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Sequencing-based assays (Page 127)
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GSE84865: Ebola virus glycoprotein variant with increased infectivity for human cells dominated the 2013-2016 outbreak
The unprecedented magnitude of the 2013-2016 Makona Ebola virus (M-EBOV) epidemic likely resulted fr...
GSE86064: Mandatory Role of HMGA1 in Human Airway Epithelial Normal Differentiation and Post-injury Regeneration
Background: High mobility group AT-hook1 (HMGA1) is essential for airway basal cell mucociliary diff...
GSE83719: Transcriptome profiling of hematopoietic cells derived from human pluripotent stem cells
We performed morphogen-directed differentiation of human PSCs into HE followed by combinatorial scre...
GSE83512: Transcriptome-wide analysis to determine miR-200a targets in melanoma cell lines
Three metastatic melanoma cell lines (BD-0548-ME, DP-0574-ME and WP-0614-ME) were transfected with m...
GSE84610 (human): CHD1 loss sensitizes prostate cancer to DNA damaging therapy by promoting error-prone double-strand break repair
BACKGROUND:; Deletion of the chromatin remodeler CHD1 is a common genomic alteration found in human ...
GSE84620: Transcriptomic changes mediated by -amyloid in human aortic endothelial cells (HAOEC)
We found that -amyloid accumulation is modulated in HAOEC cells by overexpression or blocking of lnc...
GSE84197: Benzotriazoles reactivate latent HIV-1 through inactivation of STAT5 SUMOylation (RNA-Seq)
We screened for small molecules that reactivated latent HIV-1 and identified benzotriazoles as laten...
GSE94999: H3B-8800, a novel oral splicing modulator, induces lethality in spliceosome mutant cancers [Nalm-6]
Genomic analyses of cancer have identified recurrent point mutations in the RNA splicing factors SF3...
GSE84684: Dysregulated synaptic gene expression and axonal neuropathology in a human iPSC-based model of familial Parkinson's disease
We generated de novo induced pluripotent stem cells (iPSCs) from two Parkinsons Disease patients (PD...
GSE85417: Transcriptome of iPSC-derived Cerebral Organoids with Heterozygous Knockout in CHD8
CHD8 (chromodomain helicase DNA binding protein 8), which codes for a member of the CHD family of AT...
GSE84666: Engineered human pluripotent stem cell-derived intestinal tissues with a functional enteric nervous system
The enteric nervous system (ENS) of the gastrointestinal (GI) tract controls many diverse functions ...
GSE90683: Heterogeneity of neuroblastoma cell identity revealed by transcriptional circuitries
Neuroblastoma is a tumor of the peripheral sympathetic nervous system, derived from multipotent neur...
GSE83142: Identification of rare, dormant and therapy resistant stem cells in acute lymphoblastic leukemia
Tumor relapse is associated with dismal prognosis, but responsible biological principles remain inco...
GSE84022: BCL6-centric reorganization of the genome during B cell affinity maturation
During the humoral immune response mature B-cells undergo a dramatic change in phenotype to enable a...
GSE109795: Gene expression in mature and immature human ES-derived beta cells, and sorted beta-cells from adult islets
This submission comprises RNA-Seq profiling of in vivo differentiated pancreatic beta cells types an...
GSE84694: Reprogramming of human stem cells towards a rejuvenated and transformation-resisting state by recoding a single nucleotide
Premature senescence-associated functional decay and neoplastic transformation of transplanted human...
GSE113861: Nascent RNA Sequencing after NMYC activation in SH-EP MYCNER cells
In order to distinguish transcription changes from RNA modification and post transcription changed, ...
GSE84085: Next Generation Sequencing Facilitates Quantitative Analysis of Human Primary and Pluripotent Stem Cell-Derived Epicardial Cell Transcriptomes
Next-generation sequencing (NGS) has significantly advanced the elucidation of developmental signali...
GSE84712: RNA-seq of Human neural progenitor cells exposed to lead (Pb) reveals transcriptome dynamics, splicing alterations and Pb disease risk associations
We use time series RNA-seq to conduct a genome-wide survey of the temporal transcriptome response of...
GSE85133: Recurrent somatic mutations in POLR2A define a distinct subset of meningiomas [RNA-seq]
RNA polymerase II mediates the transcription of all protein-coding genes in eukaryotic cells, a proc...
GSE84135: The NFkB subunit RELA is a master transcriptional regulator of the committed epithelial-mesenchymal transition in airway epithelial cells
The epithelial-mesenchymal transition (EMT) is a multistep dedifferentiation program important in ti...
GSE84188: Ebolavirus species associated with differential pathogenicity induce distinct host responses in human macrophages
Highly pathogenic Zaire ebolavirus (EBOV) infection is associated with a dysregulated immune respons...
GSE84730: Long non-coding RNA TYKRIL controls pericyte function and survival in the cardiovascular and central nervous system through regulation of p53 activity and PDGFR expression
Vessel maturation is dependent on platelet derived growth factor (PDGF), which signals via tyrosine ...
GSE85461: Model systems of DUX4 expression recapitulate the transcriptional profile of FSHD cells
Facioscapulohumeral dystrophy (FSHD) is caused by the mis-expression of the double-homeodomain trans...
GSE84722: Integrative classification of human coding and non-coding genes based on RNA metabolism profiles
The pervasive transcription of the human genome results in a heterogeneous mix of coding and long no...
GSE85783: Laminin-guided highly efficient endothelial commitment from human pluripotent stem cells [Single Cell RNA-Seq]
Obtaining highly purified differentiated cells via directed differentiation from human pluripotent s...
GSE85493: Cell responses to dysregulated VZV-induced cell-cell fusion
The highly conserved herpesvirus glycoprotein complex, gB/gH-gL, mediates membrane fusion during vir...
GSE109870: transcriptome studies of BRD4 inhibitor BDF-1253 on renal clear carcinoma 786-O cells
As an epigenetic reader, BRD4 is important for the recognition of acetylated lysines and regulation ...
GSE85474: RNA-dependent RNA polymerase sequence specificities of capsnatching viruses are tailored to aid viral replication
Influenza A virus (IAV) is a major respiratory pathogen that causes severe illness and mortality wor...
GSE85510: Major roles of cyclobutane pyrimidine dimers, nucleotide excision repair and ATR in the alternative splicing response to UV irradiation
Alternative splicing (AS) is the main process that amplifies DNA information and is a crucial target...
GSE90069: Transcriptional signature of human mesoangioblasts from different fetal tissues.
Purpose: We performed comparative transcriptome analysis of mesoangioblasts (MABs) derived from diff...
GSE89049: Macrophages redirect phagocytosis by non-professional phagocytes and influence inflammation
Professional phagocytes (such as macrophages) and non-professional phagocytes (such as epithelial ce...
GSE83115: Identification of Tissue-Specific Protein-Coding and Noncoding Transcripts across 14 Human Tissues Using RNA-seq
Many diseases and adverse drug reactions exhibit tissue specificity. To better understand the tissue...
GSE87585: The Aneuploid Multiple Myeloma 3D Genome Reveals Spatial Genome Disorganization Associated with Copy Number Variations and Gene Expression
Hi-C technique has been widely applied to study the three-dimensional architecture of the whole geno...
GSE90785: Reconstitution of the human pancreatic niche stimulates differentiation of hESCs into beta cells and reveals new signals for pancreatic endocrine cell maturation
RNA-seq was performed for hESC-derived endocrine progenitors (EPs) treated with WNT5A for short-term...
GSE87495: DUX4-induced dsRNA and MYC mRNA Stabilization Activate Apoptotic Pathways in Human Cell Models of Facioscapulohumeral Dystrophy
Facioscapulohumeral muscular dystophy (FSHD) is caused by the mis-expression of DUX4 in skeletal mus...
GSE89729: Quantitative Analysis of PPARD Transcriptomes in Colon Cancer Cells by Next Generation Sequencing (NGS)
Purpose: NGS has revolutionized systems-based analysis of cell signaling pathways. The goal of this ...
GSE85527: Partially exhausted CD8+ T cells are associated with clinically beneficial response to Teplizumab in new onset type I diabetes (single-cell RNA-seq of sorted CD8+ T-cells)
Biologic agents active in other autoimmune settings have had variable effectiveness in newly diagnos...
GSE86102: RNA-Seq analysis of 4N and 2N RPE1 cells following polyploid induction via cytokinesis failure by siRNA knockdown of Anillin [tpo8]
Tetraploidization, or genome doubling, is a prominent event in tumorigenesis, primarily because cell...
GSE116267: Global effects of SUPT4H1 RNAi on gene expression of HEK293 cells
SUPT4H1 is a transcription elongation factor comprising part of the RNA polymerase II complex. Recen...
GSE85531: Partially exhausted CD8+ T cells are associated with clinically beneficial response to Teplizumab in new onset type I diabetes (whole blood RNA-seq)
Biologic agents active in other autoimmune settings have had variable effectiveness in newly diagnos...
GSE106661: Inactivation of ARID1A-SWI/SNF Complex Alters Chromatin Compactness at Enhancer Regions and Affects Transcription of Key Tumor Signaling Circuitry [RNA-Seq]
Somatic mutations in ARID1A, a SWI/SNF chromatin remodeling gene, are prevalent in human malignancie...
GSE83717: Identification and validation of differentially expressed transcripts by RNA-Sequencing of formalin-fixed, paraffin-embedded (FFPE) lung tissue from patients with Idiopathic Pulmonary Fibrosis
BACKGROUND: Idiopathic Pulmonary Fibrosis (IPF) is a lethal lung disease of unknown etiology. A majo...
GSE89726: RNA Sequencing of HUES8 WT and HUES8 TET1/2/3 TKO hESCs
The TET enzymes oxidize 5-methylcytosine to 5-hydroxymethylcytosine, which can lead to DNA demethyla...
GSE83849: Gene Expression Profiling Of TTLL12 Knocked Down Cell With Sendai Virus Treatment
Upon virus infection, RIG-I-like receptors in host cells recognize viral RNA and activate type I int...
GSE86237: Targeting Glioma Stem Cells through Combined BMI1 and EZH2 Inhibition [RNA-seq]
Glioblastomas are lethal cancers defined by angiogenesis and pseudopalisading necrosis. Here, we de...
GSE87096: Methylome, hydroxymethylome, and integrative transcriptome profiling in human CRC tissue and paired normal tissues
DNA methylation (5-mC) and hydroxymethylation (5-hmC) are regarded as important epigenetic hallmarks...
GSE84133: A single-cell transcriptomic map of the human and mouse pancreas reveals inter- and intra-cell population structure
While the function of the mammalian pancreas hinges on complex interactions of distinct cell types, ...
GSE86103: RNA-Seq analysis of proliferating 4N and 2N RPE1 cells derived from single cell clones following inhibition of Aurora B to induce polyploidization [tpo10]
Tetraploidization, or genome doubling, is a prominent event in tumorigenesis, primarily because cell...
GSE138437: Sequencing of commercially-available pancreatic cancer cell lines reveals selective CYP3A5 overexpression among xenobiotic-metabolizing CYPs.
Purpose: To know the expression of all cytochrome P450 (CYP) enzymes and related drug metabolizing e...
GSE84445: Transcriptomic profile of circulating memory T cells can differentiate between latent tuberculosis individuals and healthy controls
Tuberculosis (TB) is responsible for the majority of mortality and morbidity associated with infecti...
GSE85567: DNA methylation in lung cells is a key modulator of asthma endotypes and genetic risk [RNA-seq]
We generated genome-wide RNASeq data from freshly isolated airway epithelial cells of asthmatics and...
GSE86146: Single cell RNA-seq analysis of human germline cells and their niche cells
Human primordial germ cells (PGCs) are precursors of sperm and oocytes and are crucial for the maint...
GSE84285: Genome-wide analysis of Dengue virus 2 infected cells
The goal of this study was to compare the transcriptional profile (RNA-seq) of Dengue virus 2 and mo...
GSE129505: Transcriptional landscape of human myogenesis reavels a key role of TWIST1 in maintenance of skeletal muscle progenitors
Derivation of human skeletal muscle in vitro with human pluripotent stem cells (hPSCs) opens new ave...
GSE116266: Global effects of SUPT4H1 RNAi on gene expression of primary human fibroblasts
SUPT4H1 is a transcription elongation factor comprising part of the RNA polymerase II complex. Recen...
GSE84863: RNA sequencing of MDA-MB231 and U2OS cancer cell lines exposed to the alkylating agentmethyl methanesufonate (MMS)and classical chemotherapeutics
Understanding the mechanisms by which cells respond to chemotherapeutics is key to identifying means...
GSE84385: RNA-sequencing based transcriptome-wide expression profiling of Cynomolgus monkey and human IPSCs in vitro differentiated into endothelial cells
We report a macaque in vitro endothelial cell system using induced pluripotent stem cells (IPSCs) fr...
GSE86244: Early Chronological Aging in Human Adipose-Derived Stem Cells Marked by Distinct Transcriptional Regulation Compared to Differentiated Cells
Aging is a complex process characterized by a progressive decline in physiological integrity that le...
GSE87540: Cockayne syndrome A and B proteins regulate the transcription arrest upon genotoxic stress through a ubiquitin/proteasome degradation process (RNA-seq)
The rare genetic disease Cockayne syndrome (CS) results in mutations in CSA and CSB. Upon UV irradia...
GSE130852: MCF-7 as a model for functional analysis of breast cancer risk variants
Here we report how the ER+ cell line MCF-7 can be used to inform risk mechanisms for BCa. We identif...
GSE86422: Airway epithelial cells from smokers treated with myo-inositol or placebo
Samples were obtained as part of a randomized, double blind, placebo-controlled, phase IIb study to ...
GSE95077: Amiloride, an old diuretic drug, is a potential therapeutic agent for multiple myeloma
The introduction of novel therapeutic agents has considerably improved the median survival of patien...
GSE86159: LINC00520 is Induced by Src, STAT3, and PI3K and Plays a Functional Role in Breast Cancer
Long non-coding RNAs (lncRNAs) have been implicated in normal cellular homeostasis as well as pathop...
GSE87237: Human nave pluripotent stem cells exhibit X chromosome dampening and X-inactivation (single cell RNA-Seq)
Nave human embryonic stem cells (hESCs) can be derived from primed hESCs or directly from blastocyst...
GSE119296: Whole genome transcriptomics of pre-access veins and hemodialysis arteriovenous fistula (AVF) samples from two-stage AVF patients with different maturation outcomes (matured vs. failed)
We report the RNA expression profiles of native veins used for AVF creation and of remodeled AVF sam...
GSE85082: Control of gene expression in senescence through transcriptional read-through of convergent protein-coding genes [RNA-Seq PROLIF-SEN]
Antisense RNAs are non-coding RNAs, which can regulate their corresponding sense RNAs and are genera...
GSE87626: Interaction between mitoNEET and NAF-1 in cancer cells
The NEET proteins mitoNEET (mNT) and nutrient-deprivation autophagy factor-1 (NAF-1) are required fo...
GSE86001: Binding to SMN2 pre-mRNA-Protein complex elicits specificity for small molecule splicing modifiers
Small molecule splicing modifiers have been extensively described which target the generic splicing ...
GSE86452: CD161+ Tconv and Treg share transcriptome and display a migratory phenotype which is modified at the inflamed site
Regulatory T cells (Treg) are a cornerstone of immune regulation. Recent evidence indicates that hum...
GSE103071: RNA-seq analysis of melanoma and carcinoma cells expressing FOXQ1
We report the genome wide RNA sequencing for high-throughput profiling of FOXQ1 target genes in mela...
GSE87559: Pharmacological Induction of a Progenitor State for the Efficient Expansion of Primary Human Hepatocytes
Transplantation of genetically corrected hepatocytes is an attractive alternative to liver transplan...
GSE87668: p53 activity results in DNA replication fork processivity
p53 induces cell death upon DNA damage, but this may not confer all of its tumor suppressor activity...
GSE86518: Genome-wide mRNA expression in human glioblastoma cells and glioblastoma stem cells expressing or not Omomyc
MYC deregulation is common in human cancer and has a role in sustaining the aggressive cancer stem c...
GSE93783: Cytotoxic Vibrio T3SS1 Rewires Host Gene Expression to Subvert Cell Death Signaling and Activate Cell Survival Networks
Abstract: The type three secretion system 1 (T3SS1) of the marine bacterium, Vibrio parahaemolyticus...
GSE89774: Modulation of nonsense-mediated decay by rapamycin
Rapamycin is a naturally occurring macrolide whose target is at the core of nutrient and stress regu...
GSE103630: Expression changes in melanoma cell lines pre MAPKi treatment vs. post-MAPKi resistance (RNA-seq_CellLine.batch2)
Treatment of advanced V600BRAF mutant melanoma using a BRAF inhibitor (BRAFi) or its combination wit...
GSE87254: Trac-looping measures genome structure and chromatin accessibility
Interaction between different chromatin regions plays critical roles in genome organization and regu...
GSE87750: Zika virus directly infects human peripheral neurons and induces cell death
Zika virus (ZIKV), a flavivirus transmitted primarily by Aedes mosquitoes, has spread to 59 countrie...
GSE89777: Pluripotent Reprogramming of Human AML Resets Leukemic Behavior and Models Therapeutic Targeting of Subclones [RNA-seq]
Understanding the contribution of abnormal genetic and epigenetic programs to acute myeloid leukemia...
GSE90068: REST suppression mediates neural conversion of adult human fibroblasts via microRNA dependent and independent pathways
Direct conversion of human fibroblasts into mature and functional neurons, termed induced neurons (i...
GSE86550: Deletions in the ATAD3 gene cluster cause cerebellar developmental defects with mitochondrial DNA abnormalities owing to local cholesterol insufficiency
The DNA in mitochondria is associated with the inner of two membranes and it co-fractionates with th...
GSE89063: Development of an In Vitro Human Liver System for Interrogating Non-Alcoholic Steatohepatitis
A barrier to drug development for non-alcoholic steatohepatitis (NASH) is the absence of translation...
GSE87497: Evaluating Side Effects of Nanoparticle-mediated siRNA Delivery to Mesenchymal Stem Cells Using Next-generation Sequencing and Enrichment Analysis
RNA interference (RNAi) has immense potential to modulate cell functions. However, effective deliver...
GSE150557: Genes regulated by DNMT1 in WM266.4 human melanoma cells
Gene expression data of WM266.4-Luc-mEGFP cells treated with siCtrl or siDNMT1 SOURCE: Eishu Hirata ...
GSE86577: ERK5 kinase activity is dispensable for cellular immune response and proliferation
Unlike other members of the MAPK family, ERK5 contains a large C-terminal domain with transcriptiona...
GSE87320: Cis-Regulatory Circuits Regulating NEK6 Kinase Overexpression in Transformed B Cells Are Super-Enhancer-Independent (RNA-seq)
Alterations in distal regulatory elements that control gene expression underlie many diseases, inclu...
GSE87831: Nucleoporin-mediated regulation of cell identity genes
The organization of the genome in the three-dimensional space of the nucleus is coupled with cell ty...
GSE89122: Gene expression of collecting duct carcinoma of the kidney
The genetic landscape and molecular features of collecting duct carcinoma (CDC) of the kidney remain...
GSE93156: Diffuse Large B Cell Lymphoma cell line with Acquired Resistance to PI3K Inhibitor Idelalisib
RNAseq profile of TMD8 cell lines resistant to Idelalisib treatment. Idelalisib resistant TMD8 cell...
GSE102732: RNA sequencing (RNA-SEQ) of WT and LFS patient specific iPSC derived pre-osteoblasts
Purpose: To understand molecular and cellular effects of sFRP2 overexpression in LFS patients; Metho...
GSE107514: Global Transcriptional analysis of human spinal cord and neocortical neuroepithelial stem (NES) cells
We report the transcriptional profile of human spinal cord and neocortical neuroepithelial stem cell...
GSE87326: Exploiting drug addiction mechanisms to select against MAPKi resistant melanoma
Melanoma resistant to MAPK inhibitors (MAPKi) displays loss of fitness upon experimental MAPKi withd...
GSE87535: Systematic identification of molecular pathways driving GBM invasion
Glioblastoma multiforme (GBM) is the most prevalent and deadliest adult brain tumor. To systematical...
GSE85494: RNA-sequencing of milk cells extracted from pre-partum secretions and longitudinally from mature human milk across the first year of lactation
Changes in mammary cell behavior mediating normal breast development during pregnancy and lactation ...
GSE94149: Memory CD4+ T cell subsets show differential responses to HIV latency reversing agents [LARA]
HIV-1 persists in individuals on ART in infected central (CM), transitional (TM) and effector memory...
GSE86104: RNA-Seq analysis RPE1 cells following exposure to Nutlin-3 to identify target genes of p53 [tpo12]
Tetraploidization, or genome doubling, is a prominent event in tumorigenesis, primarily because cell...
GSE87340: Conserved recurrent gene mutations correlate with pathway deregulation and clinical outcomes of lung adenocarcinoma in never-smokers
Background. Novel and targetable mutations are needed for improved understanding and treatment of lu...
GSE85839: Efficient derivation of microglia-like cells from human pluripotent stem cells
Microglia-like cells and neural cells were generated from several hES and hIPS lines. As subset was ...
GSE86101: RNA-Seq analysis of 4N and 2N RPE1 cells following polyploid induction via cytokinesis failure or Aurora kinase inhibition [tpo3]
Tetraploidization, or genome doubling, is a prominent event in tumorigenesis, primarily because cell...