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Sequencing-based assays (Page 126)
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GSE80137: HLA peptides derived from tumor antigens induced by inhibition of DNA methylation for development of drug-facilitated immunotherapy
Treatment of cancer cells with anti-cancer drugs often fails to achieve complete remission. Yet, suc...
GSE81076: A single-cell transcriptome atlas of the human pancreas
To understand organ (dys)function it is important to have a complete inventory of its cell types and...
GSE78930: Discovery of first-in-class reversible dual small molecule inhibitors against G9a and DNMTs with in vivo activity in hematological malignancies [RNA-Seq]
The indisputable role of epigenetics in cancer and the fact that epigenetic alterations can be rever...
GSE78117: A novel hydrogel-based instructive biohybrid 3D culture system for modeling human neural stem cell plasticity, neurogenesis, neurodevelopment, and neurodegeneration
Meaningful models of human neural development and neurodegeneration are extremely important when exp...
GSE80043: Chromatin environment, transcriptional regulation and splicing distinguish lncRNAs and mRNAs [NucFrac]
While long noncoding RNAs (lncRNAs) and mRNAs share similar biogenesis pathways, these two transcrip...
GSE78138: MLL1 is essential for the senescence-associated secretory phenotype [RNA-Seq]
Oncogene-induced senescence (OIS) and therapy-induced senescence (TIS), while tumor-suppressive, als...
GSE97104: Molecular transitions in early progenitors during human cord blood hematopoiesis
Hematopoietic stem cells give rise to diverse cell types in the blood system, yet our molecular unde...
GSE78688 (human): Activity-dependent transcriptional changes in human neurons
We used genome-wide sequencing methods to identify activity-regulated gene expression and regulatory...
GSE77702: Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [RNA-Seq_human]
TDP-43, FUS, and TAF15 are implicated in amyotrophic lateral sclerosis (ALS) and frontotemporal deme...
GSE77704: Distinct and shared functions of ALS-associated TDP-43, FUS, and TAF15 revealed by comprehensive multi-system integrative analyses [RNA-Seq_Stability]
TDP-43, FUS, and TAF15 are implicated in amyotrophic lateral sclerosis (ALS) and frontotemporal deme...
GSE79953: Next-generation sequencing analysis of transcriptom in gemcitabine resistant pancreatic cancer cells
Next-generation sequencing was applied to compare the transcriptom of 1) SW1990 human pancreatic can...
GSE78011: RNA-Seq Analysis of Anacardic Acid Treated MCF7 and MDA-MB-231 Breast Cancer Cell Lines
Anacardic acid (AnAc) is a mixture of 6-alkylbenzoic acid congeners that are produced in a number of...
GSE78512: Identification Of Candidate Anti-Cancer Molecular Mechanisms Of Compound Kushen Injection Using Functional Genomics
Compound Kushen Injection (CKI) has been clinically used in China for over 15 years to treat various...
GSE78959: Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors [Cell Model]
Tuberous sclerosis complex (TSC) is a rare genetic disease characterized by mTOR hyperfunction induc...
GSE78960: Modeling the Neuropathology of Tuberous Sclerosis with Human Stem Cells Reveals a Role for Inflammation and Angiogenic Growth Factors [Treatment]
Tuberous sclerosis complex (TSC) is a rare genetic disease characterized by mTOR hyperfunction induc...
GSE80366: Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer. [cell models RNA-seq]
Transcriptomic changes and estrogen and progesterone receptor binding in multiple ER+/PR+ models (ei...
GSE80170: Next Generation Sequencing Compares Effects of microRNA-9 perturbation in control and SZ hiPSC NPCs
To follow-up findings that miR-9 was abundantly expressed in control NPCs, significantly down-regula...
GSE81730: Single cell gene expression profiling in normal HSCs and CML stem cells
CML stem cells (CMLSCs) and normal hematopoietic stem cells (HSCs) display the same set of surface m...
GSE79029: KSHV Infection Mimics the Hypoxic Response Based on Next-Generation Sequencing [mRNA-Seq]
Purpose: Kaposis sarcoma associated-herpesvirus (KSHV) causes several hyperproliferative disorders, ...
GSE79988: The myelin protein PMP2 is regulated by SOX10 and drives melanoma cell invasion
The transcription factor SRY(sex related protein-Y)-box10 (SOX10) plays a key role in the developmen...
GSE90491: List of TIAM1 differentially expressed genes in SW620 cells [RNA-seq]
The T lymphoma invasion and metastasis inducing protein 1 (TIAM1) is a guanine nucleotide exchange f...
GSE80333: Spatial proximity to fibroblasts impacts molecular features and therapeutic sensitivity of breast cancer cells influencing clinical outcomes
Using a 3D co-culture model, we identified significant sub-type-specific changes in the gene express...
GSE81795: An epigenetic mark of polycomb response elements implemented by Trx/MLL/COMPASS
In Drosophila, Polycomb Response Elements (PREs) are identified as genomic sequences allowing the ma...
GSE80045: Chromatin environment, transcriptional regulation and splicing distinguish lncRNAs and mRNAs [Stability]
While long noncoding RNAs (lncRNAs) and mRNAs share similar biogenesis pathways, these two transcrip...
GSE79271: Acute loss of BRD4 halts global transcriptional elongation and collapses the core regulatory circuitry of acute lymphoblastic leukemia [NET-Seq]
Cancer arises from the malignant interplay between oncogenic signaling and cell specification. Tran...
GSE79253: Acute loss of BRD4 halts global transcriptional elongation and collapses the core regulatory circuitry of acute lymphoblastic leukemia [RNA-Seq]
Cancer arises from the malignant interplay between oncogenic signaling and cell specification. Tran...
GSE124703: CRISPR-based multimodal genetic screens in human iPSC-derived neurons
CRISPR/Cas9-based functional genomics have transformed our ability to elucidate mammalian cell biolo...
GSE80305: Role of COP1 on MAP kinase transcriptional output in gastrointestinal stromal tumor
COP1 regulates MAP kinase dependent stability Pea3 transcription factors. We determined the role of ...
GSE80386: Integrator complex subunit 12 is a key regulator of human protein synthesis pathways
Genome wide association studies of human lung function have identified a signal on 4q24 but the mech...
GSE82104: Acriflavine inhibits the epithelial-to-mesenchymal transition in vitro in liver and pancreatic cancer cells (part of study on PANC1 cells treated with CoCl2)
Background: Epithelial-to-mesenchymal transition (EMT) is considered an important driving mechanism ...
GSE80358: PR isoform-specific ER and PR chromatin binding and gene expression observed in-vitro in breast cancer cells.
Major roadblocks to developing effective progesterone receptor (PR)-targeted therapies in breast can...
GSE80064: Knockout of miR-221 and miR-222 reveals overlapping and specific function between paralogous miRNAs
MicroRNAs (miRNAs) regulate the expression of mRNAs through sequence-specific binding into their 3 u...
GSE101655: Deep sequencing of transcript levels in pluripotent stem cells and their differentiated derivatives in all three germ layers
Human pluripotent stem cells (hESCs) are an excellent model to dissect the transcriptional changes t...
GSE86654: Identifying markers predicting successful graft outcome for clinical translation of hESC-based cell therapy for Parkinsons disease
Stem cell treatments for neurodegenerative diseases are expected to reach clinical trials soon. Mos...
GSE80073: Generation of Brain Region-specific Organoids using a Miniaturized Spinning Bioreactor and Modelling ZIKV Exposure
Cerebral organoids, three-dimensional cultures that model organogenesis, provide a new platform to i...
GSE85712: Physiologic expression of Sf3b1K700E causes impaired erythropoieses, aberrant splicing, and sensitivity to pharmacologic spliceosome modulation
Over 80% of patients with the refractory anemia with ring sideroblasts subtype of myelodysplastic sy...
GSE81791: Regulation of DNA methylation landscape in human somatic cell reprogramming by miR-29 family (RNA-seq)
Reprogramming to pluripotency after overexpression of OCT4, SOX2, KLF4 and MYC is accompanied by glo...
GSE86821: Global rewiring of cis-regulatory units upon lineage commitment of human embryonic stem cells
Lineage commitment is characterised by orchestrated changes in gene expression and chromatin state. ...
GSE80082: Integrin signaling regulates YAP/TAZ to control skin homeostasis
The skin is a squamous epithelium that is continuously renewed by a population of basal layer stem/p...
GSE80492: The role of miR-17-92 in the miRegulatory landscape of Ewing Sarcoma (RNA-Seq)
MicroRNAs serve to fine-tune gene expression and play an important regulatory role in tissue specifi...
GSE80463: Divergent expression and metabolic functions of human glucuronosyltransferases through alternative splicing
Purpose: Maintenance of cellular homeostasis and xenobiotics detoxification relies on the glucuronid...
GSE79492: Ridaforolimus (MK-8669) synergizes with Dalotuzumab (MK-0646) in hormone-sensitive breast cancer
Introduction: Mammalian target of rapamycin (mTOR) represents a key downstream intermediate for a my...
GSE90014: Proliferation pause as an early blockade of human cellular reprogramming toward pluripotency [single cell RNA-seq analysis]
Human induced Pluripotent Stem cells (iPSCs) can be generated by enforced-expression of OCT3/4, SOX2...
GSE103293: RNA sequencing (RNA-SEQ) of PSPC1 Knockout in A549 cells with TGFb1 stimulation
We show that PSPC1 is required for cancer cell motilities and stemness properties in vitro and lung ...
GSE79544: Idiopathic pulmonary fibrosis bronchoalveolar lavage cells RNA-seq indicates macrophage expression of pro-inflammatory M1/M2 activation concomitant with radical species metabolism inhibition
Current concepts of idiopathic pulmonary fibrosis (IPF) are that microscopic injury drives alveolar ...
GSE83256: Aberrant transcriptional networks in neurogenesis of Paroxysmal Kinesigenic Dyskinesia-induced pluripotent stem cell lines though neural induction method of dual inhibition of SMAD signaling
Paroxysmal kinesigenic dyskinesia (PKD) is an episodic movement disorder with autosomal-dominant inh...
GSE82147: Genome wide impact of loss of mechanoluminal stimulation on neonatal intestine
Purpose: Surgical treatment of congenital and neonatal intestinal diseases often requires resection ...
GSE80551: RNA-Seq following PCR-based sorting reveals rare cell transcriptional signatures
Background: Rare cell subtypes can profoundly impact the course of human health and disease, yet the...
GSE93831: mRNA Profiling of miR-17 family inhibition using TuD lentiviral vector in HepG2 and SK-Hep1 hepatocellular carcinoma cell lines [RNA-Seq]
To functionally characterize the role of miR-17 family in HCC, lentiviral vector-based miR inhibitor...
GSE109542: Antibody-Mediated Inhibition of MICA/B Shedding Promotes NK Cell-Driven Tumor Immunity
MICA and MICB (MICA/B) are expressed by many human cancers due to cellular stress and tag cells for ...
GSE80753: LSD1 mediates MYCN control of epithelial-mesenchymal transition through silencing of metastatic suppressor NDRG1 gene
Neuroblastoma (NB) with MYCN amplification is a highly metastatic tumor in children, and unraveling ...
GSE80741: Identification and characterization of androgen receptor splice variants preferred bindings that drive prostate cancer progression [RNA-seq]
Androgen receptor (AR) splice variants (ARVs) are implicated in developing castration-resistant (CR)...
GSE80774: ENL Links Histone Acetylation to Oncogenic Gene Expression in AML
Cancer cells are characterized by aberrant epigenetic landscapes and often exploit the chromatin mac...
GSE134510 (human): RNA sequencing of PD-L1 knock out human MDA-MB231 cells and mouse CT26 cells
Although membrane-anchored PD-L1 has been well-studied for its engagement with PD-1 on T cells to ev...
GSE81080: Differentiation of human embryonic stem cells to HOXA+ hemogenic vasculature that resembles the aorta-gonad-mesonephros
The production of definitive haematopoietic stem/progenitor cells from human pluripotent stem cells ...
GSE80819: Transcriptome analysis of ECFCs treated with GSK-343 and Panobinostat
Human endothelial colony-forming cells (ECFCs) represent one of the most promising sources of adult ...
GSE91010: DRB/GRO-Seq -/+ UV
The transcription-related DNA damage response was analyzed on a genome-wide scale with great spatial...
GSE79782: Amnion as a surrogate tissue reporter of the effects of maternal preeclampsia on the fetus [RNA-Seq]
Background:; Preeclampsia, traditionally characterized by high blood pressure and proteinuria, is a ...
GSE91051: Gene expression changes due to PARP knockdown in human cells
To address the global impact of PARP-1 on the transcriptome, we knocked down PARP1 using siRNA from ...
GSE84824: hCLE/RTRAF-HSPC117-DDX1-FAM98B: A new cap-binding complex that activates mRNA translation
hCLE/C14orf166/RTRAF, DDX1 and HSPC117 are components of cytoplasmic mRNA-transporting granules kine...
GSE81965: RNA-sequencing of human skeletal myocytes from healthy, obese, and type 2 diabetic subjects
Skeletal muscle is one of the primary tissues involved in the development of type 2 diabetes (T2D). ...
GSE81074: Differentiation of human embryonic stem cells to HOXA+ hemogenic vasculature that resembles the aorta-gonad-mesonephros
The production of definitive haematopoietic stem/progenitor cells from human pluripotent stem cells ...
GSE82071: A Basal Stem Cell Signature Identifies Aggressive Prostate Cancer Phenotypes
Aggressive cancers and normal stem cells often share similar molecular and functional traits. It is ...
GSE82241: A herpesvirus protein selectively inhibits cellular mRNA nuclear export
Nuclear export of mRNA is essential for eukaryotic cells to establish the flow of genetic informatio...
GSE82236: Whole-transcriptome profilings between a pair of HCA7-derived KRAS-wildtype cetuximab sensitive and resistant colon cancer cells from 3D culture
We report the results of RNA-Seq and small RNA-Seq from a pair of HCA7-derived, KRAS wildtype CC and...
GSE86855: A cytoplasmic COMPASS is necessary for cell survival and triple-negative breast cancer pathogenesis by regulating metabolism
Mutations and translocations within the COMPASS (complex of proteins associated with Set1) family of...
GSE81429: Transcriptome analysis in HT29 and SW480 cells depleted of Prdx2
Prdx2 is the thioredoxin-dependent peroxidase that reduces H2O2 using reducing power NADPH in the pr...
GSE79955: CDK7 targeting in peripheral T-cell lymphomas abrogates STAT activity causing apoptosis and sensitization to BCL2 inhibitors
Peripheral T-cell lymphomas (PTCL) are clinically aggressive diseases with poor response to availabl...
GSE82207: Total RNA sequencing of WT intestinal orgaonids.
We report elevated expression levels of genes involved in small intestine or colon regional identity...
GSE85294: Profiles of Long Noncoding RNAs in Human Naive and Memory T Cells
We employed whole-genome RNA-sequencing to profile mRNAs and both annotated and novel long noncoding...
GSE81345: Sensing self and nonself circular RNAs
Circular RNAs (circRNAs) are single-stranded RNAs that are joined head to tail. Initially discovered...
GSE82320: Nuclear Actin Regulates Inducible Transcription by Enhancing RNA Polymerase II Clustering
Nuclear actin dynamics regulate enhanced RNA polymerase II clustering on specific genes upon serum s...
GSE127886: Intrinsic Resistance to MEK Inhibition Through BET Protein Mediated Kinome
Mutation or deletion of Neurofibromin (NF1), an inhibitor of RAS signaling, frequently occurs in epi...
GSE86884: Differentially Expressed Gene Transcripts Using RNA Sequencing from the Blood of Immunosuppressed Kidney Allograft Recipients
We performed RNA sequencing (RNAseq) on peripheral blood mononuclear cells (PBMCs) to identify diffe...
GSE82289: BRD4 localization to lineage-specific enhancers is associated with a distinct transcription factor repertoire [mRNA-Seq]
We examined context specific function of BRD4 in promoting lineage specific gene expression and show...
GSE82291: Quantitative profiling of the UGT transcriptome in human drug metabolizing tissues [Total RNA]
Purpose: Maintenance of cellular homeostasis and xenobiotics detoxification relies on the glucuronid...
GSE84891: Expression analysis of the TAF1 syndrome
The goal of this study was to perform a transcriptomic analysis on individuals from the TAF1 syndrom...
GSE79362: A blood RNA signature for tuberculosis disease risk: a prospective cohort study
Identification of blood biomarkers that prospectively predict progression of Mycobacterium tuberculo...
GSE86021 (human): Crenolanib in combination with azacitidine abrogates stromal protection and survival of leukemia-initiating cells in FLT3-ITD+ AML
Effectively targeting leukemia-initiating cells (LIC) in FLT3-internal-tandem-duplication (ITD)-muta...
GSE103308: Simultaneous and systematic analysis of cellular and viral gene expression during Enterovirus 71-induced host shutoff
Enterovirus 71 (EV71) infection causes a profound shutoff of cellular protein synthesis. Deep RNA-se...
GSE82329: Adaptation of the Kinome Promotes Resistance to BET Bromodomain Inhibitors in Ovarian Cancer
Small molecule BET bromodomain inhibitors (BETi) are actively being pursued in clinical trials for t...
GSE83402: Benchmarking of RNA-sequencing analysis workflows using whole-transcriptome RT-qPCR expression data
RNA-sequencing has become the gold standard for whole-transcriptome gene expression quantification. ...
GSE99392: PGE2 mediated gene expression changes in human cervical stromal cells
The cervix represents a formidable structural barrier for successful induction of labor. Approximate...
GSE81405: Convergent roles of ATF3 and CSL in chromatin control of CAF activation [RNA-seq]
Cancer associated fibroblasts (CAFs) play an important role in initiating and promoting epithelial c...
GSE85353 (human): DNA methylation repels binding of hypoxia-inducible transcription factors to maintain tumour immunotolerance [RNA]
Background: Hypoxia is pervasive in cancer and other diseases. Cells sense and adapt to hypoxia by a...
GSE84639: Enriched retinal ganglion cells derived from human embryonic stem cells (RNA-seq)
We performed the whole transcriptome analysis in human H9 ES cells and in retinal ganglion cells (RG...
GSE83443: Pericyte-like cells generated from human pluripotent stem cells support hematopoietic stem and progenitors ex vivo
Various mesenchymal cell types have been identified as critical components of the hematopoietic stem...
GSE83475: RNA sequencing reveals levamisole target genes PTPRZ1 and MDK and their links to interferon pathway in human podocytes
To investigate the mechanisms underlying levamisole's efficacy in disease, we performed RNA sequenci...
GSE84582: Global gene expression profiles of cardiac progenitors differentiated from human pluripotent stem cells in 3D culture under simulated microgravity
Methods: RNA-seq libraries were prepared using the Illumina TruSeq RNA kit and the TrueSeq method wa...
GSE84080: Regulators of cellular heterogeneity in basal-like breast cancer influence symmetric versus asymmetric division rates (Expression profiles)
Differentiation events contribute to cellular heterogeneity within tumors and influence disease prog...
GSE83126: Effect of 48h treatment with 100nM GSK2879552 on T-ALL cell lines LOUCY and PEER
RNA sequencing was performed on biological triplicates of LOUCY and PEER cells treated with 100nM GS...
GSE83638: Modeling human brain evolution using induced pluripotent stem cells: comparative analysis of neuronal development in humans and chimpanzees
Understanding evolutionary mechanisms underlying expansion and reorganization of the human brain rep...
GSE85378: Depicting early human development and germ cell origin with porcine embryos
Human primordial germ cells (hPGCs), the precursors of sperm and eggs, originate in early postimplan...
GSE137912: Single cell RNA sequencing of cells treated with a KRAS G12C specific inhibitor
KRAS GTPases are activated in one-third of cancers and KRASG12C is the most common activating altera...
GSE83886: Identification of a unique gene expression signature in mercury and 2,3,7,8-tetrachlorodibenzo-p-dioxin co-exposed cells
Mercury (Hg) and 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD) are major environmental contaminants tha...
GSE84603: Novel KDM1A inhibitors induce differentiation and apoptosis of glioma stem cells via unfolded protein response (UPR) pathway
We examined the transcriptional changes modulated by KDM1A inhibitor NCD-38 by performing global tra...
GSE87809: Epigenetic alterations affecting transcription factors and signaling pathways in stromal cells of endometriosis: Expression data (RNA-seq)
Endometriosis is characterized by growth of endometrial-like tissue outside the uterine cavity. Sinc...
GSE83493: hnRNP C is a key regulator of protein synthesis in mitosis
Purpose: The goal of this study is to characterize the role of hnRNP C in translation regulation of ...
GSE83484: RNA sequencing of human fibroblasts after SUPT4H1 siRNA treatment
Asses the transcriptome-wide changes associated with depletion of transcription elongation factor, S...
GSE83479: Three different in vivo models of synovial sarcoma (xenograft: Fuji; PDX: CTG-0331 and CTG-0771) treated with or without the indicated dose of the EZH2 inhibitor, tazemetostat
The catalytic activities of covalent and ATP-dependent chromatin remodeling are central to regulatin...