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Sequencing-based assays (Page 134)
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GSE115898: Transcriptional landscape of epithelial and immune cell populations revealed through FACS-seq of healthy human skin
Human skin consists of multiple cell types, including epithelial, immune, and stromal cells. Transcr...
GSE114519: Mitochondrial hypoxic stress induces RNA editing by APOBEC3G in lymphocytes
Protein recoding by RNA editing is required for normal health and evolutionary adaptation. However, ...
GSE113165: Age-dependent skeletal muscle transcriptome response to bed rest-induced atrophy
Short-term bed rest is used to simulate muscle disuse in humans. In our previous reports, we found ...
GSE119700: Transcription-dependent control of stem cell self-renewal and differentiation by the splicing factor U2AF1
Purpose: Here we describe the modulation of a gene expression program involved in cell fate.; Method...
GSE117038: lncRNA expression analysis in patients with eosinophilic and neutrophilic asthma
Long non-coding RNA (lncRNA) are known to be important in many diseases. There has been some reports...
GSE119402: DUX4-induced histone variants H3.X and H3.Y mark DUX4 target genes for expression (RNA-seq)
We determined the effects of short pulses of DUX4 expression on genome-wide transcription, mimicking...
GSE117906: GATA3 enhances the neurogenic potential of primary human astrocytes after traumatic injury [exp2]
Astrocytes are an abundant cell type in the vertebrate central nervous system and can act as neural ...
GSE114297: Pseudotime Ordering of Single Human Beta-Cells Reveals States of Insulin Production and Unfolded Protein Response
We report the pseudotime ordering of single non-diabetic human beta-cells detected by large-scale RN...
GSE129630: Human iPSC-derived microglia are genetically relevant to Alzheimers disease
Microglia is a primary brain immune cell type that has been implicated in the pathogenesis of neurod...
GSE128163: The human fetal thymus generates effector invariant T cells in a Lin28b-dependent manner
In the mouse thymus, invariant T cells are generated at well-defined times during development and a...
GSE129637 (human): MLL-Menin inhibition reverses pre-leukemic progenitor self-renewal induced by NPM1c mutations [RNA-Seq]
Menin binding to MLL1 is required to maintain self-renewal properties of NPM1c progenitors at differ...
GSE115853: Organoids derived from directly reprogrammed human hepatocytes for modeling liver cancer initiation
Hepatocellular carcinoma (HCC) and cholangiocarcinoma (ICC) are two main forms liver cancers with po...
GSE118980: GATA2 promotes hematopoietic development and represses cardiac differentiation of human mesoderm
In vertebrates, GATA2 is a master regulator of hematopoiesis and is expressed throughout embryo deve...
GSE114311: Regulation of pre-mRNA splicing by m6A through the low-complexity protein hnRNPG and co-transcriptional pausing
Co-transcriptional processing of nascent transcripts is coupled with transcription through the carbo...
GSE137946: Radiotherapy and IFN treatment effect on transcriptome in HT1080 cells
Immune checkpoint blockade is a powerful oncologic treatment modality for a wide variety of human ma...
GSE115565: Human iPSC-derived GABAergic Interneuron Transplants Attenuate Neuropathic Pain
Neuropathic pain causes severe suffering and most patients are resilient to current therapies. A cor...
GSE116580: SMUG1 promotes telomere maintenance through telomerase RNA end-processing
Single-strand selective uracil DNA-glycosylase (SMUG1) associates with the DKC1-H/ACA ribonucleoprot...
GSE113209: Acute viral bronchiolitis (NMS)
Background: A subset of infants are hyper-susceptible to severe/acute viral bronchiolitis (AVB), for...
GSE114569: Cellular recruitment by podocyte-derived pro-migratory factors in assembly of the human renal filter
Analysis of monogenic kidney disease-causing genes, and secondary pathology resulting from systemic ...
GSE113121: Widespread and Functional RNA Circularization in Localized Prostate Cancer
Standard RNA analyses using microarrays and low-coverage polyadenylation enriched RNA-Sequencing (RN...
GSE113218: Epigenetic changes induced by Bacteroides fragilis toxin (BFT) [RNA-seq]
Purpose: The goal of this study is to determine how BFT2 alters chromatin accessibility at relativel...
GSE114326: Transcriptome profiling of CXCR2+ neuroendocrine (NE) tumor cells purified from patients' fresh prostate adenocarcinoma
The development of therapy resistance is inevitable in prostate cancer (PCa) despite maximal inhibit...
GSE128576: mRNA-sequencing of 293T-no dice transfected with miR-16, miR-214, or KSHV-miR-K6-5p
The viral miRNA miR-K6-5p encoded by the DNA tumor virus Kaposis sarcoma-associated herpesvirus exhi...
GSE126232: Molecular effects of ISRIB during asparagine deprivation
The integrated stress response (ISR) is a conserved pathway which is activated by cells that are exp...
GSE116631: Loss of SFPQ is synthetically lethal with BRAFV600E in colorectal cancer cells
Oncogenes such as BRAFV600E kinase entrust cancer cells with novel properties that increase their fi...
GSE113399: SETDB1 compacts the inactive X chromosome in part through silencing an enhancer in the IL1RAPL1 gene
The product of dosage compensation in human females is the compacted inactive X chromosome (Xi). Her...
GSE115103: The CD4+ alike CD8+ memory T cell compartment diversification reveales CD8+ T cell subsets with cytotoxic and non-cytotoxic properties
CD4+ memory T helper cells are organized in different subsets characterized by distinct functions an...
GSE128683: RNA sequencing data of paired parental and therapy resistant cancer cell lines
RNA sequencing data of paired parental and therapy resistant cancer cell lines. Parental cell lines ...
GSE113008: mRNA sequencing of Aniridia limbal epithelial cells.
PAX6-related Aniridia is a sight-threatening disease due to progression of secondary glaucoma and an...
GSE117084: Safeguarding nucleolar homeostasis by CBX4 alleviates senescence and osteoarthritis
Chromobox homolog 4 (CBX4), a component of polycomb repressive complexes 1 (PRC1), plays important r...
GSE113426: RNAseq Study in CC-671 Treated Cal-51 Cells
CC-671 has been identified as an inhibitor of Cdc2-like kinase 2 (CLK2) and TTK in direct enzyme ass...
GSE121273: Gene expression profiles of BxPC-3, MiaPaCa-2 and PANC-1 cell lines treated with DMSO and THZ1 respectively
By screening an epigenetic-related compound library, we identified THZ1, a covalent inhibitor of CDK...
GSE113472: RNA Sequencing of si-Contol treated M010817 and siSMAD7 treated M010817 human melanoma cell line
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular path...
GSE113215: Enhancer Domains in Gastrointestinal Stromal Tumor Regulate KIT Expression and are Targetable by BET Bromodomain Inhibition [RNA-seq]
Gastrointestinal stromal tumor (GIST) is a mesenchymal neoplasm characterized by activating mutation...
GSE113485: ELF1 expression in prostate cells reduces oncogenic ETS functions and promotes senescence and sensitivity to chemotherapy through distinct gene expression programs [RNA-seq]
Aberrant overexpression of oncogenic ETS factors through chromosomal rearrangments is the most commo...
GSE113659: Genome-wide transcriptome profiling of NEDD9-regulated genes using RNA-seq
Purpose:This study is to examine NEDD9-regulated and aldosterone-induced gene expression to understa...
GSE115397: Non-inflammatory tumor microenvironment of Diffuse Intrinsic Pontine Glioma (DIPG)
Diffuse intrinsic pontine glioma (DIPG) is a universally fatal malignancy of the childhood central n...
GSE138042: RNA sequencing profiles for thyroid tumor tissue specimens
There is a challenge of thyroid cancer versus benign follicular denoma differential diagnostics usin...
GSE113519: Identification of Nrf2 regulated genes by RNA sequencing
The transcription factor Nuclear factor (erythroid-derived 2)-like 2 (Nrf2) is activated by the meta...
GSE115407: Robust Hi-C maps of enhancer-promoter interactions reveal the function of non-coding genome in neural development and diseases
Despite recent progress in mammalian 3D genome studies, it remains experimentally and computationall...
GSE113695: EIF1AX-A113 splice and RAS mutations cooperate to drive thyroid tumorigenesis through ATF4 and c-MYC
Translation initiation in higher eukaryotes is orchestrated by the tight regulation of the cap bindi...
GSE121238: Transciptomic profiling of human fetal lung samples
Fibroblast Growth Factor (FGF) signaling plays an important role in lung organogenesis. Over recent ...
GSE114493: Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma [RNA-Seq; normal samples]
Many high-grade serous carcinomas (HGSCs) of the pelvis are thought to originate in the distal porti...
GSE124017: Transcriptional analysis of THs-responding genes during human hepatocyte development
Liver is one of the major targets of thyroid hormones (THs), as well as many industrial chemicals re...
GSE114412: Charting in vitro beta cell differentiation by single cell RNA sequencing
In vitro differentiation of human stem cells can produce pancreatic beta cells, the insulin-secretin...
GSE115653: Aberrant splicing in B-cell acute lymphoblastic leukemia [B-ALL]
Aberrant splicing is a hallmark of leukemias with mutations in splicing factor (SF)-encoding genes. ...
GSE117155 (human): LEDGF and HDGF2, histone H3K36 methyl-binding proteins that assist RNA polymerase II transcription through nucleosomes
FACT (facilitates chromatin transcription) is a protein complex that allows RNAPII to overcome the n...
GSE114938: DUX4-induced transcripts from pericentric human satellite II repeats form double-stranded RNA [stranded-RNAseq]
The DUX4 transcription factor is normally expressed in the cleavage stage embryo and regulates genes...
GSE116121: Pro-angiogenic Ginsenoside F1 and Rh1 Inhibit Vascular Leakage by Modulating NR4A1
Angiogenesis is an essential process in human physiology and disease pathology. Particularly, in isc...
GSE113734: Loss of the Chr16p11.2 candidate gene QPRT leads to aberrant neuronal differentiation
Background: Altered neuronal development is discussed as underlying pathogenic mechanism of Autism S...
GSE115941: Sex-specific gene expression differences are evident in human embryonic stem cells and during in vitro differentiation of human placental progenitor cells
Here, we examine sex-specific gene expression differences during in vitro differentiation of male an...
GSE113505: A high-throughput screening strategy identifies regulators of alternative splicing via interaction with RNA G-quadruplexes
RNA secondary structures have been increasingly reported to serve critical regulatory roles in post-...
GSE113711: CAGE profiling after treatment with JQ1 BET inhibitor in lung cancer cell line.
The bromodomain and extra-terminal domain (BET) proteins are promising drug targets for cancer and i...
GSE113753: DAOY-Notch1/Notch2 knockout: transcriptome comparison
Hyperactivation of Notch signaling and the cellular hypoxic response are frequently observed in canc...
GSE114446: Combining mathematical and statistical modeling to simulate time course bulk and single cell gene expression data in cancer with CancerInSilico [RNA-seq]
We develop an R/Bioconductor package CancerInSilico to simulate bulk and single cell transcriptional...
GSE125606: A non-canonical role ofYAP/TEADis required for activation ofestrogen-regulated enhancers in breast cancer [RNA-seq]
Estrogen and estrogen receptor alpha (ER) signaling plays an essential role in ER-positive breast ca...
GSE124396: RNA-sequencing in irradiated and normal A549 cells.
The aim of this study is to investigate the role of circRNAs/miRNAs/lncRNAs in radioresistance in A5...
GSE113891: Transcriptomic profile of circulating CD4+ T cells from TCM and TEM memory compartments from donors vaccinated at birth either with whole or acellular Pertussis vaccine
In the mid-1990s vaccine-related side effects prompted the replacement of the whole Pertussis (wP) b...
GSE113871: Cardiac organoid model of human myocardial infarction
While human organoid systems have provided a powerful platform in modeling diseases caused by geneti...
GSE115939: Expression Profiling of Cisplatin Resistant IGROV1 Cell Lines vs. Wild Type IGROV1 Cell Lines
Ovarian cancer IGROV1 cells were studied to profile the expression of wild type (WT, Cisplatin Susce...
GSE115639: Transcriptome of cord blood derived subsets of human haematopoietic stem cells, LMPP and MLP myelo-lymphoid restricted progenitors [49f+ Subset2, Subset2, LMPPs, MLPs]
Integration of index sorting and single cell functional assays allowed identification of novel haema...
GSE115377: Displacement of WDR5 from chromatin by a pharmacological WIN site inhibitor with picomolar affinity
We discovered potent small molecule inhibitors against the WIN site of WDR5. These inhibitors select...
GSE117966: Oxygen Controls Metabolic Flux and Influences Global Acetylation and Methylation in Human Pluripotent Stem Cells
Purpose: The goals of this study are to compare the effects of 5% and 20% oxygen culture on human em...
GSE113881: DNMT3B maintains mCA landscape and regulates mCG status of bivalent promoters in human embryonic stem cells
In mammalian cells, DNMT3B is known as a de novo DNA methyltransferase. However, its preferential ta...
GSE115307: Race-specific transcriptome and Long non-coding RNA of ADT-resistant African-American prostate cancer cell models.
Purpose: The goals of this study are to compare NGS-derived Androgen Deprivation Therapy (ADT) resis...
GSE113902: Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing (Total RNA sequencing)
In females with X-linked genetic disorders, wild-type and mutant cells coexist within brain tissue b...
GSE117322: Identification of the role of polydom in neurofibromas
Dermal neurofibromas in von Recklinghausen's disease (vRD) develop in the dermis. Therefore, we hypo...
GSE113976: mRNA-seq Whole Transcriptome Profiling of Fresh Frozen versus Archived Fixed Tissues
Background: The main bottleneck for genomic studies of tumors is the limited availability of fresh f...
GSE113942: Genome-wide profiling of cervical RNA-binding proteins identified HPV regulation of RNASEH2A expression by viral E7 and E2F1
RNA-binding proteins (RBPs) have been shown to control mRNA processing, stability, transport, editin...
GSE117511: Inhibition of BET proteins rescues neural defects in Rett syndrome [RNA-seq]
Rett syndrome (RTT) is a severe X-linked neurodevelopmental disorder caused by mutations in the meth...
GSE115400: Mutant KRAS/BRAF Reprograms the Enhancer Landscape via GATA1 to Drive Chemoresistance
Despite advances in the detection and management of colorectal cancers, resistance to anti-cancer th...
GSE115462 (human): TP63-mediated enhancer reprogramming drives the squamous subtype of pancreatic ductal adenocarcinoma (RNA-seq)
The aberrant expression of squamous lineage markers in pancreatic ductal adenocarcinoma (PDA) has be...
GSE114541: Transcriptome profiling of microRNA-mediated neuronal reprogramming with REST repression at day 7
Ectopic expression of neuronal microRNAs (miRNAs), miR-9/9* and miR-124 (miR-9/9*-124) in adult huma...
GSE122743: Single-cell Transcriptomics reveals multi-step adaptations to endocrine therapy
Resistant tumours are thought to arise from the action of Darwinian selection on intratumoral geneti...
GSE115654: Aberrant splicing in B-cell acute lymphoblastic leukemia [cell line]
Aberrant splicing is a hallmark of leukemias with mutations in splicing factor (SF)-encoding genes. ...
GSE118131: Transcriptomic profiling of human Lung Carcinoids (LCs)
Lung carcinoids (LCs) are rare and slow growing primary lung neoplasms that are understudied. Here, ...
GSE120057: ARID1A regulates condensin II distribution and chromosomal partition [RNA-seq]
ARID1A, a subunit of the switch/sucrose non-fermentable (SWI/SNF) chromatin remodeling complex, infl...
GSE116778: Inhibition of O-GlcNAc transferase renders prostate cancer cells dependent on CDK9
O-GlcNAc transferase (OGT) is a nutrient-sensitive glycosyltransferase that is overexpressed in pros...
GSE120233: BRD9 defines a novel SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors [RNA-seq]
Bromodomain-containing protein 9 (BRD9) was recently identified to be associated with the chromatin ...
GSE114677: Distinct imprinting signatures and biased differentiation of human androgenetic and parthenogenetic embryonic stem cells [RNA-Seq II]
Genomic imprinting is an epigenetic mechanism that results in parent-of-origin monoallelic expressio...
GSE115655: Bone marrow derived human B cells [normal proB]
Aberrant splicing is a hallmark of leukemias with mutations in splicing factor (SF)-encoding genes. ...
GSE114643: Small molecule-mediated reprogramming of human hepatocytes into bipotent progenitor cells
Currently, much effort is directed to the development of new cell sources for clinical therapy using...
GSE115414: Discovery of lncRNA biomarkers of prostate cancer
In the last decade, new high-throughput sequencing techniques have revealed the complexity of the hu...
GSE131422: CD34+ AML cells with low mitochondrial activity show increased expression of stemness-genes and can be targeted by the BCL-2 inhibitor Venetoclax
It has been shown that AML cells with low levels of reactive oxygen species (ROS) have characteristi...
GSE114765: Antioxidant metabolism in activated CD8+ T cells regulates stem-like human memory T cell formation and anti-tumor immunity
Adoptive T cell transfer (ACT) immunotherapy benefits from early-differentiated memory stem-like T (...
GSE115509: mRNA-sequencing of U87 glioblastoma and DAOY medulloblastoma spheroidal aggregates undergoing electrotaxis
Treatment of neuroepithelial cancers remains a daunting clinical challenge, particularly due to an i...
GSE136032: Effect of venetoclax, tedizolid, and combination treatment on gene expression in a venetoclax-resistant AML cell line
The goal of this study was to profile the changes in gene expression in an AML cell line with acquir...
GSE122714: Transcriptomic analysis of different human cardiac cell types produced in vitro from human pluripotent stem cells or derived from patients.
The epicardium, an epithelium covering the heart, is essential for cardiac development. During embry...
GSE139327: Contrasting inflammatory signatures in peripheral blood and bronchoalveolar cells reveal compartment-specific effects of HIV infection
The mechanisms by which HIV increases susceptibility to tuberculosis and other respiratory infection...
GSE114647: Targeting FGFR overcomes EMT-mediated resistance in EGFR mutant non-small cell lung cancer
Acquired drug resistance to tyrosine kinase inhibitor (TKI) targeted therapies remains a major clini...
GSE114873: Global hyperactivation of enhancers stabilizes human and mouse nave pluripotency [RNA-Seq 2]
The transition of pluripotent stem cells (PSCs) from primed to nave states constitutes a prototypica...
GSE114771: Comparison of transcriptome profiles of human embryo cultured in either closed or standard incubator
Measuring transcriptomic profiles of human embryos cultured in time-lapse imaging (TLI) incubator an...
GSE117945: Co-expression of CD163 and CD141 Identifies Human Circulating IL-10-Producing Dendritic Cells (DC-10) [RNA-seq]
Tolerogenic dendritic cells (DC) are key players in maintaining immunological homeostasis, dampening...
GSE114976: Derivation of ventrical and atrial cardiomyocytes and maturation using biowires
Tissue engineering using cardiomyocytes derived from human pluripotent stem cells holds a promise to...
GSE120271: RNA-seq and ChIP-seq for human-specific regulation of neural maturation identified by cross-primate transcriptomics
Brain development is exceptionally delayed in humans compared to nonhuman primates (NHPs), a finding...
GSE122735: RNA-seq of resting and activated CD4+ T cells +-JQ1
HIV-1 recurrently targets active genes that are positioned in the outer shell of the nucleus and int...
GSE128066 (human): A Bayesian mixture model for clustering droplet-based single cell transcriptomic data from population studies
Abstract: The recently developed droplet-based single cell transcriptome sequencing (scRNA-seq) tech...
GSE116780: RNA sequencing of CRISPR/Cas9-generated A20 DUB-inative and A20 knock-out U937 cells to elucidate the role of human A20 DUB-domain
Objectives: Genetic variations in TNFAIP3 (A20) de-ubiquitinase (DUB) domain increase the risk of sy...
GSE115031: Cardiac organoid model of human myocardial infarction (batch2)
While human organoid systems have provided a powerful platform in modeling diseases caused by geneti...
GSE114946: The NORAD lncRNA assembles a topoisomerase complex critical for genome stability [RNA-seq]
Thousands of long non-coding RNAs (lncRNAs) have been identified in the human genome, but specific b...