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Sequencing-based assays (Page 73)
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GSE118997: JMJD3 and UTX Determine Fidelity and Lineage Specification of Human Neural Progenitor Cells [RNA-seq]
Neurogenesis entails a highly orchestrated process from pluripotent to neural cell fates including p...
GSE108718: Resistin-like molecule provides vitamin A-dependent antimicrobial protection of the skin
The skin is the human bodys largest organ and is in contact with a diverse community of microorganis...
GSE89179: CHD1 regulates cell fate determination by activation of differentiation-induced genes
We describe here a novel role for CHD1 in regulating the osteoblast cell fate by studying the effect...
GSE116870: Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques [HCC1599_RNA-seq]
Purpose: To investigate the impact of oncogenic Notch on the 3D genome organization of cancer cells....
GSE117138: CBF-MYH11 fusion blocks hematopoietic differentiation via repression of a GATA2 gene program
The CBF-MYH11 fusion generated by inv(16) aberration is proposed to block normal myeloid differentia...
GSE117270: Membrane Metallo-Endopeptidase (Neprilysin) Regulates Inflammatory Response and Insulin Signaling in White Preadipocytes (RNA-Seq)
Accumulation of subcutaneous white adipose tissue (WAT) is associated with increased insulin sensiti...
GSE108653: Single-cell dissection of long non-coding RNAs pivotal for embryonic hematopoietic stem cell development
In mammalian embryos, the stepwise generation of hematopoietic stem cells (HSCs) from endothelial pr...
GSE118064: Maternal Nematode Infection Up-regulates Expression of Genes Associated with Long-Term Potentiation in Brains of Uninfected Pups
Pregnant mice were infected with Heligmosomoides bakeri nematode on gestation day 7, 12 and 17 and o...
GSE116850: The THO Complex-Dependent Posttranscriptional Control Contributes to Vascular Smooth Muscle Cell Fate Decision
We applied RNA-Seq to analyze the effects of silencing of Thoc2 or Thoc5, two components of the THO ...
GSE117212: ZBTB10 binds the telomeric variant repeat TTGGGG and interacts with TRF2 [RNA-Seq]
To study if ZBTB10 influences gene expression, we used CRISPR/Cas9 knockout HEK293 and U2OS cells to...
GSE120891: Differential expression of genes in fibroblasts and epithelial cells infected with dsDNA viruses
We studied changes in a whole transcriptome during dsDNA virus infection. SOURCE: Thomas Shenk Princ...
GSE108483: Transcriptome of the visual cortex in WT or Chrdl1 KO mice at post-natal day 14
Chrdl1, a BMP antagonist, is an astrocyte-secreted factor that promotes synapse maturation in the up...
GSE120612: Transcriptomic response to etoposide treatment in immune cell lines
RNA-seq analysis of the effects of etoposide treatment on transcriptomes of human pre-B, mature B, T...
GSE108717: Setd2-dependent H3K36me3 is required for Acrbp1 and protamine transcriptions and spermiogenesis in mice
Spermatogenesis is precisely cotrolled by complex gene expression programs and involves epigenetic r...
GSE125469: Effect of circPTPRM on the biological behaviors of hepatocellular carcinoma cells in vitro and its clinical significance.
In this paper, a new circRNA was discovered by RNA sequencing, and its relationship with hepatocarci...
GSE112566: Expression data from mouse CD19-targeted CAR (chimeric antigen receptor) T cells after antigen stimulation [RNA-seq]
Second-generation CD19-targeted chimeric antigen receptors (CAR) have an antigen-binding domain fuse...
GSE119017: Adult Connective Tissue-Resident Mast Cells Originate from Late Erythro-Myeloid Progenitors [development]
Purpose: The purpose is to systemically identify RNA expression changes along mast cell development ...
GSE125493: Feedforward regulation of Myc coordinates lineage-specific with housekeeping gene expression during progenitor cell differentiation
Chromatin-associated RNA-Seq of pre-B cell line B3 transduced with Ikaros (Ikaros-ERt2) or Myc (Myc-...
GSE117238: Transcriptome profiling identified a 3-lncRNA regulatory network in transthyretin against glucose induced hRECs dysfunction
Transcriptome of human retinal endothelial cells (hRECs) treated with low glucose (LG), high glucose...
GSE121484: Transcriptional profiling of 5 days post LPC lesion after microglia ablation
Following all types of neurological injury, resident macrophages are activated locally, and blood-de...
GSE125479: RNA-seq of Wild-type and Math5-/- mouse dLGN (dorsolateral geniculate nucleus) at postnatal day 3, postnatal day 7, postnatal day 14 and postnatal day 23
We performed transcriptome profiling for mouse dLGN (dorsolateral geniculate nucleus) tissues derive...
GSE110574: FoxK1/2 New Components in Insulin Regulation of Cellular and Mitochondrial Metabolism
A major target of insulin signaling is the FoxO family of Forkhead transcription factors, which tran...
GSE111540: Transcriptional profiling of pancreatic acinar to ductal metaplasia using laser capture microdissection
Pancreatic ductal adenocarcinoma (PDAC) is a deadly disease when diagnosed at a late stage, however ...
GSE120732: Transcriptome analysis of hiHepPCs in various culture conditions, human liver-derived hepatocytes, human liver-derived cholangiocytes, HUVECs, and HPBECs
Transcriptome analysis of human induced hepatic progenitor cells (hiHepPCs) in various culture condi...
GSE124919: Essential functions of the Glucocorticoid Receptor require direct DNA binding [RNA-seq]
We performed RNA sequencing in Mouse Embryonic Fibroblasts (MEFs) of GR wild-type and GR Zn. Cells w...
GSE116928: Recapitulating the Human Segmentation Clock with Pluripotent Stem Cells - RNAseq analysis of step-wise in vitro induction/differentiation of human presomitic mesoderm and its derivatives
Pluripotent stem cells (PSCs) have increasingly been used to model different aspects of embryogenesi...
GSE133494: RNA sequencing of hippocampal sample from normal male mice, stress induced depressive male mice and male offspring born to stress-induced depressed male mice
We demonstrated that the offspring of depressed fathers display reduced resilience to stress and enh...
GSE110585: Identification of the tumour transition states occurring during EMT [RNA-seq]
EMT in cancer has been associated with tumour stemness, metastasis and resistance to therapy. It has...
GSE120714: Extracellular vesicle based therapeutic targeting of b-catenin to modulate anti-cancer immune responses in Hepatocellular Cancer
Combination therapy with anti PD-1 and -catenin siRNA delivered using biological nanoparticles prov...
GSE116863: Restoring Mitofusin balance in the nervous system prevents axonal degeneration in a CMT2A mouse model
MFN2 is a mitochondrial outer membrane protein that plays a pivotal role in mitochondrial dynamics i...
GSE117280: RNA-seq analysis of Pten's function in regulating embryonic stem cell transition from nave to primed pluripotent state
The goals of this study are to explore the function of Pten in regulating the pluripotency transitio...
GSE117279: Investigsting the role of NF-B p50 S80 phosphorylation in regulating TNF-induced transcription in HEK293T cells
Phosphorylation of the NF-B p50 subunit is known to regulate target gene expression. Here, we invest...
GSE117248: Isogenic hPSC model of Fragile X Syndrome reveals COMT deficiency coupled with neurodevelopmental defects
We report the generation of isogenic hPSC model of FXS and characterize the neurodevelopmental capac...
GSE108864: Long noncoding RNA Hoxb3os is dysregulated in autosomal dominant polycystic kidney disease and regulates mTOR signaling
Autosomal dominant polycystic kidney disease (ADPKD) is a debilitating disease that is characterized...
GSE120767: Genome-wide expression analysis of human hTert immortalized fibroblasts after donwregulation of MCM7
Minichromosome maintenance (MCM) proteins facilitate replication by licensing origins and unwinding ...
GSE129730: Single cell RNA-seq shows cellular heterogeneity and lineage expansion in a mouse model of SHH-driven medulloblastoma support resistance to SHH inhibitor therapy
Cellular diversity within tumors and reduced lineage commitment can undermine targeted therapy by in...
GSE116127: Transcriptomic analysis of the effect of trastuzumab in human iPSC-CMs
We used human iPSC-CMs generated from healthy individuals and performed RNA-sequencing after 7 days ...
GSE145186: Microenvironmental Th9- and Th17-lymphocytes induce epithelial-mesenchymal transition in lung cancer cells, thereby promoting metastatic spreading
Analysis of gene expression profile of cancer cells after T lymphocyte-cancer cell co-culture SOURCE...
GSE117312: Pharmacologic activation of G protein-coupled estrogen receptor inhibits pancreatic ductal adenocarcinoma
We examine the effect of GPER activation on murine pancreatic ductal adenocarcinoma cell lines SOURC...
GSE138224: Inflammation induced by incomplete radiofrequency ablation accelerates tumor progression and hinders PD-1 immunotherapy
High-throughput RNA-seq analysis was performed using fresh residual CT26 tumors 3 days after incompl...
GSE118082: Gene expression profiling in mice with the depletion of prolyl hydroxylase domain proteins in endothelial cells
To evaluate gene expression changes in response to prolyl hydroxylase domain protein 2 and 3 (PHD2/3...
GSE120080: Next Generation Sequencing Facilitates Quantitative Analysis of Ventilator-Induced Lung Injury Animal Model and Control Lung Transcriptomes
Purpose: Long non-coding RNAs (lncRNAs) have been implicated in the inflammatory response of many di...
GSE120406: A neutropenia-associated transcription factor mutation differentially impacts target genes in the cell-states traversed during granulocyte specification and commitment [Gfi1-R412X-HTZ]
Advances in genetics and sequencing have lead to a deluge of disease-associated and disease-causing ...
GSE119027: Truncating variant in MYOF gene is associated with limb-girdle type muscular dystrophy and cardiomyopathy
Even though genetic studies of individuals with neuromuscular diseases have uncovered the molecular ...
GSE109173: Males undergo a transient X-chromosome inactivation-like state at the onset of nave cell differentiation
A hallmark of nave cell identity is the presence of two active X-chromosomes in females. However, li...
GSE119088: Transcriptomes change differerntly in differernt cancer cells upon EPZ-6438 treatment
Purpose: The goals of this study are to compare NGS-derived transcriptome profiling (RNA-seq) to fin...
GSE119255: Cytokeratin 18 knockdown decreases cell apoptosis by regulating the transcription and alternative splicing in Hela cell
Cytokeratin 18(CK18), one of the major components of intermediate filaments (IF) in simple-type epit...
GSE118989: KCNH2-3.1 mediates aberrant complement activation to impair hippocampal-medial prefrontal pathway associated with schizophrenia
Although elevated KCNH2-3.1 potassium channel expression is associated with cognitive dysfunctions a...
GSE119026: m6A-RNA mapping, SND1-RNA binding profile mapping and SND1-depletion in KSHV-infected B-lymphocytes
We have mapped m6A sites and endogenous SND1 binding sites in the viral and cellular transcriptome u...
GSE119290: Expression-based drug screening of neural progenitor cells from individuals with schizophrenia [RNA-seq]
Integration of in silico and in vitro approaches to design and conduct transcriptomic drug screening...
GSE119118: Gene expression profile in mouse back skin after cyclophosphamide treatment
Chemotherapy-induced hair loss (alopecia; CIA) is a highly distressing adverse effect that many canc...
GSE118762 (mouse): Transcriptome-wide analysis of adipose circular RNAs reveals their dynamic regulation in obesity and functional role in adipogenesis
Non-coding RNAs are emerging as novel regulators in adipocyte differentiation and function. Circular...
GSE121447: Transcriptomic analysis of Kidney Machine normothermic perfusion and comparision to cold storage
Kidneys which had been taken for transplant but later declined were perfused for up to 4 hours using...
GSE108736: Defining the Essential Function of Yeast Hsf1 Reveals a Compact Transcriptional Program for Maintaining Eukaryotic Proteostasis
We used the conditional chemical genetics approach known as anchor away (AA) to rapidly inactivate t...
GSE119119: Transcriptome-wide analysis of TRIM21-mediated changes in gene expression after challenge with virus and antibody
We report that TRIM21 plays a crucial role in mediating antibody interference of adenovirus gene del...
GSE118075 (mouse): Dynamics and Topology of Human Transcribed Cis-regulatory Elements
Promoters and enhancers are key cis-regulatory elements, but how they orchestrate to generate cell-t...
GSE117643: Gene expression profiles of differentiating BMSCs from WT and Irx5 knockout mice during osteoblastogenesis (day 4 post differentiation)
Functional mutagenic screening has been used to identify key factors required for a wide range of de...
GSE116934: Recapitulating the Human Segmentation Clock with Pluripotent Stem Cells - RNAseq-based comparison of patient and isogenic rescue / healthy control iPSC lines during in vitro differentiation of human presomitic mesoderm and its derivatives
Pluripotent stem cells (PSCs) have increasingly been used to model different aspects of embryogenesi...
GSE119192: Human Treg NaCl stimulation
Human Tregs isolated from PBMCs were cultured in the absence or presence of additional NaCl (40mM) f...
GSE124394: Role of p110a subunit of PI3-kinase in skeletal muscle mitochondria
Skeletal muscle insulin resistance, decreased phosphatidylinositol 3-kinase (PI3K) activation and al...
GSE138235: NAIL: an evolutionarily conserved lncRNA essential for coordinating p38 activation and NFB mediated chromatin remodelling in inflammation_2
We report the differential gene expression analysis of DSS treated colon tissues obtained from WT an...
GSE109545: A novel role of Tet1/2 proteins in cell cycle progression of trophoblast stem cells
The ten-eleven translocation (Tet) proteins are well known for their role in maintaining naive pluri...
GSE118717: Influence of endothelial Cx40 under atheroprone and atheroprotective flow
High laminar shear stress (HLSS), as observed in straight parts of arteries, assures a quiescent non...
GSE120261 (human): In situ 10-cell RNA sequencing in tissue and tumor biopsy samples
We combined the tissue preservation and single-cell resolution of laser capture with an improved pre...
GSE122206: Ezh2 regulates Langerhans cell migration and host protection against allergic contact dermatitis
We analysed by bulk RNA seq the impact of the depletion of EZH2 on Langerhans cells SOURCE: Kaibo D...
GSE125518: Targeting HuH7 cells with JumonjiC Lysine Demethylase Inhibitors (RNA-Seq)
Characterization of gene expression changes in HuH7 HCC cells upon treatment with the Jumonji KDM in...
GSE108493: RNA seq analysis of regenerating hearts from three models of successful cardiac regeneration
Defining conserved molecular pathways in animal models of successful cardiac regeneration could yiel...
GSE127233: Differential cellular transcriptional profiles during virus-induced neuroinflammation identified new microglial- and macrophage-specific genes
Goal: Determine differences in gene expression profile between microglia and macrophages isoalted fr...
GSE121486: Transcriptomics analysis of human jejunal enteroendocrine cells after vertical sleeve gastrectomy
We report here the transcriptome of a population enriched in enteroendocrine cells from human jejunu...
GSE109297: The Effect of TLR2 Activation on Transcriptome of IFN-induced Microglia
In murine glioma models, TLR2 is selectively upregulated in glioma-associated microglia. We found th...
GSE118707: RNA-Seq study of Cell lines rendered resistant to idelalisib and ibrutinib
BCR pathway inhibitors idelalisib and ibrutinib are the first small molecule targeted agents for B-c...
GSE121416: A peninsular structure coordinates asynchronous differentiation with morphogenesis to generate pancreatic islets
This scRNA-seq data is an integral part of a manuscript with the above title. Using computational me...
GSE116904: Interferon Regulatory Factor-8 (IRF8) Expression in Macrophages Governs an Anti-Metastatic Program in Breast Cancer
High macrophage infiltration in cancer is associated with reduced survival in animal models and in p...
GSE125569: 3Pool-seq: an optimized cost-efficient and scalable method of whole-transcriptome gene expression profiling (Run0064)
The advent of Next Generation Sequencing has allowed transcriptomes to be profiled with unprecedente...
GSE116094: Kidney-resident macrophages promote a proangiogenic environment in the normal and chronically ischemic mouse kidney
Renal artery stenosis (RAS) caused by narrowing of arteries is characterized by microvascular damage...
GSE119517: Transcriptome Profiling of PanIN Cells Exposed to Tobacco Carcinogen
Purpose: The goals of this study are to compare transcriptome profiling (RNA-seq) in pancreatic intr...
GSE131100: RNASeq differential expression analysis from the lung tissue of IL-33 transgenic mice
To identify the up & down regulated genes in IL-33 transgenic mice SOURCE: Daniel,Rothschild,OBrien ...
GSE116943: RNA expression in BRCA2-depleted breast cancer cell lines
Next generation RNA sequencing was performed to analyze changes in gene expression upon BRCA2 deplet...
GSE127975: Heterotypic cell-cell communication regulates multipotency in glandular epithelial stem cells
Glandular epithelia including the mammary gland (MG) and the prostate are composed of basal cells (B...
GSE118739: Leukodystrophy-associated POLR3A mutations down-regulate the RNA polymerase III transcript and important regulatory RNA BC200
RNA polymerase III (Pol III) is an essential enzyme responsible for the synthesis of several small n...
GSE124303: Liver, Adipose Tissue, and Skeletal Muscle from adult male offspring of maternal nutrient restriction in mice
Pregnant CD-1 mice were fed control (ad libitum) and 70% total food (g) (MNR) diets from E6.5-birth....
GSE125546: RNAseq analysis of hematopoietic stem cells isolated from control and Regnase1 null mice
The balance between self-renewal and differentiation of hematopoietic stem and progenitor cells (HSP...
GSE116867: Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques [MB157_RNA-seq]
Purpose: To investigate the impact of oncogenic Notch on the 3D genome organization of cancer cells....
GSE118849: Integrated analysis of a compendium of RNA-Seq data reveals putative master splicing factors underlying Rett syndrome and thermogenesis
Cold exposed mice were studied to investigate the genes changed in cold-induced thermogenesis. SOURC...
GSE127172: Gene expression profiles of mouse colonic epithelial monolayer cultured in air-liquid interface
The colonic epithelium can undergo multiple rounds of damage and repair, often in response to excess...
GSE118808: Comparative analysis of mesenchymal stem cells derived from amniotic membrane, umbilical cord and chorionic plate under serum-free condition
We performed RNA-Seq and identified the differnetially expressed gene information among human AM-MSC...
GSE117299: mRNA circularization by METTL3-eIF3h enhances translation
N6-methyladenosine (m6A) modification of mRNA catalyzed by METTL3 is enriched at a subset of stop co...
GSE118945: Myocardial-specific ablation of Jarid2 leads to dilated cardiomyopathy in mice
Analysis of heart from myocardil specific deletion of Jarid2 by crossing Jarid2 floxed mice with aMH...
GSE118879: Transcriptomic analysis of wild type and Nr4a1-/- adipose progenitors.
The project aims to identify differentially expressed genes in adipose progenitors that were freshly...
GSE120041: Theilers Virus-Mediated Immunopathology in the CNS and Heart: Roles of Organ-Specific Cytokine and Lymphatic Responses [RNA-Seq]
Theilers murine encephalomyelitis virus (TMEV) induces different diseases in the central nervous sys...
GSE127119: Variant PRC2.1 and PRC2.2 co-operate to direct H3K27 methylations in ESCs [RNA-seq]
Polycomb repressive complex 2 (PRC2) is composed of EED, SUZ12, and EZH1/2, and mediates mono-, di- ...
GSE117330: Global gene expression profiling of lung-resident CD8+ T cells from uninfected, Mtb-infected and BCG-infected mice
Transcriptomics on lung-resident CD8+ T cells reveals how global gene expression patterns diverge ov...
GSE111642: Transcriptional analysis of murine norovirus infection of primary bone marrow-derived macrophages
Murine norovirus is genetically similar to human norovirus, and offers both an efficient in vitro ce...
GSE122471: Epithelial retinoic acid receptor beta regulates serum amyloid A expression and vitamin A-dependent intestinal immunity
Retinoic acid receptor beta regulates intestinal immune transcriptional programs SOURCE: Zheng Kuang...
GSE109012: CHD4 and the NuRD complex directly control cardiac sarcomere formation
Cardiac development relies on proper cardiomyocyte differentiation including expression and assembly...
GSE117329: Transcriptomic analysis of primary human hepatic stellate cells undergoing TGFb mediated activation and JQ1 mediated attenuation of activation
Comparison of longitudinal transcriptomic profiles of activated human primary hepatic stellate cells...
GSE119562 (mouse): Definition of Natural Killer cell heterogeneity in humans and mice by high-throughput single-cell RNA sequencing
Natural Killer (NK) cells are innate lymphoid cells (ILCs) involved in antimicrobial and antitumoral...
GSE127971: Expression analysis of Lgr5 hair follicle stem cells following skin injury in the presence and absence of regulatory T cells
The goal of this study was to identify transcripts that were differentially regulated in Lgr5 hair f...
GSE122875: Transcriptional profile of stemness in the ovarian surface epithelium
We leverage RNA sequencing to identify the transcriptional changes assocaited with several experimen...
GSE109480: Hepatocytes direct the formation of a pro-metastatic niche in the liver.
The liver is the most common site of metastatic disease in gastrointestinal malignancies, including ...