-SoonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensA total of 1,301 differentially expressed genes were identified: 521 upregulated and 780 downregulated. Furthermore, p21 and PAI levels decreased, which coincided with decreases in E-cadherin and increases in fibronectin expression, in cells stimulated with Clonorchis sinensis excretory/secretory products (ESPs) and NDMA. Cancer-related proteins, such as EGFR, K-ras, and PCNA, were significantly upregulated in cells exposed to C. sinensis ESPs and NDMA. Our results showed that C. sinensis ESPs an...
Source: GEO: Gene Expression Omnibus - October 14, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE138801 Sequencing of the 3' end of RNA using BRB-seq in Drosophila heterozygous cross
Contributors : Michael V Frochaux ; Maroun B Sleiman ; Bart DeplanckeSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterResistance to enteric pathogens is a complex trait at the crossroads of multiple biological processes. We have previously shown in the Drosophila Genetic Reference Panel (DGRP) that resistance to infection is highly heritable, but our understanding of how the effects of genetic variants are channeled through distinct molecular layers is still limited. To address this, we employed a systems genetics approach on the gut transcriptomes from 38 control and orally...
Source: GEO: Gene Expression Omnibus - October 13, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Drosophila melanogaster Source Type: research

GSE51571 Expression data from human embryonic kidney 293 (HEK-293) cells transiently transfected with Human endogenous retrovirus (HERV) (K-HML2) Rec protein compared to empty expression vector control
Contributors : Sven Stengel ; Joachim DennerSeries Type : Expression profiling by arrayOrganism : Homo sapiensHERV-K protein Rec functions as RNA transport protein shuttling unspliced viral genomic RNA from the nucleus to the cytoplasm.Rec was found to be expressed in several tumors and transformed cell lines and contributes to cell transformation by inhibiting the transcription factor Promyelocytic Leukemia Zinc Finger Protein (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE74071 DNA methylation in human pancreatic cancer vs. adjacent normal pancreatic tissue
Contributors : Po-Hsien Huang ; Yan-Shen ShanSeries Type : Methylation profiling by genome tiling arrayOrganism : Homo sapiensHumanMethylation 450K microarrays were used to identify aberrant DNA methylation in pancreatic adenocarcinoma (n=14), juice-circulating cancer cells (n=4), cancer associated fibroblasts (n=3), against adjacent normal pancreatic tissues (n=7)Bisulphite converted DNA from the 28 samples were hybridised to the Illumina HumanMethylation450 Beadchip v1.2 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE87861 miRNAs regulate lung development and surfactant homeostasis via directly targeting SFTPC and TTF-1 in reprogramming-derived bovine model of NRDS
In this study, We proposed a reprogramming-derived bovine model of NRDS based on typical phenotypes of neonatal respiratory distress syndrome (NRDS) and high reproducibility and replication rates as well as a steerable background of neonatal cloned cows suffering from NRDS. With the aid of miRNA sequencing, construction of the miRNA –gene network and functional enrichment of target genes, the effects of specific miRNAs on lung development and surfactant homeostasis were determined in this model. We identified 12 miRNAs targeting SFTPB, SFTPC and NKX2-1 genes, demonstrated repression effects of three miRNAs on NKX2-1 ...
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Bos taurus Source Type: research

GSE105042 The influence of CCL5 to the exprssion profile of tumor associated macrophages (TAMs)
Contributors : Sheng B Zhang ; Wei Q Gao ; Yan ZhangSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe aim of the dataset was to demonstrate that the gene expression profile of CD11bhiF4/80low TAMs are different from CD11blowF4/80hi TAMs in WT and CCL5-/- BALB/c mice which subcoutinious incubated with CT26 WT or CT26 CCL5 knockdown cell line. Furthermore, we also want to determine the different gene expression profile of CD11bhiF4/80low TAMs which seperated from the colonrectal tumor of WT mice and CCL5-/- mice (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE121180 Gene expression in basal progenitors in the cerebral cortex of Tbr2 conditional knockout mice
Contributors : Tanay Ghosh ; Matthias GroszerSeries Type : Expression profiling by arrayOrganism : Mus musculusDuring cortical development neurons are generated from basal progenitors (BPs) which specifically express the transcription factor Tbr2. We used fluorescent-activated cell sorting (FACS) to isolate BPs from Tbr2-conditional knockout mice brain at early (E13) and late (E16) stages of cortical neurogenesis and determined mRNA expression profiles using microarray (Illumina MouseWG-6 v2).Role of transcription factor Tbr2 in basal progenitors during corticogenesis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE121768 Transcriptomics and chromatin accessibility analysis of MLL-AF9 early responses in mouse bone marrow cells
Contributors : Shangqin Guo ; Xinyue Chen ; Daniel BurkhardtSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusWe investigated early changes of gene expressions and chromatin accessibilities in hematopoietic stem and progenitor cells (HSPCs) in response to MLL-AF9 oncogene expressions. Using RNA-Seq and ATAC-Seq, we analyzed HSPCs briefly exposed to MLL-AF9 for one or two days. Such analysis addressed the initial changes during malignant transformation, and provided insights into the primary functions of MLL-AF9 oncogene....
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE128122 The piRNA Response to Retroviral Invasion of the Koala Genome
Contributors : Yu Tianxiong ; Koppetsch Birgit ; Weng Zhiping ; Theurkauf E William ; Keith Chappell ; Jeremy LubanSeries Type : Expression profiling by high throughput sequencing ; Non-coding RNA profiling by high throughput sequencing ; OtherOrganism : Mus musculus ; Phascolarctos cinereusAntisense piRNAs guide silencing of established transposons during germline development, and sense piRNAs drive ping-pong amplification of the antisense pool, but how the germline responds to genome invasion is not understood. The KoRV-A gammaretrovirus infects the soma and germline and is sweeping through wild koalas by a combination o...
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Non-coding RNA profiling by high throughput sequencing Other Mus musculus Phascolarctos cinereus Source Type: research

GSE138751 Therapeutic targeting MDR1 expression by ROR γ antagonists resensitizes cross-resistant CRPC to taxane via coordinated induction of cell death programs
We report here that ROR γ, a nuclear receptor family member, unexpectedly mediates MDR1/ABCB1 overexpression. RORγ plays an important role in controlling the functions of subsets of immune cells and has been an attractive target for autoimmune diseases. We found that its small-molecule antagonists are efficacious in re-s ensitizing DTX and CTX cross-resistant CRPC cells and tumors to taxanes in both androgen receptor (AR)-positive and -negative models. Our mechanistic analyses revealed that combined treatment with RORγ antagonists and taxane elicited a robust synergy in killing the resistant cells, which ...
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE138764 miRNA profiling by array of astrocytic tumors
Contributors : Chen-Xue Mao ; Zhao-Qian LiuSeries Type : Non-coding RNA profiling by arrayOrganism : Homo sapiensAstrocytoma is a common pathologic type of glioma, its survival and prognosis remain poor. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE138766 hNSCs siRNA NOVA2
Contributor : Amelie PitonSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensinactivation of NOVA2 gene in human neural stem cells (hNSCs). Two independent series (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE138768 DUX4 promotes mitochondrial impairment in skeletal muscle
Contributors : Kevin I Watt ; Mark Ziemann ; Richard J Mills ; Man-Kit-Sam Lee ; Adam Hagg ; Hongwei Qian ; Fergus L Sully ; Assam El-Osta ; Andrew J Murphy ; Stephen J Tapscott ; James E Hudson ; Paul GregorevicSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensFacioscapulohumeral muscular dystrophy (FSHD) is characterised by a progressive degeneration and weakness of skeletal muscle fibers attributed to inappropriate expression of the transcription factor double homeobox 4 (DUX4). However, the cellular events that precede pathology in DUX4 expressing muscle fibers remain incompletely u...
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE138770 Neonatal injury increases gut permeability by epigenetically suppressing E-cadherin in adulthood
Contributors : Kevin T Kline ; Haifeng Lian ; Xiaoying S Zhong ; Xiuju Luo ; Syed Z Nayeem ; John H Winston ; Zingzi Cong ; Tor C Savidge ; Roderick H Dashwood ; Don W Powell ; Qingjie LISeries Type : Non-coding RNA profiling by arrayOrganism : Rattus norvegicusEpithelial cell juntion integrity is thought to play an important role in the pathogenesis of inflammatory bowel disease (IBD). Early life stressors are suspected to impact epithelial barrier function later in life. We postulated that based on our previous findings that early life exposure to an inflammatory event could lead to epigegenetic changes mediating an exag...
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Rattus norvegicus Source Type: research

GSE138772 Genomic profiling of biliary tract cancer cell lines reveals molecular subtypes and actionable drug targets
Conclusions: Cell lines harbor similar genomic alterations to primary BTCs. Integration of cell line and primary cancer data identify novel molecular subsets, and highlight specific molecular vulnerabilities in BTC. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE138774 RNA-seq analysis using glomeruli isolated from control and podocyte-specific bPIX deficient mice
Contributors : Jun Matsuda ; Tomoko TakanoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe found that podocyte-specific bPIX deficient (KO) mice developed progressive proteinuria starting at ~8 weeks of age, and glomerulosclerosis and podocyte loss by 13 weeks of age. To investigate the mechanism of podocyte loss induced by bPIX deficiency, we analyzed mRNA expression by RNA-sequence using isolated glomeruli from control (CTRL) and KO mice. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE138775 Deletion of intestinal Hdac3 remodels the lipidome of enterocytes and protects mice from diet-induced obesity
Contributors : Mercedes D ávalos-Salas ; Sheren Al-Obaidi ; John MariadasonSeries Type : Expression profiling by arrayOrganism : Mus musculusHistone deacetylase 3 (Hdac3) regulates the expression of lipid metabolism genes in multiple tissues, however its role in regulating lipid metabolism in the intestinal epithelium is unknown. Here we demonstrate that intestine-specific deletion of Hdac3 (Hdac3IKO) protects mice from diet induced obesity. Intestinal epithelial cells (IECs) from Hdac3IKO mice display co-ordinate induction of genes and proteins involved in mitochondrial and peroxisomal b-oxidation, have an increase...
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE138782 Gene expression profiles of PGAM5-knockout brown adipose tissue
Contributors : Sho Sugawara ; Akinori Takahashi ; Lila Maekawa ; Tadashi Yamamoto ; Takao Fujisawa ; Kazuki Hattori ; Hidenori IchijoSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPGAM5 is a mitochondria-localized protein phosphatase. To analyze the effect on gene expression profiles by PGAM5 in iBAT, RNA-seq analysis was performed. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE138785 Expression data from murine gut and spleen tissues
Contributor : Yujun YangSeries Type : Expression profiling by arrayOrganism : Mus musculusTIM-1 is a gene that regulates immune responses including transplantation tolerence, allergy and asthma, autoimmunity, viral infections as well as cancer, however its role in transplantation has not been evaluated. Here we use a murine model of graft versus host disease (GVHD) to evaluate the therapeutic potential of blocking TIM-1 using an antibody.We used microarray data to look for difference in gene expession in the gut which is one of the main organs that are afffected by GVHD as well as the spleen an organ when the immune respon...
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE138789 In Vitro and In Vivo Modulation of Alternative Splicing by the Biguanide Metformin.
Contributors : Delphine Laustriat ; Jacqueline Gide ; Laetitia Barrault ; Emilie Chautard ; Clara Benoit-Pilven ; Didier Auboeuf ; Anne Boland ; Christophe Battail ; Fran çois Artiguenave ; Jean-François Deleuze ; Paule Bénit ; Pierre Rustin ; Sylvia Franc ; Guillaume Charpentier ; Denis Furling ; Guillaume Bassez ; Xavier Nissan ; Cécile Martinat ; Marc Peschanski ; Sandrine BaghdoyanSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensMajor physiological changes are governed by alternative splicing of RNA, and its misregulation may lead to specific diseases. W...
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE138794 A single cell atlas of human glioma
This study sheds light on a long-standing debate regarding lineage relationships among GSCs and presents a paradigm by which personalized combination therapies can be derived from single-cell RNA signatures, to overcome intra-tumor heterogeneity. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Other Homo sapiens Source Type: research

GSE138800 Next Generation Sequencing Facilitates Quantitative Analysis of UVB(20mJ/cm2 and 40mJ/cm2) exposed and untreated HaCaT keratinocytes Transcriptomes
Contributors : Lidan Xiong ; Hailun HeSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensPurpose: To compare the transcriptomes of UVB (20mJ/cm2 and 40mJ/cm2) exposed and untreated HaCaT keratinocytes by RNA-Seq analysis, trying to find differences in gene expression between UVB exposed and untreated of keratinocytes and then elucidate the candidate genes that may play important roles in the differentiation of UVB-induced damage in keratinocytes.Methods: HaCaT keratinocytes were subjected to 20mJ/cm2 and 40mJ/cm2 UVB irradiation.Results: To better understand the effects of UVB (20 mJ/cm2...
Source: GEO: Gene Expression Omnibus - October 12, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE138731 Next Generation Sequencing Facilitates Quantitative Analysis of control of Pseudomonas aeruginosa PAO1 and farnesol-treated P. aeruginosa PAO1 Transcriptomes
Conclusions: (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Pseudomonas aeruginosa PAO1 Source Type: research

GSE95267 Expression data from inducible ES stable cell line overexpressing specifically the human gene GTF2IRD1
Contributor : Rossella De CegliSeries Type : Expression profiling by arrayOrganism : Mus musculusIn order to identify the effects of the induction of the gene of interest (GTF2IRD1) on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the inducible not-tagged cell lineTranscriptome analysis of the inducible transgenic mouse ES cell line overexpressing the human isorofm of the gene GTF2IRD1. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE95268 Expression data from inducible ES stable cell line overexpressing specifically the human gene GTF2IRD2
Contributor : Rossella De CegliSeries Type : Expression profiling by arrayOrganism : Mus musculusIn order to identify the effects of the induction of the gene of interest (GTF2IRD2) on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the inducible not-tagged cell lineTranscriptome analysis of the inducible transgenic mouse ES cell line overexpressing the human isorofm of the gene GTF2IRD2 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE95269 Expression data from inducible ES stable cell line overexpressing specifically the human gene WBSCR1
Contributor : Rossella De CegliSeries Type : Expression profiling by arrayOrganism : Mus musculusIn order to identify the effects of the induction of the gene of interest (WBSCR1) on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the inducible not-tagged cell lineTranscriptome analysis of the inducible transgenic mouse ES cell line overexpressing WBSCR1 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE95270 Expression data from inducible ES stable cell line overexpressing specifically the human gene GTF2I
Contributor : Rossella De CegliSeries Type : Expression profiling by arrayOrganism : Mus musculusIn order to identify the effects of the induction of the gene of interest (GTF2I) on the mouse ES transcriptome, we performed Affymetrix Gene-Chip hybridization experiments for the inducible not-tagged cell lineTranscriptome analysis of the inducible transgenic mouse ES cell line overexpressing the human isorofm of the gene GTF2I (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE96701 A transcriptomic study of Williams-Beuren syndrome associated genes in mouse embryonic stem
Series Type : Expression profiling by arrayOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE104860 Pumilio-Homology Domain protein APUM9 regulates seed dormancy via decapping-dependent mRNA decay
Contributors : T ünde Nyiko ; Etienne BucherSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaAPUM9 is a conserved PUF RNA-binding protein (RBP) and the expression of this protein is under complex epigenetic regulation. A transposable element (TE)-mediates this epigenetic regulation and thereby restricts its expression in Arabidopsis. Currently, little is known about the molecular function of the APUM protein family and the biological relevance of the TE-mediated epigenetic control of APUM9 in plant development and stress responses. By combining a range of transient assays...
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE104944 Region-specific Innate Antiviral Responses of the Human Epididymis
Contributors : Ann Harris ; James BrowneSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensViral infections of the epididymis are associated with epididymitis, which damages the epithelium and impairs fertility. We showed previously that innate immune response genes were differentially expressed in the corpus and cauda region of the human epididymis in comparison to the caput. Here we investigate the antiviral defense response mechanisms of human epididymis epithelial (HEE) cells. Toll-like receptor (TLR) 3 and retinoic acid-inducible gene I (RIG-I)- like receptors (RLRs) are enriched in...
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE118534 FACT mediates cohesin function on chromatin
Contributors : Jonay Garcia-Luis ; Luis AragonSeries Type : Genome binding/occupancy profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Saccharomyces cerevisiae ; [Candida] glabrataCohesin is a key regulator of genome architecture with roles in sister chromatid cohesion and the organisation of higher-order structures during interphase and mitosis. The recruitment and mobility of cohesin complexes on DNA are restricted by nucleosomes. Here we show that cohesin role in chromosome organization requires the histone chaperone FACT. Depletion of FACT in metaphase cells affects ...
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Expression profiling by high throughput sequencing Saccharomyces cerevisiae [Candida] glabrata Source Type: research

GSE130308 A revised model for promoter competition based on multi-way chromatin interactions
Contributors : A M Oudelaar ; Jim R HughesSeries Type : OtherOrganism : Mus musculusSpecific communication between gene promoters and enhancers is critical for accurate regulation of gene expression. However, it remains unclear how specific interactions between multiple regulatory elements and genes contained within a single chromatin domain are coordinated. Recent technological advances allow for the investigation of multi-way chromatin interactions at single alleles in individual nuclei. This can provide insights into how multiple regulatory elements cooperate or compete for transcriptional activation. We have used these...
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Other Mus musculus Source Type: research

GSE134498 DNA copy number alteration analysis of radioresistant and radiosensitive prostate cancer cell lines
Contributors : Anna Dubrovska ; Claudia Peitzsch ; Vasyl Lukiyanchuk ; Klink Barbara ; Michael SeifertSeries Type : Genome variation profiling by arrayOrganism : Homo sapiensProstate cancer cell lines DU145 and LNCaP were purchased from the American Type Culture Collection. Radioresistant (RR) sublines were generated form these original parental radiosensitive (RS) cell lines. aCGH profiles of radiosensitive (RS) and radioresistant (RR) prostate cancer cell lines were measured and compared to normal DNA. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Genome variation profiling by array Homo sapiens Source Type: research

GSE134499 Comparative analysis of gene expression profiles comparing radioresistant to radiosensitive prostate cancer cell lines
Contributors : Anna Dubrovska ; Claudia Peitzsch ; Vasyl Lukiyanchuk ; Michael SeifertSeries Type : Expression profiling by arrayOrganism : Homo sapiensProstate cancer cell lines DU145 and LNCaP were purchased from the American Type Culture Collection. Radioresistant (RR) sublines were generated form these original parental radiosensitive (RS) cell lines. Gene expression profiles of radiosensitive (RS) and radioresistant (RR) prostate cancer cell lines were measured. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE134500 DNA copy number alteration analysis and gene expression profiles comparing radioresistant to radiosensitive prostate cancer cell lines
Series Type : Expression profiling by array ; Genome variation profiling by arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Genome variation profiling by array Homo sapiens Source Type: research

GSE134994 Targeted DNA methylation of the ALS/FTD gene C9orf72 via endogenous DNA damage repair pathways (I)
This study presents a novel method of targeted DNA methylation that utilizes endogenous DNA double strand break repair pathways and applies it to the neurodegenerative disease gene C9orf72. A double strand break induced by CRISPR/cas9 in the promoter of C9orf72 is sufficient to induce DNA methylation, and methylation can be precisely targeted through the process of homology directed repair (HDR) via delivery of an in vitro methylated exogenous repair template. Long methylated double stranded DNA templates induce more methylation than shorter templates and with higher efficiency than a dCas9-DNMT3a fusion protein construct....
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE134995 Targeted DNA methylation of the ALS/FTD gene C9orf72 via endogenous DNA damage repair pathways (II)
This study presents a novel method of targeted DNA methylation that utilizes endogenous DNA double strand break repair pathways and applies it to the neurodegenerative disease gene C9orf72. A double strand break induced by CRISPR/cas9 in the promoter of C9orf72 is sufficient to induce DNA methylation, and methylation can be precisely targeted through the process of homology directed repair (HDR) via delivery of an in vitro methylated exogenous repair template. Long methylated double stranded DNA templates induce more methylation than shorter templates and with higher efficiency than a dCas9-DNMT3a fusion protein construct....
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE134996 Targeted DNA methylation of the ALS/FTD gene C9orf72 via endogenous DNA damage repair pathways
Series Type : Methylation 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 - October 11, 2019 Category: Genetics & Stem Cells Tags: Methylation profiling by genome tiling array Homo sapiens Source Type: research

GSE137288 Allele-specific 4C-seq of rs2836411 located in the ERG gene in HUVEC and HASMCs
Contributors : Judith Marsman ; Gregory Gimenez ; Robert C Day ; Julia A Horsfield ; Gregory T JonesSeries Type : OtherOrganism : Homo sapiensAllele-specific circular chromosome conformation capture sequencing (4C-seq) using the single nucleotide polymorphism rs2836411 as a bait was performed in two cell types: human umibilical vein endothelial cells (HUVECs) and human aortic smooth muscle cells (HASMCs). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE138679 Influences of CDK9 on gene expressions
Contributors : Jiao Li ; Jiahong ShiSeries Type : Expression profiling by arrayOrganism : Homo sapiensTo understand better the contribution of CDK9 in P. gingivalis-stimulated gene expression, gene chips were performed. Lentiviral vectors carrying CDK9 shRNA or not were transfected into cells for 96 hours, with the assist of Envirus. NC group was transfected with non-targeting scramble and stimulated with PBS. NC and Pg group was transfected with non-targeting scramble and stimulated with P. gingivalis. CDK9 shRNA group was transfected with CDK9 shRNA and stimulated with PBS. CDK9 shRNA and Pg group was transfected with CD...
Source: GEO: Gene Expression Omnibus - October 11, 2019 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research