GSE178798 Systematic profiling of DNMT3A variants reveals protein instability mediated by the DCAF8 E3 ubiquitin ligase adaptor
Contributors : Yung-Hsin Huang ; Dapeng HaoSeries Type : Methylation profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Homo sapiens ; Mus musculusClonal hematopoiesis is a prevalent age-related condition associated with greatly increased risk of hematologic malignancies. Mutations in DNA methyltransferase 3A (DNMT3A) are the most common drivers of this state and contribute to multiple types of hematologic malignancy. DNMT3A variants occur across the gene and some are associated with particular disease states, but the functional relevance and mechanisms of pathogenesis of...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Methylation profiling by high throughput sequencing Expression profiling by high throughput sequencing Homo sapiens Mus musculus Source Type: research

GSE115843 An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [miRNA-seq]
In this study, 40 miRNAs including 38 known miRNAs representing 22 miRNA families and 2 novel miRNAs were substantially altered in response to Cd exposure. 18 differentially altered target genes were inversely correlated with 18 Cd responsive miRNAs. Majority of these targeted genes are transcript factors such as Auxin response factor 13 (ARF13), Scarecrow-like protein 6 (SCL6), Squamosa promoter-binding-like proteins (SPLs), Nuclear transcription factor Y subunit A-6 (NFYA6), Gibberellin-dependent avian myeloblastosis virus oncogene (GAMYB) and No apical meristem protein domain containing proteins (NACs), most of which we...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Oryza sativa Source Type: research

GSE116214 An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [transcriptome]
In this study, 40 miRNAs including 38 known miRNAs representing 22 miRNA families and 2 novel miRNAs were substantially altered in response to Cd exposure. 18 differentially altered target genes were inversely correlated with 18 Cd responsive miRNAs. Majority of these targeted genes are transcript factors such as Auxin response factor 13 (ARF13), Scarecrow-like protein 6 (SCL6), Squamosa promoter-binding-like proteins (SPLs), Nuclear transcription factor Y subunit A-6 (NFYA6), Gibberellin-dependent avian myeloblastosis virus oncogene (GAMYB) and No apical meristem protein domain containing proteins (NACs), most of which we...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Oryza sativa Source Type: research

GSE116275 An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress
Series Type : Non-coding RNA profiling by high throughput sequencing ; Expression profiling by high throughput sequencingOrganism : Oryza sativaThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Expression profiling by high throughput sequencing Oryza sativa Source Type: research

GSE116774 An integrated analysis of small RNAs, degradome and transcriptome in rice seedling exposure to cadmium stress [degradome]
In this study, 40 miRNAs including 38 known miRNAs representing 22 miRNA families and 2 novel miRNAs were substantially altered in response to Cd exposure. 18 differentially altered target genes were inversely correlated with 18 Cd responsive miRNAs. Majority of these targeted genes are transcript factors such as Auxin response factor 13 (ARF13), Scarecrow-like protein 6 (SCL6), Squamosa promoter-binding-like proteins (SPLs), Nuclear transcription factor Y subunit A-6 (NFYA6), Gibberellin-dependent avian myeloblastosis virus oncogene (GAMYB) and No apical meristem protein domain containing proteins (NACs), most of which we...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Oryza sativa Source Type: research

GSE138705 Multiplex genome editing uncovers a class of non-CG methylation specific for GC-rich regions in rice
We report the BS-Seq, mRNA-Seq and sRNA-Seq of the homozygous mutants and wide type in rice T1 plants, including single and multiple knock-out mutants. We found the major DNA methyltransfereases in regulating DNA methylation of rice. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Methylation profiling by high throughput sequencing Oryza sativa Source Type: research

GSE145158 Altered expression of genes in WDR5 inhibited (by OICR-9429) bladder cancer cells
Contributors : Jingtong Zhang ; Tianxin Lin ; Jian Huang ; Xu ChenSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo explore the molecular mechanism underlying OICR-9429-induced WDR5 inhibition in BCa cells, a genome-wide RNA-sequencing was conducted to compare gene expression profiles between OICR-9429 treated T24, UM-UC-3 cells and their control cells (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE148226 Epithelial cell plasticity drives endoderm formation during gastrulation
Contributors : Katharina Scheibner ; Ingo Burtscher ; Silvia Schirge ; Maren B üttner ; Michael Sterr ; Dapeng Yang ; Anika Böttcher ; Martin Irmler ; Johannes Beckers ; Filippo M Cernilogar ; Gunnar Schotta ; Fabian J Theis ; Heiko LickertSeries Type : Expression profiling by arrayOrganism : Mus musculusIt is generally accepted that epiblast cells ingress into the primitive streak by epithelial-to-mesenchymal transition (EMT) to give rise to the mesoderm; however, it is less clear how the endoderm acquires an epithelial fate. Here, we used embryonic stem cell and mouse embryo knock ‐in reporter systems to comb...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE151607 Combined inhibition of EZH2 and degradation of Ikaros has synergistic effects in germinal center B-cell diffuse large B-cell lymphoma [RNA-seq]
Contributors : Kit Tong ; Sharon Yoon ; Keren Isaev ; Robert KridelSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo explore the therapeutic opportunities to enhance the clinical efficacy of EZH2 inhibitors in treating diffuse large B-cell lymphoma (DLBCL), a genome-wide drug sensitizing CRISPR/Cas9 screen was conducted in the presence of tazemetostat. We found that the loss of IKZF1 or IKZF3 augmented the potency of tazemetostat on DLBCL. Treating cells with lenalidomide, an immunomodulatory drug that degrades IKZF1 and IKZF3, in combination with tazemetostat, recapitulated the effe...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE152028 Combined inhibition of EZH2 and degradation of Ikaros has synergistic effects in germinal center B-cell diffuse large B-cell lymphoma [ChIP-seq]
Contributors : Kit Tong ; Sharon Yoon ; Keren Isaev ; Robert KridelSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensTo explore the therapeutic opportunities to enhance the clinical efficacy of EZH2 inhibitors in treating diffuse large B-cell lymphoma (DLBCL), a genome-wide drug sensitizing CRISPR/Cas9 screen was conducted in the presence of tazemetostat. We found that the loss of IKZF1 or IKZF3 augmented the potency of tazemetostat on DLBCL. Treating cells with lenalidomide, an immunomodulatory drug that degrades IKZF1 and IKZF3, in combination with tazemetostat, recapitu...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE152069 Combined inhibition of EZH2 and degradation of Ikaros has synergistic effects in germinal center B-cell diffuse large B-cell lymphoma
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE152937 Mouse HFD Liver Skeletal Muscle SLC16A13 Knock-Out
Contributors : T Schumann ; B Hamilton ; E SimonSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusGenome-wide association identified SLC16A13 as novel type 2 diabetes gene locus. The SLC16A13 gene encodes for SLC16A13/MCT13, member of the solute carrier 16 family of monocarboxylate transporters. This transporter family recently raised interest in metabolic research with the identification of SLC16A11 polymorphisms associated with type 2 diabetes; and human as well as mouse data suggest causal relationship between SLC16A11/MCT11 transporter dysfunction and type 2 diabetes development. In...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE153159 Histone methyltransferases SDG25/ATX1 regulate heat stress memory by antagonizing DNA remethylation
Contributors : Ze-Ting Song ; Jian-Xiang LiuSeries Type : Expression profiling by high throughput sequencing ; Methylation profiling by high throughput sequencingOrganism : Arabidopsis thalianaHeat stress is a great threat to plant growth because of their sessile lifestyle. Here, we show that histone methyltransferases SDG25 and ATX1 regulate gene expression and antagonize DNA remethylation under recovery stage after long-term high temperature treatment by catalyzing the methylation of histone H3K4 loci. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Methylation profiling by high throughput sequencing Arabidopsis thaliana Source Type: research

GSE154148 Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (RNA-seq)
Contributors : Ryan L McCarthy ; Kelsey E Kaeding ; Samuel Keller ; Yu Zhong ; Liqin Xu ; Anthony Hsieh ; Yong Hou ; Greg Donahue ; Oscar Alberto ; Bomyi Lim ; Kenneth S ZaretSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensHeterochromatin, typically marked by H3K9me3 or H3K27me3, is key to the repression of genes and repetitive elements. The mechanisms responsible for establishing and maintaining heterochromatin in a locus specific manner are unclear. Heterochromatin restricts cell identity by preventing activation of alternative lineage genes. This barrier can be partially overcome b...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE154214 Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (ChIP-seq)
Contributors : Ryan L McCarthy ; Kelsey E Kaeding ; Samuel Keller ; Yu Zhong ; Liqin Xu ; Anthony Hsieh ; Yong Hou ; Greg Donahue ; Oscar Alberto ; Bomyi Lim ; Kenneth S ZaretSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Homo sapiensHeterochromatin, typically marked by H3K9me3 or H3K27me3, is key to the repression of genes and repetitive elements. The mechanisms responsible for establishing and maintaining heterochromatin in a locus specific manner are unclear. Heterochromatin restricts cell identity by preventing activation of alternative lineage genes. This barrier can be partia...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Homo sapiens Source Type: research

GSE154232 Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements (srHC-seq)
Contributors : Ryan L McCarthy ; Kelsey E Kaeding ; Samuel Keller ; Yu Zhong ; Liqin Xu ; Anthony Hsieh ; Yong Hou ; Greg Donahue ; Oscar Alberto ; Bomyi Lim ; Kenneth S ZaretSeries Type : OtherOrganism : Homo sapiensHeterochromatin, typically marked by H3K9me3 or H3K27me3, is key to the repression of genes and repetitive elements. The mechanisms responsible for establishing and maintaining heterochromatin in a locus specific manner are unclear. Heterochromatin restricts cell identity by preventing activation of alternative lineage genes. This barrier can be partially overcome by inducing ectopic transcription factors (TFs...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Other Homo sapiens Source Type: research

GSE154233 Diverse Heterochromatin-Associated Proteins Repress Distinct Classes of Genes and Repetitive Elements
Series Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy 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 - June 24, 2021 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

GSE157402 Nucleosome exchange in budding yeast
Contributors : Gilad Yaakov ; Felix Jonas ; Naama BarkaiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Saccharomyces cerevisiaeMeasuring nucleosome exchange of all four histone core subunits using novel sensors in budding yeast (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Saccharomyces cerevisiae Source Type: research

GSE162149 Identification of miRNAs that regulate hepatitis B virus replication and are potential biomarkers for therapeutic outcome
In this study we want to identify novel miRNAs that are involved in hepatitis B replication and could therefore be used as biomarkers and targeted as a potential new therapeutic option.Methods: miRNA/small RNA NGS was performed on total RNA isolated from 10 matching plasma and liver biopsy of an identification cohort of CHB patients and 10 plasma and liver controls.Results: We identified 23 and 18 miRNAs that were differentially expressed between controls and CHB patients in plasma and liver respectively, of which five were differentially expressed in both liver and plasma. Of these candidate miRNAs 3 were upregulated in l...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE162534 Epithelial cell plasticity drives endoderm formation during gastrulation
Contributors : Katharina Scheibner ; Ingo Burtscher ; Silvia Schirge ; Maren B üttner ; Anika Böttcher ; Sophie Tritschler ; Michael Sterr ; Dapeng Yang ; Martin Irmler ; Johannes Beckers ; Filippo Cernilogar ; Gunnar Schotta ; Fabian Theis ; Heiko LickertSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusWe performed 3 single-cell RNAseq experiments to identify the mechanisms of definitive endoderm formation during gastrulation. To enrich for the rare endoderm and endoderm progenitor populations we used the FVF reporter mouse line. 103 homozygous FVF embryos were isloated at t...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE167632 Dissecting OCT4 defines the role of nucleosome binding in reprogramming
Contributor : Abdenour SoufiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe aim of this study is to dissect the transcription factor OCT4 and reveal which parts of the protein are essential for interaction with nucleosomes and access to closed chromatin. We revealed that the DNA-binding domain mediates the interaction of OCT4 with nucleosomes. Remarkably, nucleosome-binding can be uncoupled from DNA-binding, diminishing the ability of OCT4 to access to closed chromatin, thus losing the pioneer function. We show that the pioneer function of OCT4 is not only essential ...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE168141 Dissecting OCT4 defines the role of nucleosome binding in pluripotency maintenance
Contributor : Abdenour SoufiSeries Type : Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusThe aim of this study is to dissect the transcription factor OCT4 and reveal which parts of the protein are essential for interaction with nucleosomes and access to closed chromatin. We revealed that the DNA-binding domain mediates the interaction of OCT4 with nucleosomes. Remarkably, nucleosome-binding can be uncoupled from DNA-binding, diminishing the ability of OCT4 to access to closed chromatin, thus losing the pioneer function. We show that the pioneer function of OCT4 is not only essential ...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE171224 Revisiting the characteristics of testicular germ cell lines GC-1(spg) and GC-2(spd)ts
Contributors : Pratibha Verma ; Priyanka ParteSeries Type : Expression profiling by arrayOrganism : Mus musculusThe study aims to explore gene expression changes associated with commerically available germ cell lines, GC-1 (spg) and GC-2 (spd)ts (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Mus musculus Source Type: research

GSE172000 The type 3 deiodinase contributes to the reduced sensitivity of the fetal brain to thyroid hormone
We examined the impact of thyroid hormone on the mouse fetal brain utilizing a model of deficiency in DIO3, the enzyme that is responsible for clearing thyroid hormones (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE173983 RECK isoforms are differentially expressed in patients with stable and unstable coronary artery disease: A pilot study.
Contributors : Chiara Vancheri ; Elena Morini ; Francesco Romeo ; Giuseppe Novelli ; Francesca AmatiSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensFour male patients were enrolled for this study in collaboration with the Cardiology Unit of Policlinico Tor Vergata-Fondazione PTV (Rome). We have performed RNA-Sequencing using NextSeq 500 ILLUMINA platform on PBMCs of patients with clinically proven healthy coronary arteries (CTR) and patients with chronic coronary artery disease (CAD) confirmed by coronary angiography. RNA sequencing results showed differentially Altenative Splicing (A...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE174540 Characterization of a novel mouse model of undifferentiated pleomorphic sarcoma that is lymphocyte poor, macrophage rich, and resistant to immune checkpoint blockade
Contributors : Karys M Hildebrand ; Kayla L Marritt ; Kurt N Hildebrand ; Arvind K Singla ; Reid McNeil ; Franz Zemp ; Jahanara Rajwani ; Doha Itani ; Pinaki Bose ; Douglas J Mahoney ; Frank R Jirik ; Michael J MonumentSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusSarcomas are rare, difficult to treat, mesenchymal lineage tumours that disproportionately affect children and young adults. Immunologically-based therapies have improved outcomes for numerous adult cancers, however, such approaches have proven ineffective for the majority of individuals with advanced sarcomas. Clinically ...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE175416 Tumor cells generate astrocytes that contribute to SHH-driven medulloblastoma relapse
Contributors : Zeng-jie Yang ; Duancheng Guo ; Shengyou Liao ; Yan ChengSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusAstrocytes, a major glial cell type in the brain, play a critical role in supporting the progression of medulloblastoma (MB), the most common malignant pediatric brain tumor. By lineage tracing analyses and single cell RNA sequencing, we demonstrate that astrocytes are predominately derived from the transdifferentiation of tumor cells in relapsed MB (but not in primary MB), although MB cells are generally believed to be neuronal-lineage committed. Such transdifferent...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE175593 Transcriptome of DLD-1 co-cultured with or without Fusobacterium nucleatum
Contributors : Xin Zheng ; Rui Liu ; Chenchen Zhou ; Haopeng Yu ; Wanyi Luo ; Jianhui Zhu ; Jiaxin Liu ; Xian Peng ; Quan Yuan ; Canhua Huang ; Xuedong ZhouSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo determine the glycolysis promoting effect of F. nucleatum and its underlying mechanisms, we performed RNA-seq to compare the gene expression profiles of DLD-1 cultured with or without F. nucleatum. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE175994 Gene expression changes by telomere shortening in human colonic organoids
Contributors : Kiichiro Tsuchiya ; Sho WatanabeSeries Type : Expression profiling by arrayOrganism : Homo sapiensGene expression changes of UC-model organoids derive from human colon indcued by telomere enlongation was assessed by Madecassoside treatemt (telomerase activator). Gene expression changes of human colon organoids induced by telomere shortening was assessd by MST-312 treatment (telomerase inhibitor). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE178510 Expression data from Minoxidil- and TCQA-2D treated HFDPCs
Series Type : Expression profiling by arrayOrganism : Homo sapiensGene expression profiling reveals a potential effect of minoxdil and TCQA in stimulating hair growth in 2D cultered dermal papilla cells.HFDPCs were human primary cells line, treated with 0,1 µM minoxidil and 10 µM TCQA for 48 h. Microarray gene expression profiling was conducted for three biological replicates (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE178548 Osteoblast-derived intraflagellar transport 140 suppresses insulin sensitivity I
Contributors : Chenyang Zhang ; Yao SunSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHyperglycemia-induced damage to bone formations and function has been recognized.However, as the largest connective tissue organ, whether bone and osteocytes in turn regulate blood sugar and insulin sensitivity has not been addressed. Here we identified a novel protein termed intraflagellar transport 140 with functional importance in regulating osteogenesis, which is also related to the osteoblastic insulin sensitivity. We established Ift140 osteoblastic conditional knockout mice model, and found th...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE178558 Osteoblast-derived intraflagellar transport 140 suppresses insulin sensitivity II
Contributors : Chenyang Zhang ; Yao SunSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusHyperglycemia-induced damage to bone formations and function has been recognized.However, as the largest connective tissue organ, whether bone and osteocytes in turn regulate blood sugar and insulin sensitivity has not been addressed. Here we identified a novel protein termed intraflagellar transport 140 with functional importance in regulating osteogenesis, which is also related to the osteoblastic insulin sensitivity. We established Ift140 osteoblastic conditional knockout mice model, and found th...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE178561 Osteoblast-derived intraflagellar transport 140 suppresses insulin sensitivity
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE178637 Expression data from Minoxidil- and TCQA-3D treated HFDPCs
Series Type : Expression profiling by arrayOrganism : Homo sapiensGene expression profiling reveals a potential higher effect of minoxdil and TCQA in stimulating hair growth in 3D cultered dermal papilla cells.HFDPCs were human primary cells line, treated with 0,1 µM minoxidil and 10 µM TCQA for 48 h. Microarray gene expression profiling was conducted for three biological replicates (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research

GSE178721 Transcriptome sequencing in serum exosomes from proliferative diabetic retinopathy (PDR)
Conclusions: Our study represents the first detailed analysis of serum exosomal transcriptomes from PDR patients by RNA-seq technology. The optimized data analysis workflows reported here should provide a framework for comparative investigations of expression profiles. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE178725 The m6A reader IMP2 directs autoimmune inflammation through an IL-17 – and TNFa-dependent C/EBP transcription factor axis
Contributors : Bechara Rami ; Gaffen SarahSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusPosttranscriptional regulation of C/EBPs through m6A/IMP2 represents a new paradigm of cytokine-driven autoimmune inflammationUsing an optimized data analysis workflow, we mapped about 40 million sequence reads per sample to the mouse genome (build mm10) and identified potential differentially regulated transcripts in the MEFs of siImp2 vs siControl with an absolute fold change ≥2 and p value (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE178737 Organoid-based drug screening reveals neddylation as therapeutic target for malignant rhabdoid tumors
Contributors : Camilla Calandrini ; Sander R van Hooff ; Irene Paassen ; Jarno DrostSeries Type : Methylation profiling by arrayOrganism : Homo sapiensMalignant rhabdoid tumors (MRT) represent one of the most aggressive childhood malignancies. No effective treatment options are available, and prognosis is therefore dismal. Previous studies have demonstrated that tumor organoids capture the heterogeneity of patient tumors and can be used to predict patient therapy response. Here, we perform drug screening on patient-derived normal and tumor organoids to identify MRT-specific therapeutic vulnerabilities. We identify neddylat...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Methylation profiling by array Homo sapiens Source Type: research

GSE178745 IL-6 promotes drug resistance through formation of polyploid giant cancer cells and stromal fibroblast reprogramming
Contributors : Na Niu ; Jun Yao ; Robert C Bast ; Anil K Sood ; Jinsong LiuSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensTo understand the role of polyploid giant cancer cells (PGCCs) in drug resistance and disease relapse, we examined the mRNA expression profile of PGCCs in ovarian cancer cells. An acute activation of IL-6 dominated senescence associated secretory phenotype lasted 2-3 weeks and declined during the termination phase of polyploidy. IL-6 activates embryonic stemness during the initiation of PGCCs and can reprogram normal fibroblasts into cancer-associated fibroblasts ...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE178753 Hsa_circ_0001021 regulates intestinal epithelial barrier function via sponging miR-224-5p in ulcerative colitis
In this study, we aim to investigate the role of circRNAs in UC pathogenesis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Non-coding RNA profiling by array Homo sapiens Source Type: research

GSE178755 Global transcriptional profiling of HCC827 lung adenocarcinoma cells in response to EGFR inhibition
Contributors : J S Gutkind ; Nadia Arang ; Toshinori AndoSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensmRNA sequencing of EGFR mutant HCC827 lung adenocarcinoma cells were treated with erlotinib (EGFR inhibitor) for 24hr to profile and characterize dysregulated pathways in response to EGFR inhibition (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE178757 A rapid and scalable PCR-based test to detect SARS-CoV-2 cellular immunity
Contributors : M Schwarz ; D Torre ; E GuccioneSeries Type : Expression profiling by high throughput sequencingOrganism : Homo sapiensThe rapid deployment of SARS-CoV-2 vaccines to a large proportion of the population argues in favor of new approaches to measure the duration of the immune response and the potential need for vaccine boosters. Here we report the development of a rapid ( (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Homo sapiens Source Type: research

GSE178758 Integrated spatial multi-omics reveals fibroblast fate during tissue repair
Contributors : Michael Januszyk ; Deshka S FosterSeries Type : Expression profiling by high throughput sequencing ; Genome binding/occupancy profiling by high throughput sequencingOrganism : Mus musculusIn the skin, tissue injury results in fibrosis in the form of scars composed of dense extracellular matrix deposited by fibroblasts. The therapeutic goal of regenerative wound healing has remained elusive in part because principles of fibroblast programming and adaptive response to injury remain incompletely understood. Here, we present a multimodal -omics platform for the comprehensive study of cell populations in complex ...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Genome binding/occupancy profiling by high throughput sequencing Mus musculus Source Type: research

GSE178764 Screening for differentially expressed circRNAs in ischemic stroke by RNA sequencing
Conclusion: The results of our study may help to elucidate the specific mechanism underlying ischemic stroke. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Non-coding RNA profiling by high throughput sequencing Homo sapiens Source Type: research

GSE178766 Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity (Salivary Gland)
Contributors : Luke C Gandolfo ; Susan N Christo ; Laura K MackaySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTissue-resident memory T cells (TRM) are non-recirculating cells that exist throughout the body. While TRM in various organs rely on common transcriptional networks to establish tissue residency, location-specific factors adapt these cells to their tissue of lodgment. Here, we chart TRM heterogeneity between organs and find that the different environments in which these cells differentiate dictate TRM function, durability and malleability. We find that unequal responsivenes...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE178767 Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity (Liver)
Contributors : Luke C Gandolfo ; Susan N Christo ; Laura K MackaySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTissue-resident memory T cells (TRM) are non-recirculating cells that exist throughout the body. While TRM in various organs rely on common transcriptional networks to establish tissue residency, location-specific factors adapt these cells to their tissue of lodgment. Here, we chart TRM heterogeneity between organs and find that the different environments in which these cells differentiate dictate TRM function, durability and malleability. We find that unequal responsivenes...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE178768 Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity (Skin)
Contributors : Luke C Gandolfo ; Susan N Christo ; Laura K MackaySeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusTissue-resident memory T cells (TRM) are non-recirculating cells that exist throughout the body. While TRM in various organs rely on common transcriptional networks to establish tissue residency, location-specific factors adapt these cells to their tissue of lodgment. Here, we chart TRM heterogeneity between organs and find that the different environments in which these cells differentiate dictate TRM function, durability and malleability. We find that unequal responsivenes...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE178769 Discrete tissue microenvironments instruct diversity in resident memory T cell function and plasticity
Series Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThis SuperSeries is composed of the SubSeries listed below. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE178770 Transcriptomics analysis of aged asthmatic lung and treated with dexamethasone during HDM induced airway inflammaton
This study was designed to evaluate the lung transcriptome analysis against dexamethasone treatment throughout HDM challenge period in the aged (80-82 Weeks) mice. The lung samples from aged inflammed mice with or without dexamethasone treatmrnt were isolated followed by RNA isolation and RNA sequence analysis. (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE178782 Gene expression in anergic and na ïve CD4 T cells deficient for Nr4a1 and Nr4a3
Contributors : Ryosuke Hiwa ; James L. Mueller ; Ravi Mandla ; Julie ZikhermanSeries Type : Expression profiling by high throughput sequencingOrganism : Mus musculusThe NR4A family of nuclear receptors are upregulated by acute and chronic antigen stimulation, and play redundant, tolerogenic roles in T and B cells. To bypass their obligate function in the Treg lineage, we generated competitive chimeras with Nr4a1-/-Nr4a3-/- (double knockout or DKO) bone marrow mixed with congenically marked WT bone marrow at a 1:5 ratio. As a result of a defect in Treg production by DKO cells, Treg in mixed chimeras are almost exclusively o...
Source: GEO: Gene Expression Omnibus - June 24, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by high throughput sequencing Mus musculus Source Type: research

GSE178708 Gene set enrichment analysis of basal and in vitro irradiation differentiates breast cancer patients with late skin radiotherapy toxicity
Contributors : Ester Aguado-Flor ; Sara Guit érrez-EnríquezSeries Type : Expression profiling by arrayOrganism : Homo sapiensRadiation-induced late effects remain a common cause of morbidity amongst cancer survivors.The purpose of this study was to investigate the molecular basis underlying the radiotherapy-induced late skin toxicity in breast cancer patients who were previously assessed for radiation-induced lymphocyte apoptosis (RILA). (Source: GEO: Gene Expression Omnibus)
Source: GEO: Gene Expression Omnibus - June 23, 2021 Category: Genetics & Stem Cells Tags: Expression profiling by array Homo sapiens Source Type: research