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Sequencing-based assays (Page 131)
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GSE101518: Large-scale low-cost NGS library preparation using a robust Tn5 purification and tagmentation protocol [i5i7]
In recent years, tagmentation-based library preparation using a hyperactive version of the Tn5 trans...
GSE130756: A single-cell survey of cellular hierarchy in acute myeloid leukemia
We applied Micro-well seq, a high-throughput and low-costing single-cell RNA platform, to 40 patient...
GSE101993: Molecular characterization of gene regulatory networks in primary human tracheal and bronchial epithelial cells.
The epithelial layer lining the airways has a central role in maintaining lung health, particularly ...
GSE101588: A Low-cost Multiplex Biomarker Assay Stratifies Colorectal Cancer Patient Samples into Clinically-relevant Subtypes: Singapore Cohort RNA-seq
Objective: In order to personalise standard therapies based on molecular profiles, we previously cla...
GSE103477: Transcription elongation regulates genome 3D structure
How transcription affects genome organization in the nucleus is poorly understood. Analyzing influe...
GSE103449: Regulation of the glucocorticoid receptor via a BET-dependent enhancer drives antiandrogen resistance in prostate cancer
In prostate cancer, resistance to the antiandrogen enzalutamide (Enz) can occur through bypass of an...
GSE102040: Base-resolution mapping reveals distinct classes of N1-methyladenosine methylome in nuclear- and mitochondrial-encoded transcripts
Gene expression can be post-transcriptionally regulated via dynamic and reversible RNA modifications...
GSE117580: Inflammation induced by influenza virus impairs innate control of human pneumococcal carriage
Secondary bacterial pneumonia following influenza infection is a significant cause of mortality worl...
GSE111310: Widespread intronic polyadenylation diversifies immune cell transcriptomes
Alternative cleavage and polyadenylation (ApA) can generate mRNA isoforms with differences in 3'UTR ...
GSE102139: Recapitulation of Human Neural Microenvironment Signatures in iPSC-Derived NPC 3D Differentiation
Brain microenvironment plays an important role in neurodevelopment and function, where extracellular...
GSE101821: The novel BETi BI894999 represses super-enhancer associated transcription and synergizes with CDK9 inhibition in AML by induction of apoptosis
Bromodomain and extra-terminal (BET) protein inhibitors have been reported as treatment options for ...
GSE128465: LINC00266-1-encoded peptide regulates mRNA splicing
The mRNA transcriptome profiling and splicing profiling mediated by LINC00266-1 and LINC00266-1-enco...
GSE129519: Brain organoids reproducibly generate the cellular diversity of the human cerebral cortex
Stem cell-derived human brain organoids hold an unprecedented degree of promise as experimental mode...
GSE107029: Total RNA deep sequencing (ribosomal depleted) of human umbilical vein endothelial cells exposed to hypoxia (0.2%) for 12h and 24h or kept under normoxic conditions.
Impaired or excessive growth of endothelial cells contributes to several diseases. However, the func...
GSE102283: Transcriptome analysis and microRNAs profile of mesodermal iPSCs derived progenitors
Mesodermal iPSC derived progenitors (MiPs) obtained from human fetal fibroblasts and skeletal muscle...
GSE102806: ARID2 promotes clear cell renal cell carcinoma in the absence of functional PBRM1 [RNA-seq]
Subunits of SWI/SNF chromatin remodeling complexes are frequently mutated in human malignancies. The...
GSE103309: UBE3A-mediated regulation of imprinted genes and epigenome-wide marks in human neurons
The dysregulation of genes in neurodevelopmental disorders that lead to social and cognitive phenoty...
GSE103501: A multidimensional blood stimulation assay reveals immune alterations underlying systemic juvenile idiopathic arthritis [RNA-Seq]
Despite great scientific and technological advances, immune alterations predisposing to sporadic hum...
GSE108749: Discovery of inhibitors of the HSP90-Calcineurin-NFAT pathway against glioblastoma
We report the application of mRNA sequencing technology for high-throughput profiling of genes expre...
GSE102272: The circular RNA of peripheral blood mononuclear cells: hsa_circ_0005836 as a new diagnostic biomarker and therapeutic target of active pulmonary tuberculosis
It has been reported that circular RNA (circRNA) is associated with human cancer. However, few studi...
GSE102237: Poly(ADP-ribosyl)ation dependent changes in CTCF-chromatin binding and gene expression in breast cells
CTCF is an evolutionary conserved and ubiquitously expressed architectural protein, which regulates ...
GSE128915: Proteomics identifies a marker signature of MAPKi resistance in melanoma
Combined proteomic and RNAseq analysis on 6 melanoma cell cultures reveals a signature for resistanc...
GSE103170: Neutrophils in systemic onset Juvenile Idiopathic Arthritis display sepsis-like features which can be reverted by IL-1 blockade
This study investigated neutrophils in systemic onset Juvenile Idiopathic Arthritis (sJIA), one of t...
GSE102311: Transcriptome variation among human embryonic stem cell lines impacts on their differentiation
Human embryonic stem cells (hESCs) have the pluripotency to form any cell type in the body, making t...
GSE104149: Epigenomes and transcriptomes of human monocytes before and after in vivo exposure to Bacillus Calmette-Gurin vaccine
Innate immune memory is the phenomenon whereby innate immune cells such as monocytes or macrophages ...
GSE106991: RNA-seq analysis of human expandable arterial endothelial precursors (eAEPs), expandable mesenchymal precursors (eMPs), and controls
The following is an excerpt from the abstract of Miller et al. In this study, we find that two trans...
GSE104744: Integration of genome-wide analysis to characterize long noncoding RNAs in diverse immune cell types of the stage IV melanoma patients
We investigated the expression profiles in the CD4+, CD8, and CD14+ peripheral blood cells (PBLs) of...
GSE109718: Enhancing human kidney organoid differentiation from pluripotent stem cells with high-throughput automation
Organoids derived from human pluripotent stem cells are a potentially powerful tool for high-through...
GSE131576: Integrated analysis of H2A.Z isoforms reveals a complex interplay in gene regulation [WI38_siPHF14-siSIRT1 RNA-seq]
The H2A.Z histone variant plays major roles in the control of gene expression. In human, H2A.Z is en...
GSE103242: The transcriptome effect of overexpressing EZH2 in MCF7
Purpose: Increasing evidence suggests that epigenetic reprogramming contributes significantly to the...
GSE102395: Lack of Repressive Capacity of Human Promoter DNA Methylation identified through Genome-Wide Epigenomic Manipulation
It is widely assumed that the addition of DNA methylation at gene promoters silences gene transcript...
GSE107637: RUVBL1/RUVBL2 ATPase Activity Drives PAQosome Maturation, DNA Replication and Radioresistance in Lung Cancer
RUVBL1 and RUVBL2 (collectively RUVBL1/2) are essential AAA+ ATPases that function as co-chaperones ...
GSE103325: Toll-Like Receptor 7 Agonist GS-9620 Induces Prolonged Inhibition of HBV in Human Hepatocytes via a Type I Interferon-Dependent Mechanism
TLR7 induced transcriptional change in HBV-infected primary human hepatocytes SOURCE: Li Li (li.li@g...
GSE130888: Single cell transcriptome of peritoneal cells
To define the transcriptomic landscape of human mesothelial cells in response to PD, we analyzed sin...
GSE105145: Bone marrow-derived and dental pulp-derived human mesenchymal stem cell RNA-Seq
Lineage commitment and tumorigenesis specify adult stem cells from different tissues or organs. To g...
GSE104526: Reversible LSD1 Inhibition with HCI-2509 induces the p53 gene expression signature in high-risk neuroblastoma cells
Lysine-Specific Demethylase 1 (LSD1) over-expression correlates with poorly differentiated neuroblas...
GSE103997: Impeding transcription of expanded microsatellite repeats by deactivated Cas9
Transcription of expanded microsatellite repeats is associated with multiple human diseases, includi...
GSE102875: Spontaneous generation of a novel fetal human retinal pigment epithelium (RPE) cell line available for investigation on phagocytosis and morphogenesis
Purpose: Primary retinal pigment epithelium (RPE) cells have a limited capacity to re-establish epit...
GSE104348: Analysis of transcriptional differences after IFN-beta (IFN-b) or IFN-lambda (IFN-l) treated human mid-gestation chorionic villus explants
Purpose: Treatment of midgestation chorionic villus explants with recombinant IFN-b leads to morphol...
GSE103350: Mechanisms of tolerance and resistance to EGFR inhibition in lung cancer [RNA-seq]
Purpose: Multiple mechanims have been proposed that lead to reduced effectiveness of EGFR tyrosine k...
GSE119204: Short-term effect of Boost versus Radical doses of Intraoperative electron Radiotherapy in breast cancer tumor bed using high-throughput approaches
Importance: Intra-operative electron Radiation Therapy as a partial-breast single high dose radiothe...
GSE103420: Respecifying human iPSC-derived blood cells into highly engraftable hematopoietic stem and progenitor cells with a single factor
Purpose: We designed this study to evaluate the feasibility of using only one factor to respecify hu...
GSE104308 (human): A TFIID-SAGA perturbation that targets MYB and suppresses acute myeloid leukemia (RNA-seq)
Targeting of general coactivators, such as BRD4, is an emerging strategy to interfere with oncogenic...
GSE132178: RNAseq of human monocyte cell line (U937-Cas9) WT or IRF2KO
We analyzed the transcriptional effect of IRF2 in the U937 human monocyte cell line. The major findi...
GSE108094: Next Generation Sequencing of human SMA and healthy control Motor Neurons
Spinal muscular atrophy (SMA) is a motor neuron (MN) disorder caused by mutations in SMN1. The reaso...
GSE103557: Expression profiles in wild-type and IDH1 R132H/WT human astroglial cells [RNA-seq]
Mutations in the isocitrate dehydrogenase 1 (IDH1) gene are critical to oncogenesis. The exact mecha...
GSE110492: Characterization of gene regulation and protein interaction networks for Matrin 3 encoding mutations linked to amyotrophic lateral sclerosis and myopathy
To understand how mutations in Matrin 3 (MATR3) cause amyotrophic lateral sclerosis (ALS) and distal...
GSE107580: Activation of neuronal genes via evolutionarily young LINE-1 elements upon global DNA demethylation in human neural progenitor cells
DNA methylation is thought to contribute to the maintenance of genomic integrity in somatic cells, i...
GSE104354: Salmonella activation of STAT3 signaling by SarA effector promotes intracellular replication and production of IL-10
Salmonella enterica is an important foodborne pathogen that utilizes secreted effector proteins to m...
GSE108198: Global transcriptional analysis of human functional hepatocytes Long-term maintained by small-molecule cocktails by RNA-seq
Functional maintenance of terminally differentiated cells outside the in vivo microenvironment has p...
GSE103711: Expression changes in MAPKi resistant M229 melanoma lines co-cultured with PD-1 overexpressing HEK293T cells [CellLine.FPKM.batch5]
Treatment of advanced V600BRAF mutant melanoma using a BRAF inhibitor (BRAFi) or its combination wit...
GSE104721: OBESITY IS ASSOCIATED WITH IMPAIRED EXPRESSION OF THE GLYCOSYLTRANSFERASE EOGT IN DECIDUALIZING ENDOMETRIUM
In pregnancy, resistance of endometrial decidual cells to stress signals is critical for the integri...
GSE106245: Human embryonic stem cell, chimpanzee induced pluripotent stem cell, orangutan induced pluripotent stem cell, rhesus embryonic stem cell, and their derived cortical organoid RNA-seq
We compared a 5 week time course of cortical organoid differentiation across human, chimpanzee, oran...
GSE103672: Longitudinal Transcriptional Response of Endothelial Cells to Shear Stress
The goal of this study was to find longitudinal transcriptional response of Human Umbilical Vein End...
GSE103688: Expression changes in melanoma cell lines under BRAFi treatment timepoints [RNA-Seq.CellLine.batch3]
Treatment of advanced V600BRAF mutant melanoma using a BRAF inhibitor (BRAFi) or its combination wit...
GSE110146: Transcriptomic-based functional characterization of adverse events following lymphatic filariasis treatment
Intro: Lymphatic filariasis (LF) is a neglected tropical disease caused by the nematode parasite Wuc...
GSE103687: Expression changes in melanoma cell lines under BRAFi treatment timepoints [RNA-Seq.CellLine.batch4]
Treatment of advanced V600BRAF mutant melanoma using a BRAF inhibitor (BRAFi) or its combination wit...
GSE106359: An EGR-Integrator axis controls monocytic enhancers during differentiation
We investigated the genomic occupancy of INTS13 during monocytic differentiation, in in vitro differ...
GSE103637: Transcriptome profiles of POM121-knockout prostate cancer cell lines
Nucleoporins are major constituents of nuclear pore complexes, molecular conglomerates embedded with...
GSE122953: Thymidylate synthase maintains the de-differentiated state of triple negative breast cancers
Cancer cells frequently boost nucleotide metabolism (NM) to support their increased proliferation, b...
GSE142198: Chromatin Topology Reorganization and Transcription Repression by PML/RAR in Acute Promyeloid Leukemia (RNA-seq)
Acute promyeloid leukemia (APL) is characterized by the oncogenic fusion protein PML/RAR, a major et...
GSE106344: Lyophilized human cells stored at room temperature preserve multiple RNA species at excellent quality for RNA sequencing
Purpose: We aimed to examine whether eukaryotic cell lyophilization and long-term storage would be f...
GSE131732: RNA-seq of primary human aortic smooth muscle cells treated with AEA
Primary human aortic smooth muscle cells (HAoSMC) were starved over night in 1% FCS. On the next day...
GSE103763: Genome-wide analysis of herpes simplex virus type 1 (HSV-1) infected cells
The goal of this study was to compare the whole transcriptional profile (RNA-seq) of herpes simplex ...
GSE107594: HMGA2 Promotes Long-Term Engraftment and Myelo-Erythroid Differentiation of Human Hematopoietic Stem and Progenitor Cells
Identification of determinants of fate choices in hematopoietic stem cells (HSCs) is essential in or...
GSE104840: LSD1-mediated enhancer silencing enables endocrine cell development through attenuation of retinoic acid signaling
Developmental progression depends on temporally defined changes in gene expression mediated by trans...
GSE103844: RORt and ROR Signature Genes in Human Th17 Cells
In an effort to study gene expression modulated by RORt and ROR in human Th17 cells, global gene exp...
GSE104442: Alteration of transcriptome by recombinant ncRNA agents
Purpose: Identify whether recombinant ncRNAs are recognized by mammalian cells and processed into ma...
GSE105782: N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis[Ribosome Profiling]
Many of the regulatory features governing erythrocyte specification, maturation, and associated diso...
GSE123976: DNA Methylation Reprograms Metabolic Gene Expression in End-Stage Human Heart Failure
Heart Failure (HF) is a complex clinical disease and leading cause of hospitalization in the United ...
GSE109228: Necroptosis inhibition protects from dopaminergic neuronal cell death in OPA1 mutant Parkinsons disease patient neurons and MPTP treated mice
Dysfunctions in mitochondria dynamics and metabolism are common pathological processes associated wi...
GSE108157: Genome-Wide DNA Methylation Encodes Cardiac Transcriptional Reprogramming in Human Ischemic Heart Failure [RNA-Seq]
Background Epigenetic alterations are stable modifications to chromatin structure that occur in res...
GSE108539: Transcriptomic analyses reveal rhythmic and CLOCK-driven pathways in human skeletal muscle
The circadian regulation of transcriptional processes has a broad impact on cell metabolism. Here, w...
GSE107633: Effect of CBL0137 on nascent transcription in HT1080 cells [RNA-seq]
Small molecule curaxin CBL0137 has broad anti-cancer activity in different preclinical models. It in...
GSE116873: Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques [DND41_RNA-seq]
Purpose: To investigate the impact of oncogenic Notch on the 3D genome organization of cancer cells....
GSE108545: Transcriptomic Reprogramming of Prostate Cancer Cells Driven by Stroma-Derived SPINK1
Recent advances in next generation sequencing (NGS) has revolutionized systems-based analysis of cel...
GSE104178: RNA-Sequencing approach for the identification of novel long non-coding RNA biomarkers in colorectal cancer
Long non-coding RNA (lncRNA) have been implicated in human pathology, however, their roles in colore...
GSE108498: Rescue of Fragile X syndrome neurons by DNA methylation editing of the FMR1 gene [RNA-seq]
Fragile X syndrome (FXS), the most common genetic form of intellectual disability in male, is caused...
GSE110872: Comparative Transcriptome analysis of hESCs- and iPSCs-derived Corneal Endothelial Cells
Purpose: We previously reported the generation of corneal endothelial cells (CECs) using the human p...
GSE105082: RNA G-quadruplexes mark repressive upstream open reading frames in human mRNAs
Translational control is a key determinant of protein abundance, which in turns defines the physiolo...
GSE111584: Neural progenitors derived from Tuberous Sclerosis Complex patients exhibit attenuated PI3K/AKT signaling and delayed neuronal differentiation
Tuberous Sclerosis Complex (TSC) is a disease caused by autosomal dominant mutations in the TSC1 or ...
GSE109373: Mutant p53 controls tumor metabolism and metastasis by regulating PGC-1
Mutant forms of p53 protein often possess pro-tumorigenic function, conferring increased survival an...
GSE106920: Epigenetic Reprogramming of Tissue-Specific Transcription Promotes Colorectal Cancer Metastasis to Liver (RNA-Seq)
Metastasis is the cause of death for 90% of cancer patients, but little is known about how cancer ce...
GSE108248: Epigenome regulation during epidermal lineage commitment [ATAC-seq, RNA-seq]
Recent advances in human pluripotent stem cell (hPSC) technology provide a unique resource for skin ...
GSE117620: Systems-level analyses reveal a convergent pathway for progression of diffuse astrocytoma and potential role for resveratrol in delaying high-grade transformation
We assembled genome-wide gene regulatory networks (modules) that are differentially co-expressed bet...
GSE105142: Identification of the networks that regulate human monocytic myeloid-derived suppressor cell differentiation into inflammatory macrophages
Background: Monocytic myeloid-derived suppressor cells (mMDSC) support immune evasion of tumors by b...
GSE112438: Cell type purification by single-cell transcriptome-trained sorting
Traditional cell type enrichment using fluorescence activated cell sorting (FACS) relies on methods ...
GSE129263: MTR4 drives tumorigenesis of hepatocellular carcinoma by controlling alternative splicing of metabolic genes through PTBP1 recruitment
Aberrant alternative splicing (AS) is implicated in cancer metabolic reprogramming that supplies can...
GSE107370: Concomitant BCORL1 and BRAF mutations in vemurafenib-resistant melanoma cells
BRAF is the most frequently mutated gene in melanoma. Constitutive activation of mutant BRAFV600E le...
GSE104193: Hypoxia-mediated translational activation of ITGB3 in breast cancer cells enhances TGF- signalling and malignant features in vitro and in vivo
We performed a polysomal RNA-Seq screen in non-malignant breast epithelial (MCF10A) and TNBC (MDA-MB...
GSE110220: USP15-dependent lysosomal pathway controls p53-R175H turnover in ovarian cancer cells
Gain-of-function p53 mutants such as p53-R175H form stable aggregates that accumulate in cells and p...
GSE106368: Cooperation of GRSF1 and the mitochondrial degradosome (hSuv3-PNPase complex) in degradation of mitochondrial RNA
Vertebrate mitochondrial genomes show extraordinary GC skew which results in the synthesis of RNAs p...
GSE107638: Contribution of differential cell-specific methylation to schizophrenia [RNA-seq]
To address the heterogeneity of gene regulation and expression in cell types of a brain region with ...
GSE108191: HDAC Inhibitor-Induced Acetylation of KRAS Confers A Pro-Oncogenic Effect Limiting Treatment Response in Colorectal Cancer
The limited clinical utility of HDAC inhibitors for the treatment of colorectal cancer (CRC) has unt...
GSE109708: Transcriptome analysis of VCaP xenografts resistant to dual therapy with abiraterone and enzalutamide
We report RNA sequencing data on serial biopsies of prostate cancer VCaP xenografts as the tumors pa...
GSE107047: Natural Killer cells control tumor growth by sensing a growth factor
Many tumors produce platelet-derived growth factor (PDGF)-DD, which promotes cellular proliferation,...
GSE106335: Loss-of-function due to MODY1/HNF4A mutation abrogates liver and pancreas differentiation from MODY1-hiPSCs
Purpose: To investigate the impact of MODY1/HNF4A mutation on foregut development using differentiat...
GSE105773: RNA editing in nascent RNA affects pre-mRNA splicing
In eukaryotes, nascent RNA transcripts undergo an intricate series of RNA processing steps to achiev...
GSE105951: Histone acetyltransferase p300 induces de novo super-enhancers to drive cellular senescence [RNA-seq]
Cellular senescence is a state of stable proliferative arrest induced by stress and is associated wi...
GSE107707: Transcriptional changes associated with resistance to JQ1 treatment in MYCN-amplified neuroblastoma
Drug resistance is a major clinical challenge in achieving durable responses to targeted cancer ther...