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Sequencing-based assays (Page 123)
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GSE59066: RNA-seq transcriptomic analysis of sarcomatoid (E/S), rhabdoid (E/R) and non-sarcomatoid (E*) clear cell renal cell carcinoma
The biphasic epithelioid (E-) and sarcomatoid(S-) components of sarcomatoid RCC and epithelioid (E-)...
GSE58535: H3K9 methylation fine-tunes coordination of transcription by regulating the conformational plasticity of chromosomal folding [RNA-Seq]
Despite that stochastic gene expression variations underlie lineage specification and adaptive respo...
GSE74493: Downregulation of LATS kinases alters p53 to promote cell migration
p53 is a pivotal tumor suppressor and a major barrier against cancer. We now report that silencing o...
GSE59531: TNF Signaling Exposes Latent Estrogen Receptor Binding Sites in Breast Cancer Cells [GRO-seq]
The interplay between mitogenic and proinflammatory signaling pathways play key roles in determining...
GSE56623: RNAseq to investigate transcriptional changes in human MM cell lines due to panobinostat, 5-Azacytidine, panobinostat+5-Azacytidine or n-methyl-2-pyrroldine (NMP) treatments.
Purpose: We applied RNA sequencing technology for high-throughput analysis of transcriptional change...
GSE59251: RNA-sequencing experiment: Treatment of MCF-7 breast cancer cells with the novel small molecule ZNA
MCF-7 cells were treated with either ZNA (30 uM) or a vehice control for 3 or 12 hours. Following R...
GSE73016: Primary human trophoblast from term placenta
We compare two groups of transcriptome profiles. They are 1) primary human trophoblasts (PHT) and 2)...
GSE79899: The MLL-AF9 and MLL-AF4 oncofusion proteins bind a distinct enhancer repertoire and target the RUNX1 program in MLLr AML
In MLL-rearranged (MLLr) leukemias the N terminal part of the MLL gene can be fused to over 60 diffe...
GSE59386: Human intestinal DC and MNP
Parallel subpopulations of CD11c+ MNPs present in the mouse intestine similarly exist in the human i...
GSE59100: Molecular mechanism underlying increased ischemic damage in the ALDH2*2 genetic polymorphism using a human iPSC model system
We investigated the ALDH2*2 genetic polymorphism and its underlying mechanisms for the first time in...
GSE58626: Suppression of the FOXM1 transcriptional program via novel small molecule inhibition
The transcription factor FOXM1 binds to sequence-specific motifs on DNA (C/TAAACA) through its DNA b...
GSE62820: RNA-Seq data for five HER2 over-expressed samples with twelve green fluorescent protein control samples using human mammary epithelial cells
Purpose: The goal was to capture the transcriptional activity due to over-expression of HER2 protein...
GSE63966: Differential susceptibility of human pleural and peritoneal mesothelial cells to asbestos exposure
We hypothesize that the observed differences in incidences of pleural and peritoneal malignant mesot...
GSE60217: Adenosine-to-inosine RNA editing controls cathepsin S expression in atherosclerosis by enabling HuR-mediated post-transcriptional regulation
Adenosine-to-inosine (A-to-I) RNA editing, which is catalyzed by a family of adenosine deaminase act...
GSE60216: Comparative Analysis of Transcriptional Responses in Monocytes from Human Neonates, Adults, and Older Adults
Human neonates and older adults frequently exhibit a reduced capacity to control microbial infection...
GSE60955 (human): The metabolome regulates the epigenetic landscape during naive to primed human embryonic stem cell transition
We performed mRNA-seq and small RNA-seq on the newly derived ELF human nave pluripotent stem cell li...
GSE55492: Gene expression profile of calcified and normal tricuspid aortic valves by RNA sequencing.
Purpose: Calcific aortic valve stenosis (AS) is a fatal disease with currently no medical therapy. S...
GSE60481: Identification of novel gene signatures in patients with atopic dermatitis complicated by eczema herpeticum
Background: A subset of patients with atopic dermatitis (AD) is prone to disseminated herpes simple...
GSE77737: Hotspots of aberrant enhancer activity punctuate the colorectal cancer epigenome
We sought to identify hotspots of aberrant enhancer activity in colorectal cancer (CRC) through inte...
GSE63122: Integrin v3 acting as membrane receptor for thyroid hormones mediates angiogenesis in malignant T cells
We have found that thyroid hormones (THs), acting as soluble integrin v3 ligands, activate growth-re...
GSE57253: An activating NLRC4 inflammasome mutation causes autoinflammation with recurrent macrophage activation syndrome
Inflammasomes are intracellular innate immune sensors that respond to pathogen and damage-associated...
GSE94587: Transcriptome analysis revealed impaired cAMP responsiveness in PHF21A-deficient human cells
We performed RNA-Seq on PHF21A-deficient patient-dervied lymphoblasts as well as two unaffected indi...
GSE56924: Ribosome profiling reveals an important role for translational control in circadian gene expression
Physiological and behavioral circadian rhythms are driven by a conserved transcriptional/translation...
GSE60462: iRNA-seq: Computational method for genome wide assessment of acute transcriptional regulation from total RNA-seq data
RNA-seq is a sensitive and accurate technique to compare steady state levels of RNA between differen...
GSE57896: White-to-brown metabolic conversion of human adipocytes by JAK inhibition
The rising incidence of obesity and related disorders such as diabetes and heart disease has focuse...
GSE61844: Genome-wide detection of DNase I hypersensitive sites in single cells and FFPE tissue samples
DNase I hypersensitive sites (DHSs) provide important information on the presence of transcriptional...
GSE60902: Restoration of Progranulin Expression Rescues Cortical Neuron Generation in Induced Pluripotent Stem Cell Model of Frontotemporal Dementia
To understand how haploinsufficiency of progranulin (PGRN) protein causes frontotemporal dementia (F...
GSE60949: EWS-Fli and LNC regulated genes in comparison to GFP samples
RNA from A673 cells with shRNA-mediated knockdown of GFP (4 libraries), EWS-FLI1 (4 libraries), or ...
GSE61491: CHD8regulates neurodevelopmental pathways associated with autism spectrum disorder in neural progenitors [RNA-Seq]
Truncating mutations of CHD8, encoding a chromodomain helicase, and of many other genes with diverse...
GSE61162: Specific molecular signatures underlie response to decitabine in CMML [RNA-seq]
Myelodysplastic syndromes and chronic myelomonocytic leukemia (CMML) are characterized by mutations ...
GSE60989: POU2AF1 Functions in the Human Airway Epithelium to Regulate Expression of Host Defense Genes [RNA-Seq]
In the process of seeking novel lung host defense regulators by analyzing genome-wide RNA sequence d...
GSE66446: The Cushing's disease adipose gene expression profile reveals effects of long term glucocorticoids on adipose tissue lipid, protein and glucose metabolism
Glucocorticoids have major effects on adipose tissue metabolism. To study tissue mRNA expression cha...
GSE62518: IL-33 activates tumor stroma to promote intestinal polyposis
Tumor epithelial cells develop within a microenvironment consisting of extracellular matrix, growth ...
GSE62483: T-bet recruits P-TEFb to super-enhancers to regulate T helper cell differentiation (RNA-Seq)
The transcription factor T-bet induces differentiation of CD4+ T cells into the Th1 lineage and also...
GSE64233: Acute TNF-induced repression of cell identity genes is mediated by NFkB-directed redistribution of cofactors from super-enhancers
The proinflammatory cytokine tumor necrosis factor (TNF) plays a central role in low-grade adipose t...
GSE63034: Integrative analysis identifies targetable CREB1/FoxA1 transcriptional co-regulation as a predictor of prostate cancer recurrence
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular path...
GSE61390: Genetic Correction and Metabolic Rescue of Pluripotent Cells from Patients with mtDNA
Mitochondria are vital due to their principal role in energy production via oxidative phosphorylatio...
GSE66430: Expression of gallstone disease-associated genes in non-diseased and diseased gallbladder and liver samples
Following a large-scale genome-wide association study of gallstone disease, we performed RNA sequenc...
GSE66385: Allogeneic mature human dendritic cells generate superior alloreactive regulatory T cells in the presence of IL-15
Introduction: Expansion of antigen (Ag)-specific natural occurring regulatory T cells (nTregs) is re...
GSE62190: Leucegene: AML sequencing (part 3)
RNA sequencing of human leukemia SOURCE: Guy Sauvageau Institute for Research in Immunology and Canc...
GSE62448: Enhanced MyoD-Induced Transdifferentiation to a Myogenic Lineage by Fusion to a Potent Transactivation Domain
Synthetic transcription factors can be applied to many areas of biotechnology, medicine, and basic r...
GSE61566: Isolation and Transcriptome Analyses of Human Erythroid Progenitors: BFU-E and CFU-E
Burst-forming unit-erythroid (BFU-E) and colony-forming unit-erythroid (CFU-E) cells are erythroid p...
GSE61549: A long non-coding RNA tunes PRC1 function during human and zebrafish development
Long non-coding RNAs (lncRNAs) are emerging as functional regulators of gene expression in many spec...
GSE62591: HEK 293T cells RNA-seq data treated with 5-aza-2-deoxycytidine
DNA methylation can be abnormally regulated in human disease and associated with effects on gene tra...
GSE61586: The histone H3.3K27M mutation in pediatric glioma reprograms H3K27 methylation and gene expression
Recent studies have identified a Lys 27-to-methionine (K27M) mutation at one allele ofH3F3A, one of ...
GSE85155: DHX9 suppresses spurious RNA processing defects originating from the Alu invasion of the human genome [uvCLAP CLIP-seq]
Transposable elements increase genetic diversity thus making them an important part of evolution and...
GSE62930: Human cells contain natural double-stranded RNAs with potential regulatory capacity
Although recent evidence suggests that overlapping sense/antisense transcription is a common feature...
GSE61966: BRG1 recruitment by transcription factors MITF and SOX10 defines a specific configuration of regulatory elements in the melanocyte lineage (RNA-seq)
Microphthalmia-associated transcription factor (MITF) is the master regulator of the melanocyte line...
GSE62613: Nuclear TIGAR mediates an epigenetic-metabolic loop via Nrf2 for cancer therapeutics resistance
Epigenetic and metabolic reprogrammings are implicated in cancer progression with unclear mechanisms...
GSE76271: TRIM28 interacts with EZH2 and SWI/SNF to activate genes that promote mammosphere formation
EZH2 is generally associated with H3K27 methylation and gene silencing. Mass spectrometry of the EZH...
GSE66158: Suppression of NAF-1 in Breast Cancer Cells Reduces their Tumorigenicity by Interfering with Cellular Iron Distribution and Metabolism and Ensuing ROS Formation and Apoptosis
Nutrient autophagy factor 1 (NAF-1) is an iron-sulfur protein found on the outer mitochondrial membr...
GSE65540: Impact of bariatric surgery on RNA-seq gene expression profiles of adipose tissue in humans
Bariatric surgery is the most effective therapy of severe human obesity. It is associated with impro...
GSE62193: Dissecting neural differentiation regulatory networks through epigenetic footprinting
Human pluripotent stem cell derived models that accurately recapitulate neural development in vitro ...
GSE63900: Dual RNA-sequencing of nontypeable Haemophilus influenzae and host cell transcriptomes reveals new aspects of host-pathogen interface
Characterization of host-pathogen interactions is critical for the development of next-generation th...
GSE64283: Tissue-specific circular RNA induction during human fetal development
The pervasive expression of circular RNA from protein coding loci is a recently discovered feature o...
GSE62966: Analysis of allele specific expression and its chromatin state to identify genes that are escaping X chromosome inactivation
Disappearance of the Barr body has long been considered a hallmark of cancer, although whether this ...
GSE62077: RNA-Seq Samples of siTFE3 in 8988T PDA Cell Line to Investigate Transcriptional Control of the Autophagy-Lysosome System
The activation of cellular quality control pathways to maintain metabolic homeostasis and mitigate d...
GSE63161: hiPSCs unravel aberrant TGF signaling as an etiology of left ventricular non-compaction
Left ventricular non-compaction (LVNC) is the third most prevalent cardiomyopathy in children and ha...
GSE63950: RNA sequencing of CACO-2 cells incubated with bifidobacteria grown on human milk oligosaccharides.
Background: Breastfed human infants are predominantly colonized by bifidobacteria that thrive on hum...
GSE112898: Transcriptome-wide identification of transient RNA G-quadruplexes in human cells
We report here on G4RP-seq, which comprises of a cross-linking step, followed by chemical-affinity c...
GSE63283: Slit2 modifies VEGF-induced angiogenic responses in rabbit skeletal muscle by inducing capillary sprouting and decreasing vascular permeability via reduced eNOS activity
Rationale: Slit2 is a possible modulator of vascular endothelial growth factor (VEGF) - induced angi...
GSE67543: Novel Observations from Next Generation RNA Sequencing of Highly Purified Human Adult and Fetal Islet Cell Subsets
Understanding distinct gene expression patterns of normal adult and developing fetal human pancreati...
GSE106476: RG/RGG boxes are common binding motifs in RNA-G-quadruplex-interacting proteins
G-quadruplexes (rG4s) are recognized as key structures involved in RNA biology and are linked to neu...
GSE67174: Proteogenomics-based identification of the repertoire of human MHC class I-associated peptides
We have develop a proteogenomics-based approach for identification of human MHC class I-associated p...
GSE63569: RNA sequencing of bone marrow CD34+ cells from myelodysplastic syndrome patients with and without SF3B1 mutation and from healthy controls
The splicing factor SF3B1 is the most commonly mutated gene in the myelodysplastic syndromes (MDS), ...
GSE73527: Modulation of Indoleamine 2, 3-dioxygenase 1 Expression by Activated Human T cells in Breast Cancer Cells is Controlled by DNA Promoter Methylation
Tumor infiltrating lymphocytes (TILs) play a critical role in modulating the immunoediting features ...
GSE64513: FOXD3 is a novel tumor suppressor in lung cancer
The transcription factor forkhead box D3 (FoxD3) is a transcriptional factor which belongs to forkhe...
GSE64741: Therapy induced tumour secretomes promote resistance and tumour progression
Drug resistance invariably limits the clinical efficacy of targeted therapy with kinase inhibitors a...
GSE63452: Knock-in of PIK3CA-H1047R into MCF-10A
We have compared the proteome, transcriptome and metabolome of two isogenic cell lines: MCF-10A, der...
GSE70404: Investigation about Monocytes in metastatic breast cancer patients under chemotherapy +/- Avastin
The goal of this study was to determine if blood circulating monocytes of metastatic breast cancer p...
GSE64486: The transcriptome of Kawasaki Disease arteritis
Background: Kawasaki Disease (KD) is a childhood illness of suspected infectious etiology that cause...
GSE64017: RNA sequencing of CACO-2 cells incubated with Bifidobacteria breve grown on human milk oligosaccharides.
Background: Breastfed human infants are predominantly colonized by bifidobacteria that thrive on hum...
GSE63546: The circadian transcriptional landscape in primary human mammary epithelial cells
Cells in peripheral tissue maintain a cell-autonomous molecular clock which is regulated through tra...
GSE63375: Pre-mRNA Splicing is Facilitated by an Optimal RNA Polymerase II Elongation Rate
Transcription and pre-mRNA alternative splicing was analyzed by in isogenic human HEK293 cell lines...
GSE64850: Molecular Biomarkers Screened by Next-generation RNA Sequencing for non-sentinel lymph node status predicting in breast cancer patients with metastatic sentinel lymph node
Six candidates (all ER/PR+, HER2, Ki-67 <20 %) with metastatic SLNs selected from 305 patients were ...
GSE94979: Single-cell RNA Sequencing as a tool for simultaneous shRNA detection and transcriptome analysis in the context of functional shRNA screens
Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram soma...
GSE63015: Self-organization of polarized cerebellar plate neuroepithelium in three-dimensional culture of human pluripotent stem cells
During cerebellar development, the main portion of the cerebellar plate neuroepithelium (NE) gives b...
GSE64962: Improved transcription and translation with L-leucine stimulation of mTORC1
Roberts syndrome (RBS) is a human developmental disorder caused by mutations in the cohesin acetyltr...
GSE73060: RNAseq analysis of impact of PNN on gene expression and alternative splicing in corneal epithelial cells
The specialized corneal epithelium requires differentiated properties, specific for its role at the ...
GSE63582: Response and resistance to BET bromodomain inhibitors in triple negative breast cancer [RNA-Seq]
Triple negative breast cancer (TNBC) is a heterogeneous and clinically aggressive disease for which ...
GSE70380: Patient Derived Xenograft for Delivery of Precision Medicine in Castrate Resistant Prostate Cancer
Developing animal models representating the cancer biology of advanced prostate cancer patients is c...
GSE63734: Next Generation Sequencing Facilitates Comparisons of Control and Schizophrenia-Patient derived hiPSC-derived neurons
Cell-based models of many neurological and psychiatric diseases, established by reprogramming patien...
GSE66507: Single-Cell RNA-seq Defines the Three Cell Lineages of the Human Blastocyst
Despite morphological similarities, relatively little is known about conserved developmental proces...
GSE63744: Large-scale profiling of intracellular signalling pathway activation reveals major distinctions between airway smooth muscle cells of asthmatics and non-asthmatics.
Signalling pathways regulate all major cellular events in health and disease, including asthma devel...
GSE66506: Ectoderm specification of H1 human embryonic stem cells
In recent years, several studies have shed light into the processes that regulate epidermal specific...
GSE73109: EZH2 and BCL6 cooperate to assemble CBX8-BCOR Polycomb complex to repress bivalent promoters, mediate germinal center formation and promote lymphomagenesis [RNA-seq]
EZH2 mediates the humoral immune response and drives lymphomagenesis through de novo formation of bi...
GSE64813: Gene Networks Specific for Innate Immunity Define Post-traumatic Stress Disorder [RNA-Seq]
The molecular factors involved in the development of Post-Traumatic Stress Disorder (PTSD) remain po...
GSE65885: Ribosome profiling and RNA sequencing of MCF10A-ER-Src and fibroblast cell transformation
We applied ribosome profiling and RNA sequencing to examine gene expression regulation during oncoge...
GSE65634: Whole cell mRNA expression profiling in control and complex I deficient patient fibroblasts incubated with DMSO, AICAR, chloramphenicol, and resveratrol
Background: Transcription control of mitochondrial metabolism is essential for cellular function. A ...
GSE65621 (human): Asymmetry of STAT action in driving IL-27 and IL-6 transcriptional outputs and cytokine specificity
IL-6 and IL-27 have antagonistic and overlapping functions, signal through a shared receptor subunit...
GSE64882: Conversion of Human Fibroblasts to Stably Self-Renewing Neural Stem Cells with a Single Zinc-Finger Transcription Factor
Direct conversion of somatic cells into neural stem cells (NSCs) by defined factors holds great prom...
GSE66539: Patient-derived xenograft platform for metastatic melanoma: a model for studying resistance to targeted therapy.
The therapeutic landscape of melanoma is rapidly changing. While targeted inhibitors yield significa...
GSE80688: Safety and Efficacy of the JAK Inhibitor Tofacitinib Citrate for Alopecia Areata and Variants
The samples include RNA from scalp biopsies before treatment and at 8 weeks of treatment with Tofaci...
GSE68919: Tumor exosome integrins determine organotropic metastasis
Stephen Paget first proposed, in 1889, that organ distribution of metastases is a non-random event, ...
GSE68623: RNA-Seq of GPR56+/- populations
Insights into the complex clonal architecture of acute myeloid leukemia (AML) unravelled by deep seq...
GSE71421: EHMT1 and EHMT2 inhibition induce fetal hemoglobin expression [RNA-seq]
Using UNC0638 and genetic assays to inhibit EHMT1/2 and derepress fetal hemoglobin in adult hematopo...
GSE70106: The role of antigen presenting cells in the induction of HIV-1 latency in resting CD4+ T-cells
BACKGROUND: Combination antiretroviral therapy (cART) is able to control HIV-1 viral replication, ho...
GSE65838: Novel roles of Dnmt3a and Dnmt3b at enhancers, genebodies, and promoters regulate human epidermal stem cell function
Here, we show that Dnmt3a and Dnmt3b show non-overlapping and unique patterns of genomic localizatio...
GSE65912: Integrative analysis of RNA, translation and protein levels reveals distinct regulatory variation across humans
Elucidating the extent and consequences of genetic differences between humans is essential for under...
GSE66627: Cross-species transcriptome profiling identifies new alveolar epithelial type I cell-specific genes
Diseases involving the distal lung alveolar epithelium include chronic obstructive pulmonary disease...