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

GSE115281 C. elegans DLC-1 is a component of diverse ribonucleoprotein complexes
Contributors : Nicholas Day ; Mary Ellenbecker ; Ekaterina VoroninaSeries Type : OtherOrganism : Caenorhabditis elegansRibonucleoprotein complexes, which contain mRNAs and their regulator proteins, carry out post-transcriptional control of gene expression. The function of many RNA-binding proteins depends on their association with cofactors. Here we use a genomic approach to identify transcripts associated with DLC-1, a protein previously identified as a cofactor of two unrelated RNA-binding proteins that act in the C. elegans germline. Among the 2732 potential DLC-1 targets, most are germline mRNAs. Removal of DLC-1 affec...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Other Caenorhabditis elegans Source Type: research

GSE115558 Gene expression signatures for human interleukin-6 (IL-6) treatment in human multiple myeloma (MM) cell lines.
Contributors : Akinobu Ota ; Ichiro HanamuraSeries Type : Expression profiling by arrayOrganism : Homo sapiensTo investigate the effect of IL-6 on gene expression in IL-6-dependent MM cell lines, we have employed whole genome microarray expression profiling as a discovery platform to identify genes with the potential to be associated with the cell proliferation of MM cells. ANBL-6 and FLAM-76 cells were incubated for 48 h in the absense of IL-6, and then the cells were treated with IL-6 (10 ng/mL) for 0, 6, 12, and 24 h in vitro. (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

GSE115889 A Rank-based Semblance kernel over Probability Spaces
Conclusions: Our kernel method providees a unique framework to study cell-to-cell similarity. (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

GSE116094 Kidney-resident macrophages promote a proangiogenic environment in the normal and chronically ischemic mouse kidney
Contributors : Irina Leaf ; Amrutesh S Puranik ; Lilach O LermanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusRenal artery stenosis (RAS) caused by narrowing of arteries is characterized by microvascular damage. Macrophages are implicated in repair and injury, but the specific populations responsible for these divergent roles have not been identified. Here, we characterized murine kidney F4/80+CD64+ macrophages in three transcriptionally unique populations. Using fate-mapping and parabiosis studies, we demonstrate that CD11b/cint are long-lived kidney-resident (KRM) while CD11chiMf,...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116276 Gene array analysis of WT and TAOK3 KO T cells
Contributors : Joao Vitor S Ormonde ; Zhigang Li ; Camille Stegen ; Joaquin MadrenasSeries Type : Expression profiling by arrayOrganism : Homo sapiensRNA from cells at steady state was subjected to gene array analysis (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

GSE116532 ZEB2, a master regulator of the epithelial-mesenchymal transition, mediates trophoblast differentiation
Contributor : Nicholas P IllsleySeries Type : Expression profiling by RT-PCROrganism : Homo sapiensComparison of genes associated with the EMT between trophoblast cell line (BeWo, JEG3) controls and cells overexpressing the ZEB2 gene (BeWo ZEB2oe, JEG_ZEB2oe). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by RT-PCR Homo sapiens Source Type: research

GSE116795 The role of the Synechocystis sp. PCC  6803 homolog of the circadian clock output regulator RpaA in day-night transitions
Contributors : Christin K öbler ; Siri-Jasmin Schultz ; Dominik Kopp ; Karsten Voigt ; Annegret WildeSeries Type : Expression profiling by arrayOrganism : Synechocystis sp. PCC 6803Like many other organisms, cyanobacteria exhibit rhythmic gene expression with a period length of 24  hours to adapt to daily environmental changes. In the model organism Synechococcus elongatus PCC 7942 the central oscillator consists of three proteins: KaiA, KaiB and KaiC and utilizes the histidine kinase SasA and its response regulator RpaA as output-signaling pathway. Synechocystis sp. PCC  6803 contains two add...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Synechocystis sp. PCC 6803 Source Type: research

GSE116797 Untreated vs. QR-110 treated retinal organoids
Contributor : Kalyan DullaSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensCEP290 c.2991+1655 homozygous retinal organoids were treated with 1 µM QR-110 for 28 days (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

GSE116910 RNA-seq of Drosophilaembryos with Lim3knockdown and normal expression of Lim3
Contributors : Olga Y Rybina ; Mikhail I Schelkunov ; Elena G PasyukovaSeries Type : Expression profiling by high throughput sequencingOrganism : Drosophila melanogasterUnderstanding the molecular mechanisms underlying variation in lifespan is central to ensure long life and postpone aging. There is growing evidence that changes in expression of key lifespan regulators during early development are crucially important for lifespan determination.To study the early developmental impact of Lim3on Drosophila lifespan we performed a Lim3knockdown at early stages of Drosophiladevelopment. We detected the significant decrease of l...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Drosophila melanogaster Source Type: research

GSE116915 RNAseq quantitative analysis of ion channel mRNA expression in microbead occlusion model
Contributors : Rebecca M Sappington ; Rachel A FischerSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe purpose of this study was to utilize RNAseq to determine if there are changes in ion channel mRNA expression in the retina of C57BL/6 mice subjected to the Microbead Occlusion Model. Whole retina was isolated from 2 month old mice that received intracameral injections of either saline or 15-um-diameter microbeads. Total RNA was isolated from the retinas and subjected to RNA sequencing using Illumina HiSeq 2500. Fold change in mRNA expression was compared between saline- and microb...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE116916 RNAseq quantitative analysis of na ïve wild type and interleukin-6 knockout mice
Contributors : Rebecca M Sappington ; Lauren K WarehamSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe purpose of this study was to investigate general trasncriptomic changes in wild type and interleukin-6 knockout 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

GSE117115 PPARg Deficiency Suppresses the Release of IL-1b and a in Macrophages via a Type 1 Interferon Dependent Mechanism
Contributor : Joel SchillingSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTG elicited Peritoneal macrophages from WT and PPARgamma KO mice were treated with control or lipid inflammatory stress in triplicate (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

GSE117144 Comparison of CWC27 knockdown in HEK293T cells compared to scrambled shRNA control
Contributors : Tara L Davis ; S R Jackson ; Beth Adams ; Anh Trinh ; Peter Naranjo ; Angie Giang ; Hetty Rodriguez ; John TobiasSeries Type : Expression profiling by arrayOrganism : Homo sapiensHEK293T cells transduced with shRNA from MISSION library TRCN0000000139 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Sequence is 5 ′-CCTAAGGTTAAGTCGCCCTCGCTCTAGCGAGGGCGACTTAACCTT-3′. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, Peter Naranjo, and Angie Giang performed primary experimental contributions to cell lines, RNA/cDNA preparation, a...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE117178 Comparison of PPIE knockdown in HEK293T cells compared to scrambled shRNA control
Contributors : Tara L Davis ; S R Jackson ; Beth Adams ; Anh Trinh ; Jennifer Ayoub ; Hetty Rodriguez ; John TobiasSeries Type : Expression profiling by arrayOrganism : Homo sapiensHEK293T cells transduced with shRNA from MISSION library TRCN0000049368 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, and Jennifer Ayoub performed primary experimental contributions to cell lines, RNA/cDNA preparation, and validation, all Drexel University College of Medicine, Philadelphia, PA. Hetty Rodriguez and John To...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE117234 Comparison of PPIG knockdown in HEK293T cells compared to scrambled shRNA control
Contributors : Tara L Davis ; S. R Jackson ; Beth Adams ; Anh Trinh ; Hetty Rodriguez ; John TobiasSeries Type : Expression profiling by arrayOrganism : Homo sapiensHEK293T cells transduced with shRNA from MISSION library TRCN0000049326 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh performed primary experimental contributions to cell lines, RNA/cDNA preparation, and validations, all Drexel University College of Medicine, Philadelphia, PA. Hetty Rodriguez and John Tobias performed Bioanalyzer and micr...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE117302 Comparison of PPIL3 knockdown in HEK293T cells compared to scrambled shRNA control
Contributors : Tara L Davis ; S. R Jackson ; Beth Adams ; Anh Trinh ; Jonathan Amora ; Peter Naranjo ; Gueil Wong-Shing ; Nii Martey ; Hetty Rodriguez ; John TobiasSeries Type : Expression profiling by arrayOrganism : Homo sapiensHEK293T cells transduced with shRNA from MISSION library TRCN0000000185 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, Jonathan Amora, Peter Naranjo, Gueil Wong-Shing, and Nii Martey performed primary experimental contributions to cell lines, RNA/cDNA preparation, and valida...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE117373 Comparison of PPIL2 knockdown in HEK293T cells compared to scrambled shRNA control
Contributors : Tara L Davis ; S. R Jackson ; Beth Adams ; Anh Trinh ; Tracey Yenilaitus ; Jessica Kopenhaver ; Alyson Hurlock ; Angie Giang ; Hetty Rodriguez ; John TobiasSeries Type : Expression profiling by arrayOrganism : Homo sapiensHEK293T cells transduced with shRNA from MISSION library TRCN0000230475 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, Tracey Yenailtus, Jessica Kopenhaver, Angie Giang, and Alyson Hurlock performed primary experimental contributions to cell lines, RNA/cDNA preparatio...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE117376 Comparison of PPWD1 knockdown in HEK293T cells compared to scrambled shRNA control
Contributors : Tara L Davis ; S R Jackson ; Beth Adams ; Anh Trinh ; Jenna Marinock ; Jennifer Ayoub ; Hetty Rodriguez ; John TobiasSeries Type : Expression profiling by arrayOrganism : Homo sapiensHEK293T cells transduced with shRNA from MISSION library TRCN0000000165 using lentiviral delivery system. HEK293T cells transduced with scrambled shRNA, gifted from Dr. Mauricio Reginato. Tara L Davis, S. RaElle Jackson, Beth Adams, Anh Trinh, Jenna Marinock, and Jennifer Ayoub performed primary experimental contributions to cell lines, RNA/cDNA preparation, and validation, all Drexel University College of Medicine, Philadelphia...
Source: GEO: Gene Expression Omnibus - October 1, 2018 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research