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Sequencing-based assays (Page 142)
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GSE139671: Transcriptome analysis of in vitro generated plasmablasts dervied from Waldenstrm macroglobulinemia (WM) or heathly control B-cells
The ability to model WM B-cell differentiation using an in vitro system was validated in comparison ...
GSE144164: RNA-seq of ABCE1-knockout cells
Nonsense-mediated decay (NMD) is a pathway that degrades messenger RNAs containing premature termina...
GSE139678: Hypoxia-mediated regulation of histone demethylases affects angiogenesis associated functions in endothelial cells
Purpose: Jumonji-containing (jmjC) family of proteins are involved in epigenetic gene regulation thr...
GSE141352: Effects of EGF, cetuximab, trastuzumab and afatinib on gene expression in gastric cancer cell lines
The antibody trastuzumab in combination with platin-fluoropyrimidine chemotherapy is the standard of...
GSE139896: Gene signatures of rifampin, rifabutin an rifapentine anti-tuberculosis drugs in human primary hepatocytes.
We report the application of next generation sequencing technology for high-throughput profiling of...
GSE139924: LSD1 mediates AKT activity in PIK3CA mutant colorectal cancer [RNA-Seq]
Activation of the epithelial-mesenchymal transition (EMT) program is a critical mechanism for initia...
GSE140057: TGF superfamily signaling regulates the state of human stem cell pluripotency and competency to create telencephalic organoids
Telencephalic organoids generated from human pluripotent stem cells (hPSC) are emerging as an effect...
GSE144140: Use of NanoLuc-Based Reporters that Monitor Nonsense Suppression and Inhibition of Nonsense-Mediated mRNA Decay to Identify Potent New Agents That Partially Reverse the Effects of Nonsense Mutations
Premature termination codons (PTCs) lead to loss of protein function by 1) ending mRNA translation b...
GSE140071: Genome-wide integration of microRNA and the transcriptome during human alveolar epithelial cell transdifferentiation identifies SGK1 as novel target of miR-424/503 [RNA-Seq]
The alveolar epithelium is comprised of two cell types, alveolar type 1 (AT1) and type 2 (AT2) cells...
GSE144232: RNA sequencing of silica gel-immobilized and cisplatin-treated ovarian cancer cells
This study aimed to look at the signaling response of ovarian cancer cells to physical confinement i...
GSE141531: Transcriptomic comparison of 3D retinal organoids derived from retinitis pigmentosa patient harboring PDE6B mutation and non-phenotype control
Retinitis pigmentosa (RP) is a hereditary retinal degenerative disease. Although an increasing numb...
GSE152255: Myeloid regulation signature persists after virus clearance in mild human primary dengue serotype 2 infection
Healthy flavivirus-naive volunteers (n=11) were infected with the live attenuated dengue serotype 2 ...
GSE144216: Robust RNA-Seq of aRNA-amplified single cell material collected by patch clamp
Most single cell RNA sequencing protocols start with single cells dispersed from intact tissue. High...
GSE145641: Recapitulation of Prostate Tissue Cell Type-specific Transcriptomes by an in vivo Primary Prostate Tissue Xenograft Model
Purpose: Validate the cell type specific (Epithelial, Endothelial, and Stromal) transcriptome profil...
GSE142025: Comparison of Kidney Transcriptomic Profiles of Early and Advanced Diabetic Nephropathy Reveals Potential New Mechanisms for Disease Progression
To identify the factors mediating the progression of di- abetic nephropathy (DN), we performed RNA s...
GSE141633: The landscape of alternative splicing in aggressive prostate cancers
We sought to define the landscape of alternative pre-mRNA splicing in prostate cancers and the relat...
GSE148216: Gene expression profiles in solid and cystic central nervous system hemangioblastomas
OBJECTIVE: Due to the common occurrence of peritumoral cysts throughout the central nervous system t...
GSE152262: A frameshift variant in the specificity protein 1 triggers superactivation of Sp1-mediated transcription in familial bone marrow failure
Inherited bone marrow failure (BMF) syndromes are a heterogeneous group of diseases characterised by...
GSE140186: ARID1A is a critical regulator of luminal identity and therapeutic response in oestrogen receptor-positive breast cancer (RNA-seq II)
Mutations in ARID1A, a subunit of the SWI/SNF chromatin remodelling complex, are the most common som...
GSE144259: RNA-seq of CRC tissues
CRC tissues plus matched normal tissues (Primary colon cancer, liver metastasis colon cancer and mat...
GSE145682: Global RNA stability profiling in human NBDY knockout using TimeLapse-seq
We previously identified a conserved human microprotein NoBody/NBDY that can interact with the mRNA ...
GSE144043: AMPK1/2 isoform-specific gene expression profile in human induced pluripotent stem cells
AMP-activated protein kinase (AMPK) is a key regulator of energy metabolism that, upon activation, p...
GSE140261: Longitudinal measures of RNA expression and disease activity in FSHD muscle biopsies
Advances in understanding the pathophysiology of facioscapulohumeral dystrophy (FSHD) have led to th...
GSE149072: Gene expression profiling of tissue and hMSC xenografts in a rat postpartum urinary injury model
Periurethral human mesenchymal stem cell (hMSC) injections are associated with functional improvemen...
GSE140226 (human): Dexamethasone inhibits respiratory syncytial virus-driven mucus production while increasing viral replication without altering antiviral interferon signaling
Purpose: To understand how dexamethasone has beneficial effects on reducing mucus production but inh...
GSE140231: A human single cell atlas of the substantia nigra reveals novel cell specific pathways associated with the genetic risk of Parkinsons disease and neuropsychiatric disorders
We describe the first human single-nuclei transcriptomic atlas for substantia nigra (SN), generated ...
GSE143549: Gene expression profiling of blood of Ebola virus disease survivors and Healthy donors by Next Generation Sequencing
Clinical follow-up of Ebola virus disease (EVD) survivors revealed a persistence of clinical symptom...
GSE149161: Massively parallel reporter assays combined with cell-type specific eQTL identified a functional melanoma risk variant in HIV-1 restriction gene, MX2 [MX2_overexpress_time]
Genome-wide association studies (GWAS) have identified twenty melanoma susceptibility loci. To ident...
GSE140275: Expression profile and potential functions of circulating long noncoding RNAs in acute ischemic stroke in the Southern Chinese Han population
Background: Long noncoding RNAs (lncRNAs) have been confirmed to be associated with ischemic stroke ...
GSE149209: H3.3G34W promotes growth and impedes differentiation of osteoblast-like mesenchymal progenitors in Giant Cell Tumour of Bone [RNA-Seq]
Glycine 34 to tryptophan (G34W) substitutions in H3.3 arise in ~90% of giant cell tumour of bone (GC...
GSE152293: Osteoporosis is characterized by altered expression of exosomal long noncoding RNAs
Osteoporosis is a metabolic bone disease characterized by a decrease in bone mass and degradation of...
GSE140432 (human): CHUK/IKKalpha loss in lung epithelial cells enhances NSCLC growth associated with HIF up-regulation
During the natural progression of Non-small-cell lung cancer (NSCLC), tumor cells evolve progressive...
GSE144025: Whole transcriptome profiling of Wildtype and EXT1-/- human embryonic stem cells by RNA-Seq
Purpose: The goals of this study are to identify whole transcriptomic changes between undifferentiat...
GSE141627: Functional plasticity and reversible growth behavior of patients acute myeloid leukemia stem cells growing in mice
Resistance against chemotherapy remains a major obstacle in treating patients with acute myeloid leu...
GSE144290: Next Generation Sequencing Facilitates Quantitative Analysis of 231 and Pep-E3 cells' Transcriptomes in breast cancer
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular path...
GSE142046: SETD5-coordinated chromatin reprogramming regulates adaptive resistance to targeted pancreatic cancer therapy
Oncogenic KRAS signaling is a hallmark of pancreatic ductal adenocarcinoma (PDAC), a lethal malignan...
GSE143492: Single-nucleus RNA-seq identifies divergent populations of FSHD2 myotube nuclei [Fluidigm]
FSHD is characterized by the misexpression of DUX4 in skeletal muscle. Although DUX4 upregulation is...
GSE144085: Transcriptome analysis reveals conditions for culturing human primitive undifferentiated spermatogonia
Spermatogonial stem cells (SSCs) are essential for the generation of sperm and have potential therap...
GSE154055: Digital Gene Expression profiles analysis of patients with HCV-related hepatic fibrosis
Hepatitis C virus (HCV) infection is an important etiology of chronic liver disease. Multiple possib...
GSE143537: A single RNA polymerase II ubiquitylation site coordinates transcription with the DNA damage response [RNA-seq]
In response to transcription-blocking DNA damage, cells orchestrate a multi-pronged reaction, invol...
GSE143583: Next Generation Sequencing Facilitates Quantitative Analysis of transcriptomes in Human PBMC-derived Ms and TAMs
The goals of NGS-derived macrophage transcriptome profiling (RNA-seq) is to identify the differences...
GSE144568: Single-Cell Analyses Reveal Megakaryocyte-Biased Hematopoiesis in Myelofibrosis and Identify Mutant Clone-Specific Targets
Myelofibrosis is a severe myeloproliferative neoplasm characterised by increased numbers of abnormal...
GSE142077: RNA-Seq identifies condition-specific biological signatures of ischemia-reperfusion injury in the human kidney
Purpose: Acute kidney injury (AKI) is defined as a sudden event of kidney failure or kidney damage o...
GSE140483: Organelle-based therapy for immune mediated disease: mitochondrial transfer elicits Tregs reprogramming
Mesenchymal stem cells (MSCs) have fueled ample translation for the treatment of immune mediated dis...
GSE144580: Non-linear relationship between chromatin accessibility and estradiol-regulated gene expression
Chromatin accessibility is central to basal and inducible gene expression. Through ATAC-seq experime...
GSE144484: MLLT6 maintains PDL1 expression and mediates tumor immune resistance
We present a CRISPR-Cas9 screen in human cancer cells to identify genes that confers tumors with the...
GSE148241: Placental Editome Profiling Reveals Widespread RNA-Editing Dysregulation in Preeclampsia
Dysregulated RNA editing is well documented in several diseases such as cancer. The extent to which ...
GSE155713: Modeling human T-cell mediated beta cell destruction
Autoimmune destruction of pancreatic cells underlies type 1 diabetes (T1D). To understand T-cell me...
GSE140482 (human): Squamous trans-differentiation of pancreatic cancer cells promotes stromal inflammation (RNA-seq)
A highly aggressive subset of pancreatic ductal adenocarcinomas undergo trans-differentiation into t...
GSE140523: Tissue specific human fibroblast differential expression based on RNAsequencing analysis
Background:Physical forces, such as mechanical stress, are essential for tissue homeostasis and infl...
GSE142822: Anti-tumor immunity induces the presentation of aberrant peptides in melanoma
Extensive tumor inflammation, reflected by high levels of infiltrating T-cells and Interferon gamma ...
GSE144108: IL-12 signaling contributes to the reprogramming of neonatal CD8+ T cells
Neonates are highly susceptible to intracellular pathogens, leading to high morbidity and mortality ...
GSE141696: Therapeutic modulation of nemo-like kinase in primary and acquired endocrine-resistant breast cancer
Purpose: To assess if NLK modulates ER target gene expression, we performed transcriptome sequencing...
GSE147091: Reversal of pre-existing NGFR-driven tumor and immune therapy resistance
In spite of the remarkable clinical benefit from immune checkpoint blockade in melanoma, both intrin...
GSE147851: SMARCB1 loss induces druggable cyclin D1 deficiency via upregulation of MIR17HG in atypical teratoid rhabdoid tumors
Atypical teratoid rhabdoid tumor (ATRT) is a fatal pediatric malignancy of the central neural system...
GSE140759: Viral determinants in H5N1 influenza A virus enable productive infection of HeLa cells
Influenza A virus (IAV) is a human respiratory pathogen that causes yearly global epidemics, and spo...
GSE145148: Cell cycle checkpoints cooperate to suppress DNA and RNA associated molecular pattern recognition and anti-tumor immune responses
The DNA dependent pattern recognition receptor, cGAS mediates communication between genotoxic stress...
GSE145028: ASXL3 bridges BRD4 to BAP1 complex and governs enhancer activity in small cell lung cancer
The bromodomain and extra-terminal (BET) protein BRD4 functions as a transcriptional activator and i...
GSE143669: Investigating cone photoreceptor development using patient-derived NRLnull retinal organoids
Photoreceptor loss is a leading cause of blindness, but mechanisms underlying photoreceptor degenera...
GSE142179: Total RNA seq transcriptome profiling of thymocytes
Circular RNAs (circRNAs) are stable RNA molecules whose deregulation can drive disease and cancer me...
GSE152430: Next generation sequencing of FFPE human colon cancer samples for validation of ColoType consensus molecular subtype (CMS) assay
Purpose: To validate the novel ColoType assay for computing consensus molecular subtypes of colon ca...
GSE145073: Transcriptomic and epigenomic dynamics associated with development of human iPSC-derived GABAergic interneurons
GABAergic interneurons (GINs) are a heterogeneous class of inhibitory neurons that collectively main...
GSE142293: NGS based identification of GD2-positive tumor-specific phenotype for cancer diagnostics and therapy
The tumor-associated glycosphingolipid ganglioside GD2 presents an attractive target for cancer immu...
GSE142347: Mouse models of neutropenia reveal progenitor-stage-specific defects [Fluidigm]
Advances in genetics and sequencing have lead to a deluge of disease-associated and disease-causing ...
GSE143692: Transcription factor POU3F2 regulates TRIM8 expression contributing to cellular functions implicated in schizophrenia
Schizophrenia (SCZ) is a neuropsychiatric disorder with aberrant expression of multiple genes. Howev...
GSE142314: PRMT1 inhibition induces differentiation of colon cancer cells
Colorectal cancer (CRC) is the third most commonly occurring cancer in men and the second most commo...
GSE148589: Thymidylate synthase drives the phenotypes of epithelial-to-mesenchymal transition in non-small cell lung cancer
Epithelial to mesenchymal transition (EMT) is a developmental process driving metastasis and chemore...
GSE142381: DNA Demethylation promotes ERV expression and activation of immune signaling in renal cell cancer cells
Recently, we reported that expression of endogenous retroviruses (ERVs), a class of transposable ele...
GSE146760: A MULTIPLEX HUMAN PLURIPOTENT STEM CELL PLATFORM DEFINES MOLECULAR AND FUNCTIONAL SUBTYPES OF AUTISM
We report a multiplex human pluripotent stem cell platform to investigate autism associated genetic ...
GSE142386: MeRIP sequencing reveals angiogenic properties of vascular endothelial cells
We report the application of MeRIP sequencing technology for high-throughput profiling of RNA m6A mo...
GSE143702: Integrative analysis of transcriptome and proteome sheds light on functional differences between human salivary glands
Saliva aids in the predigestion of food and perception of taste. It helps to maintain the integrity ...
GSE143735: RNA-sequencing analysis of forearm skin in diabetic patients with or without foot ulcerations
Diabetic foot ulcers (DFUs) and associated impaired healing, represent a major problem, that signifi...
GSE145275: Mechanistic basis and efficacy of targeting Beta Catenin-TCF7L2-JMJD6-MYC Axis to overcome resistance to BET inhibitors [no drug]
Promising activity of BET protein inhibitors (BETis) is compromised by adaptive or innate resistance...
GSE143725: Multi-tissue epigenetic analysis of the osteoarthritis susceptibility locus mapping to the plectin gene PLEC
We report an immortalised CRISPR-Cas9 mesenchymal stem cell line knockdown of Plectin, we initally n...
GSE149292: Transcriptome analysis of RFWD2 overexpression (OE) and control (WT) in Multiple myeloma
Transcriptome sequencing was used to analyze changes in related signaling pathways and gene expressi...
GSE144302: Pulmonary Eosinophilic Granulomatosis with Polyangiitis has IgG4 Plasma Cells and Immunoregulatory Features
The pathologic findings and immunologic mechanisms in eosinophilic granulomatosis with polyangiitis ...
GSE149277: Frequent mutations in the amino-terminal domain of BCL7A impair its tumor suppressor role in DLBCL
Mutations in genes encoding the various subunits of the SWI/SNF chromatin remodeling complex are fre...
GSE146536: Stimulation of LTR on human fibroblasts
LTR signaling is crucial for immune development, homeostasis, and inflammation. To identify new fact...
GSE148228: Pharmacological disruption of the Notch transcription factor complex
Notch pathway signaling is implicated in several human cancers. Aberrant activation and mutations of...
GSE143731: Genome-wide gene expression profiling of anti-tuberculosis drugs-treated macrophages
Background: Tuberculosis (TB) remains a major public health problem, especially in developing countr...
GSE147147: Three-dimensional bioprinting enables creation of tissue-informed glioblastoma microenvironments for modeling complex cellular interactions
Brain tumors are dynamic complex ecosystems with multiple cell types. To model the brain tumor micro...
GSE151024: Re-expression of SMARCA4/BRG1 in Small Cell Carcinoma of Ovary, Hypercalcemic Type (SCCOHT) promotes an epithelial-like gene signature through an AP-1-dependent mechanism [AFOS RNA-seq]
Small cell carcinoma of the ovary, hypercalcemic type (SCCOHT) is a rare and aggressive form of ovar...
GSE154112: Three-way combinatorial CRISPR screen for analyzing interactions among druggable targets
We present a CRISPR-based multi-gene knockout screening system and new toolkits for extensible assem...
GSE144332: A unique viral reservoir landscape associated with durable natural control of HIV-1 infection [RNA-seq]
Sustained, drug-free control of HIV-1 replication is naturally achieved in less than 0.5% of infecte...
GSE147735: Mechanism and Reversal of Nephrotoxicity on a Chip
The kidney plays a critical role in fluid homeostasis, glucose control, and drug excretion. Loss of ...
GSE144373: Multiplexed relative and absolute quantitative immunpeptidomics reveals MHC I repertoire alterations induced by CDK4/6 inhibition
Major histocompatibility complex (MHC) class I peptides play a critical role in immune cell recognit...
GSE148003: Genome-wide characterization of platinum persister ovarian cancer (OC) cells with upregulation of Wnt pathway receptor, Frizzled 7 (FZD7)
The goal of this study is to define molecular signature of platinum persister OC cells characterized...
GSE144682: The role of long noncoding RNAs during pancreas development
LncRNAs are developmentally regulated and highly cell type-specific non-coding RNAs that have emerge...
GSE142585: Single-cell RNA sequencing of human, macaque, and mouse testes uncovers primate-specific features of spermatogenesis
Spermatogenesis is a highly regulated process that produces sperm which faithfully transmits genetic...
GSE142591: Transcriptome profiling (RNA-seq) analysis of control and NaIO3-treated RPE cells
Purpose: The goal of this experiment is to investigate the relative contributions of various types ...
GSE142730: Human iPSC-derived astrocytes from ALS patients with mutated C9ORF72 show increased oxidative stress and neurotoxicity
Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disease that affects motor ne...
GSE152460: RNA-seq of ATF-3 overexpressing and Neomycin control melanoma cell lines
The present study demonstrates that ATF-3 plays a tumor suppressing function in melanoma. Overexpres...
GSE145160: Characterization of the ZFX family of transcription factors that bind downstream of the start site of CpG island promoters
Our study focuses on a family of ubiquitously expressed human C2H2 zinc finger proteins comprised of...
GSE142831: Sacrificial cell death of adipose mesenchymal stem cells by autophagy facilitates cartilage formation in co-cultures with chondrocytes
Objective: Cartilage formation is stimulated in mixtures of chondrocytes and human adipose-derived m...
GSE154057: Pharmacological modulation of H3K9me2 deposition in human intestinal models and transformed ES cells
Transformed variant of H9 human ES cells (t-hESC) represent a surrogate model for cancer stem cells ...
GSE151073: Transcriptional comparison of in vitro and in vivo generated human dendritic cells
Dendritic cells (DC) are antigen presenting cells controlling T cell activation. In human, the diver...
GSE146792: Drop-seq of normal mammary cells pre and post- conditional reprogramming (CR)
Normal mammary cells obtained from reduction mammoplasty samples were processed into single cells an...
GSE147236: Enhancer and promoter usage in the normal and failed human heart
The failed heart is characterized by re-expression of a fetal gene program, which contributes to ada...
GSE146309: Nanoengineered Osteoinductive Bioink for Three-Dimensional Bioprinting Bone Tissue
Bioprinting is an emerging additive manufacturing approach to the fabrication of patient-specific, i...
GSE150196: Activation of clustered IFN target genes drives cohesin-controlled transcriptional memory [RNA-seq]
Cytokine activation of cells induces gene networks involved in inflammation and immunity. Transient ...