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Sequencing-based assays (Page 141)
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GSE138025: Vascular fate in misidentified pluripotent-derived blood-brain-barrier endothelial cells rescued by transcriptional reprogramming.
A single-cell suspension was loaded into the Bio-Rad ddSEQ Single-Cell Isolator on which cells were ...
GSE155337: Aging of preleukemic thymocytes drives CpG island hypermethylation in T-cell acute lymphoblastic leukemia [RNAseq_DAC_celllines]
Cancer cells display DNA hypermethylation at specific CpG islands in comparison to their normal heal...
GSE138167: RNA sequencing of primary bronchial airway epithelial cells from young children with and without CF, including those with and without rhinovirus infection in vitro
Early life viral infections are responsible for pulmonary exacerbations that can contribute to disea...
GSE136638: An Optimized Chemical-Genetic Method for Cell-Specific Metabolic Labeling of RNA
We demonstrate that mammalian cells are able to salvage uracil analogs, yielding high background inc...
GSE152101: Nave human embryonic stem cells can give rise to cells with trophoblast-like transcriptome and methylome [RNA-Seq]
Human embryonic stem cells (hESCs) readily differentiate to somatic or germ lineages but have impair...
GSE137390: Lineage-restricted regulation of SCD and fatty acid saturation by MITF controls melanoma phenotypic plasticity
Phenotypic and metabolic heterogeneity within tumors is a major barrier to effective cancer therapy....
GSE137238: Profiling gene expression changes in primary ovarian tumors compared to matched normal fallopian tubes
Ovarian cancer is the deadliest gynecologic malignancy and the fifth leading cause for cancer relate...
GSE140442: Targeted RNA sequencing enhances gene expression profiling of ultra-low input samples
RNA-seq is the standard method for profiling gene expression in many biological systems. Due to the ...
GSE137612: Distinct and redundant roles of nuclear RNA exosome targeting complexes
Degradation of transcripts in mammalian nuclei is primarily facilitated by the RNA exosome. To obtai...
GSE140440: Single Cell Analysis Reveals NUPR1 Promotes Docetaxel Resistance in Prostate Cancer
The majority of prostate cancer (PCa) patients treated with docetaxel develop resistance to it. In ...
GSE146009: Immune-Related Gene Expression and Cytokine Secretion is Reduced Among African American Colon Cancer Patients
Background: Colorectal cancer is the third most deadly cancer among African Americans (AA). When com...
GSE143448: Transcriptomic signatures and chromatin structure in adipocytes isolated from premenauposal women subcutaneous fat [RNA-seq]
Our data showed that lipid and glucose metabolic pathways genes were expressed at higher levels in g...
GSE137237: Profiling gene expression changes in primary ovarian tumors compared to matched metastasis
Ovarian cancer is the deadliest gynecologic malignancy and the fifth leading cause for cancer relate...
GSE138177: Restoring chromatin accessibility for MLL reactivates latent tumor suppression-mediated vulnerability to proteasome inhibitors.
MLL undergoes multiple distinct chromosomal translocations to yield aggressive leukemia with dismal ...
GSE137239: Profiling gene expression changes in ovarian cancer cells seeded on 3D organotypic culture of omentum
Ovarian cancer is the deadliest gynecologic malignancy and the fifth leading cause for cancer relate...
GSE137380: A distinct CD38+CD45RA+ population of CD4+, CD8+ and double-negative T cells is controlled by FAS (I)
The identification and characterization of rare immune cell populations in humans can be facilitated...
GSE137727: A unified allosteric/torpedo mechanism for transcriptional termination on human protein-coding genes
The so-called allosteric and torpedo models have been used for the past thirty years to explain how ...
GSE138058: G3BP1-linked mRNA partitioning supports selective protein synthesis in response to oxidative stress
Cells limit energy-consuming mRNA translation during stress to maintain metabolic homeostasis. Seque...
GSE137619: The choroid plexus in progressive multiple sclerosis presents hypoxia and secretory changes that may be related to neuroprotection
The choroid plexus (CP) is a key regulator of central nervous system (CNS) homeostasis through its s...
GSE140768: Senescence induced by BMI1 inhibition is a therapeutic vulnerability in H3K27M-mutant DIPG
We studied the effect of BMI1 inhibition in diffuse intrinsic pontine glioma cells (DIPG).; We repor...
GSE138082: Hippocampal Subfield Transcriptome Analysis in Schizophrenia Psychosis
We have previously demonstrated functional and molecular changes in hippocampal subfields in individ...
GSE144986: Small-Molecule PAPD5 Inhibitors Restore Telomerase Activity in Patient Stem Cells
Genetic lesions that reduce telomerase cause a range of incurable diseases including dyskeratosis co...
GSE137403: SWI/SNF inhibition leads to epigenetic reprogramming in rhabdoid tumor [RNA-seq]
Rhabdoid tumor is a pediatric cancer characterized by the biallelic inactivation of SMARCB1, a subun...
GSE140813: The BET inhibitor CPI203 promotes ex-vivo expansion of long-term repopulating human hematopoietic stem cells and megakaryocyte
RNA sequencing reveals the transcriptomic differences between cord blood cells expanded by CPI203/cy...
GSE135485: Gene expression signature of endometrial samples from women with and without endometriosis.
Endometriosis is a benign gynecological disease characterized by the presence of endometrial-like ce...
GSE135550: MLL4 establishes enhancer-associated condensates to counterbalance Polycomb-mediated nuclear mechanical stress in Kabuki Syndrome [3'UTR RNA-seq]
The genetic elements required to tune gene expression are partitioned in active and repressive nucle...
GSE135618 (human): Transcriptional profiling of microglia; current state of the art and future perspectives
Microglia are the tissue macrophages of the central nervous system (CNS) and the first to respond to...
GSE137290: Distinct mechanisms of acquired resistance to oncogenic kinase inhibition in cancer cells revealed using a single-step, high-dose selection scheme
Despite the remarkable clinical efficacy demonstrated by molecularly-targeted cancer therapeutics, t...
GSE135552: The Influence of Met Receptor Level on HGF-Induced Glycolytic Reprogramming in Head and Neck Squamous Cell Carcinoma
Head and neck squamous cell carcinomas (HNSCC) are known to overexpress a variety of receptor tyrosi...
GSE141143: RNA-Seq for a differential gene expression bewteen KLHL14 wild-type(+/+) and KLHL14 knockout(-/-) TMD8 ABC-DLBCL cell line upon treatment with a BTK inhibitor, ibrutinib
The goal of this study is to examine gene expression changes in TMD8 KLHL14(+/+) or TMD8 KLHL14(-/-...
GSE145996: Pre- Treatment Mutational and Transcriptomic Landscape of Responding Metastatic Melanoma Patients to Anti-PD1 Immunotherapy
Immunotherapy, such as anti-PD1, has improved the survival of patients with metastatic melanoma; Ho...
GSE135773: Evolutionary conserved NSL complex/BRD4 axis controls transcription activation via histone acetylation
Cells rely on a diverse repertoire of genes for maintaining homeostasis, but the transcriptional net...
GSE141839: MAT2A as key regulator and therapeutic target in MLL leukemogenesis
Epigenetic dysregulation plays a pivotal role in MLL pathogenesis, therefore serving as suitable the...
GSE143452: Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei [ddSeq]
FSHD is characterized by the misexpression of DUX4 in skeletal muscle. Although DUX4 upregulation is...
GSE139074: AKAP8 inhibits tumor metastasis by antagonizing EMT-associated RNA alternative splicing
Tumor metastasis is the most lethal attribute of breast cancer, and the epithelial-mesenchymaltransi...
GSE137338: Linking the effects of helminth infection, diet and the gut microbiota with human whole-blood signatures
Purpose: Helminth infection and dietary intake can affect the intestinal microbiota, as well as the ...
GSE140074: KIF20A promotes the development of soft tissue sarcoma by activating the PI3K-AKT signaling pathway
Soft tissue sarcoma (STS) is a group of malignancies that can appear in any part of the body. The pr...
GSE137480: Essential Oil from Pinus Koraiensis pinecones Inhibits Gastric Cancer Cells via the HIPPO/YAP Signaling Pathway
The purpose of this study was to investigate the anti-tumor activity of PEO on MGC-803 cells and its...
GSE139061: Transcriptomic Signatures of Kidney Injury in Human Renal Biopsy Specimens
The pathogenesis and molecular signature of human acute kidney injury (AKI) remain incompletely unde...
GSE137450: Pharmacological inhibition of the HEG1-KRIT1 interaction
The Krppel-like Factors 4 and 2 (KLF4/2) are transcription factors and master regulators of endothel...
GSE138772: Genomic profiling of biliary tract cancer cell lines reveals molecular subtypes and actionable drug targets
Purpose: Biliary tract cancers (BTCs) carry a very poor prognosis and have no approved targeted ther...
GSE146070: EDEM3 modulates plasma triglyceride level through its regulation of LRP1 expression
Human genetics studies have uncovered genetic variants that can be used to guide biological research...
GSE137311: Epigenomic Profiling and Single_Nucleus_RNA_Seq of Adult Human Retina, Macula, and RPE/Choroid
Cis_regulatory elements (CREs) orchestrate the dynamic and diverse transcriptional programs that ass...
GSE139078: RNA-sequencing of airway epithelial cells from individuals with cystic fibrosis; with and without infection with human rhinovirus and treatment with CFTR corrective therapy
Background: Respiratory viruses including rhinovirus can cause pulmonary exacerbations in cystic fib...
GSE137939: Rescuing over-activated microglia by acetaminophen treatment restores cognitive performance in the Dp(16) mouse model of Down syndrome.
Microglia are the resident immune cells of the brain and have been implicated in mechanisms essentia...
GSE146066: Impact of sustained TGF-receptor inhibition on chromatin accessibility and gene expression in cultured endometrial MSC [RNA-Seq]
Endometrial mesenchymal stem cells (eMSC) drive the extraordinary regenerative capacity of the human...
GSE155431: Fatty acid metabolism mediates venetoclax resistance in acute myeloid leukemia stem cells
The combination of venetoclax with azacitidine (ven/aza) has recently emerged as a promising regime...
GSE140845: Integrative analysis of microRNAs and mRNAs in liver tissue and exosomes from blood of hepatitis C virus (HCV) related hepatocellular carcinoma (HCC) patient to identify biomarker and regulators of HCC [Total RNA-Seq]
Chronic hepatitis C (CHC) is one of the major risk factor for the progressive development of end sta...
GSE142744: High-throughput single-cell mitochondrial DNA genotyping reveals properties of clonal variation in human contexts [CLL-scRNA]
Natural mitochondrial DNA (mtDNA) sequence variation plays a fundamental role in human disease and e...
GSE137786 (human): Molecular determinants of nephron vascular specialization in the kidney
The kidney vasculature is specialized to filter waste products from the blood, regulate blood pressu...
GSE137663: Artificial escape from XCI by DNA methylation editing of the CDKL5 gene [RNA-seq]
A significant number of X-linked genes escape from X-chromosome inactivation and are associated with...
GSE139091: Hemopexin is a novel tumor suppressor that blocks cancer metastasis by modulating heme:DNA G-quadruplex dynamics to control c-myc expression
Treamtent of PC3 prostate cancer cell line results in enhanced colony growth and c-myc expression. F...
GSE137811: Time series single-cell transcriptomic analysis of AEC2 directed differentiation
We perform time-series global transcriptomic profiling of a directed differentiation protocol for ge...
GSE137802: IQGAP3 interacts with Rad17 to activate the MRN/ATM/Chk2 signaling and promote radioresistance in lung cancer
IQ motif containing GTPase activating protein 3 (IQGAP3) has been implicated in diverse cellular pro...
GSE148372: RNA-Seq of brain metastatic breast cancer cell lines after knockout of lipid metabolism genes using CRISPR/Cas9 gene editing
Brain metastasis is one of the lethal causes of breast cancer. Here we identified an altered lipid m...
GSE137893: Glucocorticoids paradoxically facilitate steroid resistance in subsets of T-cell acute lymphoblastic leukemias and normal thymocytes (CCRF-CEM)
Glucocorticoids (GCs) are a central component of therapy for patients with T-cell acute lymphoblasti...
GSE139101: Developmental GABA polarity switch and neuronal plasticity in Bioengineered Neuronal Organoids
Brain organoids are promising tools for disease modelling and drug development. For proper neuronal ...
GSE137961: Identification of a LIF-responsive replication-competent human cell
The beta () cell mass formed during embryogenesis is amplified by cell replication that occurs prima...
GSE146095: Transcriptomic profiling of human cardiac cells predicts protein kinase inhibitor-associated cardiotoxicity [Conv]
Kinase inhibitors (KIs) represent an important class of anti-cancer drugs. Although cardiotoxicity i...
GSE138741: LIN28B Regulates Transcription and Potentiates MYCN-induced Neuroblastoma in a let-7-independent Manner [RNA-seq]
LIN28B is highly expressed in neuroblastoma and promotes tumorigenesis at least in part through inhi...
GSE139436: BET protein inhibition disrupts transcription without altering enhancer-promoter interactions [RNA-seq]
In higher eukaryotes, enhancers are DNA sequences that allow for the complex temporal and tissue-spe...
GSE141136: A Stem Cell-Derived Endothelial Cell Model that Responds to Tobacco Smoke Like Primary Endothelial Cells
To clarify how smoking leads to heart attacks and stroke, we developed an endothelial cell model (iE...
GSE140898: Direct reprogramming of fibroblasts identifies signatures of vascular dysfunction in physiological aging and Hutchinson-Gilford Progeria Syndrome
Our goal was to identify gene expression and functional differences between directly reprogrammed va...
GSE138852: A single-cell atlas of the human cortex reveals drivers of transcriptional changes in Alzheimers disease in specific cell subpopulations
There is currently little information about how individual cell types contribute to Alzheimers disea...
GSE149005: USP37 Promotes Deubiquitination of HIF2a in Kidney Cancer
Clear cell renal cell carcinoma (ccRCC) is characterized by a loss of tumor suppressor Von Hippel Li...
GSE143780: Shear Stresses Associated with Cardiopulmonary Bypass Activate Expression Inflammatory Cytokines and Induce Necroptosis in Monocytes Via Calcium Dependent Signaling
Cardiopulmonary bypass (CPB), the mechanical support required during the majority of cardiac surgeri...
GSE139144: Correction of ALS-related phenotypes in iPSC-derived motor neurons carrying a hexanucleotide expansion mutation in C9orf72 by CRISPR/Cas9 genome editing and homology-directed repair
The G4C2 hexanucleotide repeat expansion (HRE) in C9orf72 is the commonest cause of familial amyotro...
GSE145229: Sex differences in neutrophil biology modulate response to type I Interferons and immunometabolism (bulkRNA-seq)
Differences in female and male immunity may contribute to variations in response to infections and p...
GSE138367: In vitro and in vivo antitumor activity of cucurbitacin C, a novel natural product from cucumber
Cucurbitacin C (CuC), a novel analogue of triterpenoids cucurbitacins, confers a bitter taste in cuc...
GSE139533: Intratumoral heterogeneity and longitudinal changes in gene expression predict differential drug sensitivity in newly diagnosed and recurrent glioblastoma
We investigated longitudinal transcriptomic patterns associated with glioblastoma (GB) recurrence by...
GSE139497: Effects of newly developed pulp-capping materials on early response of stem cells from exfoliated deciduous teeth: cell differentiation, migration, and proliferation based on next gene sequencing analysis
Aim : This study aimed to identify early effect of newly developed pulp capping materials on differe...
GSE139505: Comprehensive analysis of transcriptomic changes in cutaneous squamous cell carcinoma
Purpose: We report the coding and non-coding transcriptomic changes in primary cutaneous squamous ce...
GSE141496: CNOT1 and Transcriptomic Landscape of a HeLa Cell Line
Purpose: The goals of this study are to compare NGS-derived total transcriptome profiling (RNA-seq) ...
GSE138057: FLT3 inhibition upregulates HDAC8 via FOXO to inactivate p53 and promote maintenance of FLT3-ITD+ acute myeloid leukemia
Internal tandem duplication (ITD) mutations within the FMS-like receptor tyrosine kinase-3 (FLT3) ca...
GSE139253: Visualization and Sequencing of Accessible Chromatin Reveals Cell Cycle and Post-HDAC inhibitor Treatment Dynamics
Chromatin accessibility in the nucleus is a predictor of gene expression, cell division and cell typ...
GSE139581: Quantitative analysis of AP-1 dependent gene expression in CRISPR/Cas9 negative control and AP-1 depleted human uterine smooth muscle cells (HUtSMCs).
Down-regulation of genes belonging to the JUN, FOS, and ATF families of transcription factors has pr...
GSE139151: Gene architecture and sequence composition underpin selective dependency of long RNAs on components of the nuclear export pathway
The nuclear export pathway transports long RNAs produced in the nucleus to the cytoplasm. The core c...
GSE149008: Analysis of differentially expressed long noncoding RNAs and the associated TFmRNA network in tongue squamous cell carcinoma
Purpose: The purpose of this study was to identify aberrantly expressed lncRNAs and the associated T...
GSE146197: IL-6 derived from therapy-induced senescence facilitates the glycolytic phenotype in glioblastoma cells
In this study, we aimed to determine the fate of GBM cells following cAMP-induced differentiation. W...
GSE138853: Impact of transcriptional mutagenesis on p53 transactivation
The transcriptional error rate can be significantly increased by the presence of DNA lesions that in...
GSE138207: RNAseq experiments for "THAP11F80L cobalamin disorder-associated mutation reveals normal and pathogenic THAP11 functions in gene expression and cell proliferation"
Twelve human THAP proteins share the THAP domain, an evolutionary conserved zinc-finger DNA-binding ...
GSE139273: Transcriptional Programming of Human Mechanosensory Neuron Subtypes from Pluripotent Stem Cells
In vitro generation of human peripheral sensory neurons may provide a framework for novel drug scree...
GSE139929: Combined use of astragalus polysaccharide and berberine attenuates insulin resistance in IR-HepG2 cells via regulation of the gluconeogenesis signaling pathway
Insulin resistance (IR) is likely to induce metabolic syndrome and type 2 diabetes mellitus (T2DM). ...
GSE144206: Gene Expression Differences in Host Response to Schistosoma haematobium Infection
Schistosome worms infect over 200 million people worldwide. They live in the hosts bloodstream and a...
GSE138209: Selective therapeutic targeting of the first and second bromodomains of the BET proteins in cancer and immuno-inflammation [SLAM-seq]
The evolutionarily conserved BET bromodomain family contain a distinctive tandem bromodomain structu...
GSE141013: Integrated analyses of early responses to radiation in glioblastoma identify new alterations in RNA processing and candidate targets to improve treatment outcomes
High-dose radiation is the main component of glioblastoma therapy. Unfortunately, radio-resistance i...
GSE138988: Transcriptome-wide comparison of stress granules and P-bodies reveals that translation plays a major role in RNA partitioning
The eukaryotic cytosol contains multiple RNP granules including P-bodies and stress granules. Three ...
GSE139342: Single cell RNA-seq revealed different cell types induced by loss of ARID1A in undifferentiated and differentiation (day 10) H9 hESCs.
We reported loss of ARID1A promoted neurogenesis and inhibited cardiogenesis. Under microscopy, we o...
GSE146170: Single-cell transcriptomic analysis of allergen-specific T cells in allergy and asthma [scRNA-Seq]
CD4+ helper T cells (TH) and regulatory T cells (Treg) that respond to common allergens play an impo...
GSE146225: Wild-type and TP53 genetic knockout BOBSC hiPS cells were maintained in the undifferentiated state or differentiated to definitive endoderm over 72 hours, with or without 5 ppm MMS treatment at 24 hours.
The ability of human induced pluripotent stem cells (hiPSCs) to differentiate in vitro to each of th...
GSE146184: Therapeutic Responses to Roseomonas mucosa in Atopic Dermatitis Involve Lipid-Mediated TNF-related Epithelial Repair
Dysbiosis is increasingly implicated as a targetable contributor to the pathogenesis of atopic derma...
GSE152201: RNA-seq of DEX induced and ethanol control Basal-like breast cancer cell lines
Breast cancers can be divided into subtypes with different prognoses and treatment responses based o...
GSE139685: Functional interactions between Mi-2 and AP1 complexes control response and recovery from barrier disruption
Keratinocytes respond to environmental signals by eliciting induction of genes that preserve skins i...
GSE139262: Transcriptomic data of established human AT/RT cell lines BT-12.
The multi-subunit ATP-dependent chromatin remodeling complex BAF ('mammalian SWI/SNF complex') regul...
GSE152246: Gene expression changes following dihydrotestosterone (DHT) treatment in HCI-009 PDXs
Triple-negative breast cancer (TNBC) is aggressive and difficult, and few targeted therapies are ava...
GSE138979: Single-Cell RNA-Seq and Patient-Specific iPSCs Reveal Endocardial Abnormalities in Hypoplastic Left Heart Syndrome
Hypoplastic left heart syndrome (HLHS) is one of the most devastating forms of congenital heart defe...
GSE148842: Deconvolution of Cell Type-Specific Drug Responses in Human Tumor Tissue with Single-Cell RNA-seq
Precision oncology requires the timely selection of effective drugs or drug combinations for individ...
GSE144157: Variation of human neural stem cells generating organizer states in vitro before committing to cortical excitatory or inhibitory neuronal fates [human RNAseq #2]
Better understanding the progression of neural stem cells (NSCs) in the developing cerebral cortex i...
GSE140997: Sequence- and structure-specific cytosine-5 methylation in mRNAs by NSUN6
Methylation is the most common internal modification in mRNA. While the highly abundant N6-methylado...
GSE141350: Epigenomic analyses of FOXA1-mediated enhancer reprogramming to control tumor subtype plasticity through HH-BMP-FOXA1 signalling feedback between urothelial tumor and stromal fibroblasts [RNA-seq]
Consistent with the previous study, we showed that tumor molecular subtypes switched between the lum...