GSE104447 The abundantly expressed microRNA locus miR-144/451 regulates only about 100 target mRNAs during erythroid development [RNA-seq]
We examined microRNA activities in primary cells by combining genetic loss of function with RNA-sequencing, quantitative proteomics and High-Throughput Sequencing of RNA isolated by Crosslinking Immunoprecipitation (HITS-CLIP), focusing on miR-144/451, the most highly expressed microRNA locus during red blood cell (RBC) formation. We show that Argonaute (Ago) protein binds over one thousand different mRNAs in a miR-144/451-dependent manner, accounting for one third of all Ago-bound mRNAs. However, only about 100 mRNAs are stabilized in RBC precursors after ablation of the miR-144/451 locus. Thus, Ago-miRNA complexes destab...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE104455 The abundantly expressed microRNA locus miR-144/451 regulates only about 100 target mRNAs during erythroid development
Series Type : Expression profiling by high throughput sequencing ; Other ; Non-coding RNA 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 - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Non-coding RNA profiling by high throughput sequencing Mus musculus Source Type: research

GSE104515 The 3 ’UTR of ArgR regulates the arc operon
Contributors : S B Van der Meulen ; A Hesseling-Meinders ; A de Jong ; J KokSeries Type : Expression profiling by high throughput sequencingOrganism : Lactococcus lactis subsp. cremorisArgR and the sRNA from its 3 ’UTR, ArgX, both regulate the arc operon by influencing transcription and RNA stability/translation respectively (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Lactococcus lactis subsp. cremoris Source Type: research

GSE104582 Transcriptome and metabolome analysis support that nitrate primarily promotes N and C metabolism in soybean roots and reduces those in nodules.
Contributors : Takuji Ohyama ; Shinji Ishikawa ; Yuki Ono ; Norikuni Ohtake ; Kuni SueyoshiSeries Type : Expression profiling by arrayOrganism : Glycine maxTo dissect differences in gene expression profile of soybean roots and root nodules, we have employed microarray analysis. Seeds of soybean (Glycine max L. cv. Nourin No. 2) were inoculated with rhizobia (Bradyrhizobium diazoefficiens USDA110) and were hydroponically cultivated under controlled conditions with nitrogen free culture solution (Saito et al. 2014). At 19 days after planting, each plant were treated with or without 5 mM nitrate for 24 hours. Roots and nodule...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Glycine max Source Type: research

GSE104615 Expression data of synchronised mouse embryonic fibroblasts (MEF)
Contributors : Bruno Giotti ; David Chen ; Mark W Barnett ; Tom C FreemanSeries Type : Expression profiling by arrayOrganism : Mus musculusTranscriptional programmes involved in the eukaryotic cell cycle are activated sequentially throughout the process. In particular, the set of genes required for S and G2-M phases are highly conserved and induced one after the other.We used gene expression microarrays to analyse the global programme of gene expression of mouse embryonic fibroblast from a quiescence state (G0) to a synchronised cell proliferation (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE104616 Expression data of synchronised primary human fibroblasts (NHDF, Data Set 1)
Contributors : Bruno Giotti ; Mark W Barnett ; David Chen ; Tom C FreemanSeries Type : Expression profiling by arrayOrganism : Homo sapiensTranscriptional programmes involved in the eukaryotic cell cycle are activated sequentially throughout the process. In particular, the set of genes required for S and G2-M phases are highly conserved and induced one after the other.We used gene expression microarrays to analyse the global programme of gene expression of human primary fibroblasts from a quiescence state (G0) to a synchronised cell proliferation (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE104617 Expression data of synchronised primary human fibroblasts (NHDF, Data Set 2)
Contributors : Bruno Giotti ; Mark W Barnett ; David Chen ; Tom C FreemanSeries Type : Expression profiling by arrayOrganism : Homo sapiensTranscriptional programmes involved in the eukaryotic cell cycle are activated sequentially throughout the process. In particular, the set of genes required for S and G2-M phases are highly conserved and induced one after the other.We used gene expression microarrays to analyse the global programme of gene expression of human primary fibroblasts from a quiescence state (G0) to a synchronised cell proliferation (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE104618 Expression data of synchronised primary human fibroblasts (NHDF, Data Set 3)
Contributors : Bruno Giotti ; Mark W Barnett ; David Chen ; Tom C FreemanSeries Type : Expression profiling by arrayOrganism : Homo sapiensTranscriptional programmes involved in the eukaryotic cell cycle are activated sequentially throughout the process. In particular, the set of genes required for S and G2-M phases are highly conserved and induced one after the other.We used gene expression microarrays to analyse the global programme of gene expression of human primary fibroblasts from a quiescence state (G0) to a synchronised cell proliferation (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE104619 Expression data of synchronised mouse embryonic fibroblasts (MEF) and synchronised primary human fibroblasts (NHDF)
Series Type : Expression profiling by arrayOrganism : Homo sapiens ; Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Mus musculus Source Type: research

GSE104669 Deletion of the FlbA-regulated transcription factor msnB of Aspergillus niger affects protein secretion
Contributors : David Aerts ; Robin A Ohm ; Han A W östenSeries Type : Expression profiling by high throughput sequencingOrganism : Aspergillus nigerColonies of Aspergillus niger secrete proteins throughout the colony except for the sporulating zone. Strains in which the sporulation gene flbA is deleted do not reproduce asexually and secrete proteins throughout the mycelium. Moreover, ΔflbA hyphae lyse and have thinner cell walls. This pleiotropic phenotype is associated with differential expression of 36 transcription factor genes, of which msnB was inactivated in this study. Whole genome expression analysis of ...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Aspergillus niger Source Type: research

GSE104737 Neo-Adjuvant Oncolytic Virotherapy Prior to Surgery Sensitizes Triple-Negative Breast Cancer to Immune Checkpoint Therapy
Contributors : M-C Bourgeois-Daigneault ; Adrian Pelin ; John C BellSeries Type : Expression profiling by arrayOrganism : Mus musculusTriple-negative breast cancer (TNBC) is an aggressive disease for which treatment options are limited and associated with severe toxicities.In this experiment we evaluated the response of 2 murine TNBC models to oncolytic Maraba virus infection. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE104768 mRNA expression of cytokine treated KYSE410 cells
Contributors : Jie Chen ; Qimin ZhanSeries Type : Expression profiling by arrayOrganism : Homo sapiensKYSE410 cells were treated with PBS, TNF α, IL1β, and LPS respectively and mRNA expression profiles were assayed by Nimblegen gene expression microarray human HG18 (12x135K)Investigation of the critical gene participating various inflammatory stimuli in the process of ESCC progression. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE104929 ACC-MESO1 cells: Control shRNA vs USP22 shRNA
Contributors : T Okamoto ; C MorimotoSeries Type : Expression profiling by arrayOrganism : Homo sapiensUSP22 plays oncogenic role and in order to study molecular mechanism of USP22 to promote tumorigenesis, microarray analysis was performed on USP22 knockdowned cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE104977 HDAC3 ChIP sequencing of L4-L6 Dorsal Root Ganglia upon spinal or sciatic axonal injury
Contributors : Ilaria Palmisano ; Matt C Danzi ; Eilidh McLachlan ; Arnau A Hervera ; Simone Di GiovanniSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusPurpose: A) compare the response to an axonal injury in the peripheral vs central nervous system B) clarify the role of HDAC3 in axonal regenerationResults: we found that after peripheral axonal injury there is a higher number of differentially expressed genes regulated by HDAC3 with respect to central injury with a number of genes associated with regenerative pathways (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE106108 The gene expression signatures in young and aging C57BL/6 mouse kidney
Contributors : Shun Xu ; Xinguang LiuSeries Type : Expression profiling by arrayOrganism : Mus musculusTo monitor the mRNA expression profiling in aging process, we initially established a physiological aging mouse model (20-month old male C57BL/6 mouse), compared with 2-month old male C57BL/6 mouse. Then, the Agilent mRNA microarray was performed to profile the gene expression levels in kidney from 20-month old male C57BL/6 mouse (designated as Aging) and 2-month old male C57BL/6 mouse (designated as Young). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE106109 The miRNA expression signatures in young and aging C57BL/6 mouse kidney
Contributors : Shun Xu ; Xinguang LiuSeries Type : Non-coding RNA profiling by arrayOrganism : Mus musculusTo identify novel aging-related miRNAs, we initially established a physiological aging mouse model (20-month old male C57BL/6 mouse), compared with 2-month old male C57BL/6 mouse. Then, the Agilent miRNA microarray was performed to profile miRNA expression levels in kidney from 20-month old male C57BL/6 mouse (designated as Aging) and 2-month old male C57BL/6 mouse (designated as Young). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by array Mus musculus Source Type: research

GSE106213 Gene expression analyses of GI eosinophils under homeostatic conditions
Contributors : Hadar Reichman ; Ariel MunitzSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRNA-seq was performed on eosinophils isolated from colons of naive C57/BL6 mice. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE106375 Cecum and liver gene expression profiles in response to dietary fibre
Contributors : Janice Drew ; Claus-Dieter MayerSeries Type : Expression profiling by arrayOrganism : Mus musculusTo dentify cecal and liver gene expression changes associated with altered microbiota profiles and reduced weight gain in mice consuming a high-fat diet supplemented with the inulin, or with inulin esterified with propionate and butyrate. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE106404 Identification of enhancer regulating Il9 gene
Contributors : Mark Kaplan ; Byunghee KohSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusEnhancers regulating Th cell specific cytokine gene expression were studied and identified. However, Il9 regulating enhancer was not identified yet. Active enhancers are characterized with P300, STATs binding and active histone modifications such as H3K4me1 and H3K27ac.Based on P300 ChIP seq analysis, we narrowed down enhancer candidates for Il9 gene expression. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE107721 BART-seq: cost-effective massively parallel targeted sequencing for genomics and transcriptomics [transcriptomics]
We report the application of a novel workflow, BART-Seq (Barcode Assembly foR Targeted Sequencing), the first highly sensitive, quantitative, and inexpensive technique for enriching selected cohorts of transcripts and genomic regions from thousands of samples in parallel, for next-generation sequencing (NGS). Multiplexing is based on a simple method for producing virtually unlimited matrices of barcoded primer sets. The method provides sample-specific amplicon labels for hundreds-fold enrichment compared to unbiased transcriptomics and genomics approaches. We demonstrated the technique by quantitative analysis of pluripote...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Homo sapiens Source Type: research

GSE107722 BART-seq: cost-effective massively parallel targeted sequencing for genomics and transcriptomics [genotyping]
We report the application of a novel workflow, BART-Seq (Barcode Assembly foR Targeted Sequencing), the first highly sensitive, quantitative, and inexpensive technique for enriching selected cohorts of transcripts and genomic regions from thousands of samples in parallel, for next-generation sequencing (NGS). Multiplexing is based on a simple method for producing virtually unlimited matrices of barcoded primer sets. The method provides sample-specific amplicon labels for hundreds-fold enrichment compared to unbiased transcriptomics and genomics approaches. We demonstrated the technique by screening cancer patients for BRCA...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE107723 BART-seq: cost-effective massively parallel targeted sequencing for genomics and transcriptomics
Series Type : Expression profiling by high throughput sequencing ; OtherOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Homo sapiens Source Type: research

GSE108399 Expression data of endoploidy-specific cells (with DNA content 2C, 4C, 8C and 16C)
Contributors : V éronique Boudolf ; Gert Van Isterdael ; Georgina Lambert ; Rahul Bhosale ; Steven Maere ; Lieven De VeylderSeries Type : Expression profiling by arrayOrganism : Arabidopsis thalianaEndocycle is an alternative cell cycle during which the DNA is replicated in the absence of cytokinesis, resulting in cellular endopolyploidy. The endocycle is frequenctly observed in plant species that grow under extreme conditions. Thus, endopolyploidy has been postulated to be a mechanism facilitating adaptive growth.We used microarrays to assess endoploidy-dependant gene expression profiles in Arabidopsis thaliana roo...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Arabidopsis thaliana Source Type: research

GSE108464 4 NSCLC cell lines treated with GDC-0973, AZ-628 or a combination of both
Series Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensRNA was purified cancer cell lines. The "SAMPLE_ID" sample characteristic is a sample identifier internal to Genentech. The ID of this project in Genentech's ExpressionPlot database is PRJ0013114 (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE108749 Discovery of inhibitors of the HSP90-Calcineurin-NFAT pathway against glioblastoma
This study yields a global view on molecular response to YZ29 treatment in GBM cells at mRNA level. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE108773 Role of SETMAR in gene expression in U2OS cells
Contributors : Michael Tellier ; Ronald ChalmersSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensChIP-exo of Flag-SETMAR in U2OS-SMF cell line, RNA-seq in duplicates for the U2OS control cell line, U2OS Flag-SETMAR cell line and U2OS Flag-SETMAR N210A cell line (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 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

GSE108912 Ethylene-independent Promotion of Photomorphogenesis by Cytokinin Requires a Functional Cytokinin and Light Signaling Pathway.
Contributors : Henrik Johansson ; Anne Cortleven ; Stephanie Ehert ; Thomas SchmuellingSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaThe transition of skotomorphogenesis to photomorphogenesis is induced by the perception of light and is characterized by the inhibition of hypocotyl elongation and opening of cotyledons. Although it is known that the plant hormone cytokinin, when applied in high concentrations, inhibits hypocotyl elongation in the dark-grown Arabidopsis plants, it is unclear to what extent this response is the result of cytokinin alone or cytokinin-induced ethy...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE111318 Ribonucleotide excision repair prevents intestinal tumorigenesis
Conclusion: We propose a hitherto unappreciated role for RNase H2 as a tumor suppressor gene in CRC. Our mouse model provides a novel tool to study the impact of abrogated RER on intestinal carcinogenesis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE111446 Transgenerational expression data from adult zebrafish exposed to low level TCDD
Contributor : Tracie R BakerSeries Type : Expression profiling by arrayOrganism : Danio rerioExposure to TCDD early in development produces reproductive abnormalities and decreased reproductive capacity in males in subsequent generationsWe used microarrays to investigate the global programme of gene expression in testicular tissue and identified distinct multigenerational and transgenerational gene expression changes due to legacy TCDD exposure in males. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Danio rerio Source Type: research

GSE111455 Array-based genome-wide transcriptome analysis of Minimally invasive follicular thyroid carcinomas
This study was conducted to identify novel prognostic factors for metastatic MI-FTC by use of the formalin-fixed paraffin-embedded (FFPE) specimens of this carcinoma. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE111497 Regulation of neuroregeneration by long noncoding RNAs [RNA-seq]
Contributors : Igor Ulitsky ; Rotem Ben-Tov PerrySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusIn mammals, neurons in the peripheral nervous system (PNS) have regenerative capacity following injury, a capacity which but it is generally absent in the central nervous system (CNS). This difference is attributed, at least in part, to the intrinsic ability of PNS neurons to activate a unique regenerative transcriptional program following injury. Long noncoding RNA (lncRNA) transcripts are typically expressed in a small subset of cell types and may facilitate specificity in regulatory pro...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE111671 Next Generation Sequencing Analysis of Wild Type and SRSF1-MKO Skeletal Muscle Transcriptomes
Contributor : Yuguo LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSkeletal muscle specific SRSF1 KO mice were generated by mating SRSF1flox/flox and MyoD-Cre mice, Total RNA from muscle sample were analyzed by Next Generation Sequencing (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE112517 A Kelch domain-containing KLHDC7B and a long non-coding RNA ST8SIA6-AS1 act oppositely on breast cancer cell proliferation via the interferon signaling pathway (KLHDC7B knockdown)
Contributors : Gookjoo Jeong ; Hansol Bae ; Sun J KimSeries Type : Expression profiling by arrayOrganism : Homo sapiensKelch domain-containing 7B (KLHDC7B) was revealed hypermethylated at promoter but upregulated in breast cancer. And we identified a long non-coding RNA, ST8SIA6-AS1 (STAR1), of which expression was highly associated with KLHDC7B in breast cancer (r = 0.5887). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE112518 A Kelch domain-containing KLHDC7B and a long non-coding RNA ST8SIA6-AS1 act oppositely on breast cancer cell proliferation via the interferon signaling pathway (KLHDC7B overexpression)
Contributors : Gookjoo Jeong ; Hansol Bae ; Sun J KimSeries Type : Expression profiling by arrayOrganism : Homo sapiensKelch domain-containing 7B (KLHDC7B) was revealed hypermethylated at promoter but upregulated in breast cancer. And we identified a long non-coding RNA, ST8SIA6-AS1 (STAR1), of which expression was highly associated with KLHDC7B in breast cancer (r = 0.5887). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE112519 A Kelch domain-containing KLHDC7B and a long non-coding RNA ST8SIA6-AS1 act oppositely on breast cancer cell proliferation via the interferon signaling pathway (LOC100128098 knockdown)
Contributors : Gookjoo Jeong ; Hansol Bae ; Sun J KimSeries Type : Expression profiling by arrayOrganism : Homo sapiensKelch domain-containing 7B (KLHDC7B) was revealed hypermethylated at promoter but upregulated in breast cancer. And we identified a long non-coding RNA, ST8SIA6-AS1 (STAR1), of which expression was highly associated with KLHDC7B in breast cancer (r = 0.5887). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE112587 A Kelch domain-containing KLHDC7B and a long non-coding RNA ST8SIA6-AS1 act oppositely on breast cancer cell proliferation via the interferon signaling pathway
Series Type : Expression profiling by arrayOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE113089 Spontaneous functional network activity in organoids resembles programmed early human brain development
We describe the different cell types and their differential gene expression patterns present in six-month-old cortical organoids following single cell analysis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE113306 Epigenetic enhancer marks and transcription factor binding influence Vk gene rearrangement frequencies in pre-B cells and pro-B cells
Contributors : Eden Kleiman ; Salvatore Loguercio ; Ann J FeeneySeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusDeep sequencing has the potential to provide great insight into the composition of the antibody repertoire and is now widely used. To date there has not been a study directly comparing relative rearrangement frequencies obtained with unbiased amplification from genomic DNA (gDNA) and cDNA from the same set of cells to elucidate any differences. Here we use a recently developed method for unbiased amplification of gDNA and directly compare the data to the unbias...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE113758 Histological, transcriptomic and in vitro analysis reveal an intrinsic activated state of myogenic precursors in hyperplasic muscle of trout
In this study, we aimed to characterize intrinsic properties of myogenic cells originating from fish hyperplasic muscle. For this purpose, we compared in situ proliferation, in vitro cell behavior and transcriptomic profile of myogenic precursors originating from hyperplasic muscle of juvenile trout (JT) and from non-hyperplasic muscle of fasted juvenile trout (FJT) and adult trout (AT). For the first time, we showed that myogenic precursors proliferate in hyperplasic muscle from JTas shown by in vivo BrdU labeling. This proliferative rate was very low in AT and FJT muscle. Transcriptiomic analysis revealed that myogenic c...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Oncorhynchus mykiss Source Type: research

GSE113863 An assessment of prognostic immunity markers in breast cancer
Contributors : Zhiyuan Hu ; Benlong Yang ; Jeff Chou ; Yaozhong Tao ; Dengbin Wu ; Xinhong Wu ; Xueqing Li ; Yan Li ; Yiwei Chu ; Tong Zhou ; William Kaufmann ; Jiong WuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensWe used Targeted RNA-seq to generate a gene expression data set of the 72-gene panel (TARGETSEQ) including 483 targeted RNA-seq data of 225 breast cancer FFPE samples from Shanghai and 258 breast cancer FFPE samples from UNC at Chapel Hill. The identified gene panel and risk evaluation model iRDM were developed in training data set AFFY1951 (p (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE114191 Repurposing of promoters and enhancers during mammalian evolution
Contributors : Francesco N Carelli ; Ang élica Liechti ; Jean Halbert ; Maria Warnefors ; Henrik KaessmannSeries Type : Expression profiling by high throughput sequencingOrganism : Callithrix jacchus ; Homo sapiens ; Macaca mulatta ; Mus musculus ; Oryctolagus cuniculus ; Rattus norvegicusThe spatiotemporal control of gene expression exerted by promoters and enhancers is central for organismal development, physiology and behaviour. These two types of regulatory elements have long been distinguished from each other based on their function, but recent work highlighted common architectural and functional features. It a...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Callithrix jacchus Homo sapiens Macaca mulatta Mus musculus Oryctolagus cuniculus Rattus norvegicus Source Type: research

GSE114810 Development of Trypanosoma brucei EATRO 1125 in the host bloodstream
Contributors : Eleanor Silvester ; Alasdair C Ivens ; Keith R MatthewsSeries Type : Expression profiling by high throughput sequencingOrganism : Trypanosoma brucei bruceiTrypanosoma brucei EATRO 1125 parasites were grown in adult MF1 mice with parasites harvested on day 3 post-infection ('ascend/slender') or on day 6 post-infection ('peak/stumpy'). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Trypanosoma brucei brucei Source Type: research

GSE114811 Development of Trypanosoma congolense IL3000 in the host bloodstream
Contributors : Eleanor Silvester ; Alasdair C Ivens ; Keith R MatthewsSeries Type : Expression profiling by high throughput sequencingOrganism : Trypanosoma congolenseTrypanosoma congolense IL3000 parasites were grown in adult MF1 mice with parasites harvested on day 5 post infection ('ascend') or on day 6/7 post infection ('peak'). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Trypanosoma congolense Source Type: research

GSE114813 Development of Trypanosoma brucei EATRO 1125 and Trypanosoma congolense IL3000 in the host bloodstream
Series Type : Expression profiling by high throughput sequencingOrganism : Trypanosoma brucei brucei ; Trypanosoma congolenseThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Trypanosoma brucei brucei Trypanosoma congolense Source Type: research

GSE115001 A spatiotemporal DNA endoploidy map of the Arabidopsis root reveals roles for the endocycle in root development and stress adaptation
Contributors : Rahul Bhosale ; Veronique Boudolf ; Fabiola Cuevas ; Thomas Eekhout ; Steven Maere ; Lieven De VeylderSeries Type : Expression profiling by high throughput sequencingOrganism : Arabidopsis thalianaSomatic polyploidy caused by endoreplication is observed in arthropods, molluscs, and vertebrates, but is especially prominent in higher plants where it has been postulated to be essential for cell growth and fate maintenance. However, a comprehensive understanding of the physiological significance of plant endopolyploidy has remained elusive. Here, we modeled and experimentally verified a high-resolution DNA endop...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE115054 Metabolic reprogramming with the induction of toxin production of Clostridioides difficile during the stationary phase
Contributors : Julia D Hofmann ; Andreas Otto ; Mareike Berges ; Rebekka Biedendieck ; Annika-Marisa Michel ; D örte Becher ; Dieter Jahn ; Meina Neumann-SchaalSeries Type : Expression profiling by arrayOrganism : Clostridioides difficile 630Systems biology approach of Clostridioides difficile to analyze the temporal changes in the intracellular and extracellular metabolme, transcriptome and proteome along the growth curve in casamino acids medium and the connection to toxin production. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Clostridioides difficile 630 Source Type: research

GSE115055 RNA-seq showed suppressed immune-related profile rescue pregnancy in an abotion mouse model
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPurpose:We hypothesize that there were some beneficial  effects in survive fetal and protected fetal from demise in placenta. Here we use RNA-seq to characterize the transcriptome changes of placenta tissue and pay more attention to immune-related genes.Methods: Female CBA/J mice were randomly allocated into two groups , abortion-prone group(A) and normal pregnance group(N), which mated with DBA/2J and BALB/c respectively. Male and female mice were mated 2 ∶1 at 18:00 and checked for vaginal plugs at 8:00 next day. Females wi...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE115102 Cryptochrome deletion in p53 mutant mice enhances apoptotic and anti-tumorigenic responses to UV damage at the transcriptome level
In this study, an RNA-seq approach was taken to identify the differentially regulated genes and pathways in p53-/- and p53-/-Cry1-/-Cry2-/- mouse embryonic fibroblasts fol lowing UV-induced DNA damage. Gene Set Enrichment Analysis demonstrated that immune surveillance associated genes regulated by IFN-γ showed increased responses, as well as genes involved in TNFα signaling via NF-κB. Protein network analysis helped identify key genes such as p21, Egr3, Sirt1, Jun and Casp1 among differentially regulated genes, and revealed their interaction partners. Collectively, the present study suggests that addition...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE115110 NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region
We report that NF-Y maintains the region upstream of TSSs in a nucleosome-depleted state while simultaneously protecting this accessible region against aberrant and/or ectopic transcription initiation. We find that loss of NF-Y binding in mammalian cells disrupts the promoter chromatin landscape, leading to nucleosomal encroachment over the canonical TSS. Importantly, this chromatin rearrangement is accompanied by upstream relocation of the transcription pre-initiation complex and ectopic transcription initiation. Further, this phenomenon generates aberrant extended transcripts that undergo translation, disrupting gene exp...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Other Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE115268 human pulmonary artery (endothelial and smoorh muscle) cells : control vs ARSB-siRNA transfected
Contributors : Anna Lalik ; Adam Golda ; Sebastian StudentSeries Type : Expression profiling by arrayOrganism : Homo sapiensTranscriptional profiling of human pulmonary artery endothelial (HAPEC) and smooth muscle (PASM) cells comparing control untreated cells with cells transfected with ARSB-siRNA. Goal was to determine the effects of silenced of arylsufatase B on global gene expression in HAPEC and PASM cells. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research