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Sequencing-based assays (Page 133)
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GSE113660: UMI-count modeling and differential expression analysis for single-cell RNA sequencing
Single cell RNA-seq of the human alveolar rhabdomyosarcoma cell line Rh41. We also inlcude a bulk RN...
GSE109673: Dual inhibition of EZH1/2 depletes stem cells and over-activates WNT signaling in multiple myeloma [RNA-seq]
Multiple myeloma (MM) is a hematological malignancy caused by accumulation of abnormal clonal plasma...
GSE140472: ZBTB7A prevents RUNX1-RUNX1T1 dependent clonal expansion of human hematopoietic progenitor cells
ZBTB7A is frequently mutated in acute myeloid leukemia (AML) with t(8;21) translocation. However, th...
GSE112145: FMR1 reactivating treatments in Fragile X iPSC-derived neural progenitors in-vitro and in-vivo
Fragile X syndrome (FXS) is caused primarily by a CGG repeat expansion mutation in the FMR1 gene tha...
GSE111853: Screening in Human Cardiac Organoids Identifies a Requirement for the Mevalonate Pathway in Cardiomyocyte Proliferation
Purpose: Induction of endogenous proliferation is a promising strategy for cardiac regeneration. We ...
GSE118954: Multiple modes of PRC2 inhibition elicit global chromatin alterations in H3K27M pediatric glioma
A methionine substitution at lysine 27 on histone H3 variants (H3K27M) characterizes ~80% of diffuse...
GSE111049: The commensal-derived metabolite butyrate imprints an antimicrobial program in macrophages
The balance between tolerogenic and inflammatory responses determines immune homeostasis in the gut....
GSE112509: RNA-seq analysis identifies different transcriptomic types and developmental trajectories of primary melanomas
Recent studies revealed trajectories of mutational events in early melanomagenesis, but the accompan...
GSE116282: Targeting MYC dependency in ovarian cancer through inhibition of CDK7 and CDK12/13
High-grade serous ovarian cancer is characterized by extensive copy number alterations, among which ...
GSE110397 (human): NK cell-mediated cytotoxicity contributes to tumor control by a cytostatic drug combination
Accumulating evidence suggests that molecularly targeted therapies, which were originally developed ...
GSE112589: XBP1s Activation Globally Remodels N-Glycan Structure Distribution Patterns
The unfolded protein response (UPR), as its name implies, safeguards secretory pathway proteostasis....
GSE110820: Developmental origins define epigenomic differences between subcutaneous and visceral adipocytes [RNA-Seq]
To understand the molecular differences between adipocytes and their contribution to cell-type speci...
GSE111210: The multiple myeloma risk allele at 5q15 lowers ELL2 expression and increases ribosomal gene expression [ELL2 rescue]
To understand the biological mechanism of ELL2 in multiple myeloma (MM), we show that the MM risk al...
GSE117685: Analysis of chromatin accessibility uncovers TEAD1 as a regulator of migration in human glioblastoma
The intrinsic drivers of migration in glioblastoma (GBM) are poorly understood. To better capture th...
GSE109281 (human): Subclonal cooperation drives metastasis through modulating local and systemic immune microenvironments
Bulk RNA-Seq: Gene expression analysis of stromal and tumor fractions of primary and metastatic lesi...
GSE110467: KMT2D regulates p63 target enhancers to coordinate epithelial homeostasis [RNA-Seq]
KMT2D plays a critical role in the control of epithelial enhancers and p63 target gene expression, i...
GSE113255: Gene expression profiling study to identify distinct subtypes in diffuse type gastric cancer
Although recent advances in high-throughput technology have provided many insights into gastric canc...
GSE109562: GLIS3 Transcriptionally Activates WNT Genes to Promote Differentiation of Human Embryonic Stem Cells to Posterior Neural Progenitors
Anterior-posterior (A-P) specification of the neural tube involves initial acquisition of anterior f...
GSE109607: Mechanistic insights into anti-cancer properties of oligomeric proanthocyanidins from grape seeds in colorectal cancer
Although the anti-cancer properties of Oligomeric Proanthocyanidins (OPCs) from grape seeds has been...
GSE111905: Recruitment of BRCA1 limits MYCN-driven accumulation of stalled RNA Polymerase in neuroblastoma
Deregulation of the MYCN gene drives the development of neuronal and neuroendocrine tumors and is of...
GSE110798: Single-cell transcriptomics of human oocytes: environment-driven metabolic competition and compensatory mechanisms during oocyte maturation
Aim: The mechanisms coordinating maturation with an environment-driven metabolic shift, a critical s...
GSE109986: Genome-wide transcriptional profile for the GSK3 selective inhibitor BRD3731
Exploiting an Asp-Glu switch in glycogen synthase kinase 3 to design paralog selective inhibitors fo...
GSE111920: Metabolic adaptations underlie epigenetic vulnerabilities in chemoresistant breast cancer. [RNA-Seq1]
Purpose:Assess the difference in gene expression of taxol-resistant TNBC cells relative to parental ...
GSE109752: Increased Serine and One Carbon Pathway Metabolism by PKCl/i Deficiency Promotes Neuroendocrine Prostate Cancer [RNA-seq]
Increasingly effective therapies targeting the androgen receptor have paradoxically promoted the inc...
GSE109822: Spatial and single-cell transcriptional profiling identifies functionally distinct human dermal fibroblast subpopulations
Fibroblasts synthesize the extracellular matrix of connective tissue and play an essential role in m...
GSE116391 (human): Mutations in splicing factor SF3B1 promote transformation through MYC stabilization
Although mutations in the RNA splicing factor SF3B1 are frequently observed in multiple human cancer...
GSE110469: Helios enhances the preferential differentiation of human fetal CD4+ nave T cells into regulatory T cells. [RNA-Seq - ex vivo]
RNA sequencing was used to compare the transcriptome of ex vivo isolated adult and fetal nave and re...
GSE115871: Pressure-Driven Mitochondrial Transfer Pipeline Generates Mammalian Cells of Desired Genetic Combinations and Fates
Generating mammalian cells with desired mtDNA sequences is enabling for studies of mitochondria, dis...
GSE114069: Transcriptional Targeting Of Oncogene Addiction In Medullary Thyroid Cancer [RNA-Seq]
Metastatic medullary thyroid cancer (MTC) is a currently incurable disease. FDA approved therapies t...
GSE113492: Human gut derived-organoids as model to study gluten response and effects of microbiota bioproducts in celiac disease
Celiac disease (CeD) is an intestinal immune-mediated disorder caused by gluten ingestion in genetic...
GSE109830: MYR1-dependent effectors are the major drivers of a host cells early response to Toxoplasma including counteracting MYR1-independent effects
The intracellular parasite Toxoplasma gondii uses a diverse repertoire of effector molecules to mani...
GSE117769: White blood cells from rheumatoid arthritis patients and matched healthy donors
The experiment was designed to assess gene expression differences between rheumatoid arthritis patie...
GSE113655: PTex - Purification of Cross-linked RNA-Protein Complexes by Phenol-Toluol Extraction
PTex is a protocol to purify UV-cross-linked ribonucleoproteins (RNPs) in an unbiased and sequence-i...
GSE119630 (human): Extraction-Free Whole Transcriptome Profiling from Specific Subareas of Unstained or H&E Stained FFPE Tissues
We describe the use of a ligation-based targeted whole transcriptome expression profiling assay, Tem...
GSE110513: Integrating single-cell transcriptomic data across different conditions, technologies, and species
Computational single-cell RNA-seq (scRNA-seq) methods have been successfully applied to experiments ...
GSE110709: RNA-seq of GSK-J4 Treated Neuroblastoma Cell Lines
High-risk neuroblastoma is often distinguished by amplification of MYCN and loss of differentiation ...
GSE122827: BNC1 is a master regulator of human epicardial cell heterogeneity and function
Single cell RNAseq of a model of epicardium derived from human pluripotent stem cell (hPSC-epi) reve...
GSE111878: The m 6 A-methylase complex recruits TREX and regulates mRNA export.
N6-methyladenosine (m6A) is the most abundant internal modification of eukaryotic mRNA. This modific...
GSE110952: Functional studies of missense TREM2 mutations in human stem cell-derived microglia
The derivation of microglia from human pluripotent stem cells provides systems for understanding mic...
GSE121277: RNA seq data of Hep3B-control, Hep3B-sertraline, Hep3B-XL413, Hep3B-XL413-sertraline, Huh7-control, Huh7-sertraline, Huh7-XL413, Huh7-XL413-sertraline cells
Hep3B and Huh7 cells pre-treated with XL413 for 10 days to induce senescence prior to sertraline tre...
GSE114725: Single-cell Map of Diverse Immune Phenotypes in the Breast Tumor Microenvironment 3' RNA Sequencing
Knowledge of immune cell phenotypes in the tumor microenvironment is essential for understanding mec...
GSE112962: Endogenous interaction profiling identifies DDX5 as an oncogenic coactivator of transcription factor Fra-1 [RNA-seq]
Fra-1, a member of the activator protein 1 (AP-1) family, is overexpressed in triple-negative breast...
GSE111177: Identification of Transcription Factor Relationships Associated with Androgen Deprivation Therapy Response and Metastatic Progression in Prostate Cancer
Background: Patients with locally advanced or recurrent prostate cancer typically undergo androgen d...
GSE117828: Primary human monocytes either mock treated, infected with A/California/07/2009 and A/Victoria/361/2001
241 genes differentially expressed between two viruses SOURCE: Lisa,M,Kronstad (lmkronstad@gmail.com...
GSE117469: Profiling of vascular organoid endothelial cells and pericytes from iPS cells
Diabetes is prevalent worldwide and associated with severe health complications, including blood ves...
GSE113482: cis-Regulatory Chromatin Contacts in Neural Cells Reveal Contributions of Genetic Variants to Complex Neurological Disorders [RNA-Seq]
Mutations in gene regulatory elements have been associated with a wide range of neurological disorde...
GSE111929: Long noncoding RNA CCDC144NL-AS1 knockdown induces nave-like state conversion of human pluripotent stem cells
Human nave pluripotency state cells can be derived from direct isolation of inner cell mass or prime...
GSE111222: A Multi-Parameter Analysis of Cellular Coordination of Major Transcriptome Regulation Mechanisms
To understand cellular coordination of multiple transcriptome regulation mechanisms, we simultaneous...
GSE113191: CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia
We analyzed RNA-seq, ATAC-seq, ChIP-seq and 4C-seq data to find that CTCF binding site located betw...
GSE111485: Multi-omic measurements of heterogeneity in HeLa cells across laboratories
Reproducibility in research can be compromised by both biological and technical variation, but most ...
GSE135964: Mild, moderate and severe enterovirus 71 (EV71) isolates infection in human PBMCs
Hand, foot and mouth disease (HFMD), caused by enterovirus 71 (EV71), presents mild to severe diseas...
GSE117033: Genome wide mapping of polyadenylation sites in proliferating and contact-inhibited cells and cells with knockdown of cleavage and polyadenylation factors
Purpose: Quiescence is a state of reversible cell cycle exit. Levels of polyadenylation factors decr...
GSE112883: Combined Targeting of Estrogen Receptor alpha and XPO1 prevent Akt activation, remodel metabolic pathways and induce autophagy to overcome tamoxifen resistance
Majority of breast cancer specific deaths in women with ER (+) tumor occur due to metastases that ar...
GSE119688: CHD7 is Suppressed in the Perinecrotic/Ischemic Microenvironment and is a Novel Regulator of Angiogenesis
In a study focused on the role for CHD7 in angiogenesis we completed RNA-sequencing of D456, a gliob...
GSE113581: Determining effects of microbial metabolite, Urolithin A on colon epithelial cells
Numerous studies signify that diets rich in phytochemicals reduce the risk of inflammatory bowel dis...
GSE111908: Pluripotent stem cell model of Nakajo-Nishimura syndrome untangles proinflammatory pathways mediated by oxidative stress
Nakajo-Nishimura syndrome (NNS) is an immunoproteasome-associated autoinflammatory disorder caused b...
GSE134431: Deregulated immune signature orchestrated by FOXM1 impairs human diabetic wound healing
We performed RNA-seq on tissue biopsies derived from patients with DFUs and compared it to human ora...
GSE111404: Small Sample-Big Data: Integrative Indexed Systems Biology Reveals Dramatic Molecular Ontogeny over the First Week of Human Life
Systems biology provides a powerful approach to unravel complex biological processes yet it has not ...
GSE112122: Differential gene expression of static and intermittent compressive force treated human periodontal ligament cells
Mechanical force has been shown to regulate periodontal ligament cells (PDLs) behaviors. However, di...
GSE129590: Studying the selectivity of a small molecule Synucleozid on transcriptome
One strategy to drugging undruggable proteins is to directly target the mRNA that encodes them, ther...
GSE121127: Three-component mixed cell lines RNA-seq experiment
To generate this dataset in RNA-seq, we performed a mixing experiment, in which we mixed mRNAs from ...
GSE112277: MKL1 augments megakaryocyte maturation by enhancing the SRF regulatory axis [RNA-seq]
SRF is a ubiquitous transcription factor that binds DNA in association withmyocardin-family proteins...
GSE111930: An endogenous retrovirus-derived long non-coding RNA promotes fetal cardiomyocyte migration in primates
The protein-coding gene networks regulating heart development are well known. Less understood are th...
GSE112202: Digoxin treatment is associated with thyroid cancer differentiation and radioactive iodide treatment response
Non-medullary thyroid cancer (NMTC) is the most frequent endocrine tumor with in most cases a good p...
GSE116405: Gene activation precedes DNA demethylation in response to infection in human dendritic cells
DNA methylation is considered to be a relatively stable epigenetic mark. Yet, a growing body of evid...
GSE111918: RUNX1 mutations lead to a myeloid differentiation block by altering the RUNX1 transcriptional program (RNA-Seq)
Mutations in the RUNX1 gene (RUNX1mut) have been established in myelodysplasia (MDS), de novo and se...
GSE119678: Defective transcription elongation in a subset of cancers confers immunotherapy resistance (human cell lines RNA-Seq)
The nature and the role of global transcriptional deregulations in cancers are not fully understood....
GSE130006: Transcriptomes analysis for the regulation of Z36 induced autophagy in HeLa cell death
Z36 is a small molecule that induces Beclin1-dependent autophagy and autophagic cell death in HeLa c...
GSE112297: Enhanced cardiac repair by human telomerase reverse transcriptase over-expression in human cardiac mesenchymal stem cells
RNA-seq profiling of gene expression of human telomerase reverse transcriptase (hTERT)-expressing hu...
GSE112692: Use single cell RNA sequencing to study the molecular siganature of primary human Megakaryocytic-erythroid progenitor
Megakaryocytic-Erythroid Progenitors (MEP) produce circulating red blood cells and platelets. Althou...
GSE114191 (human): Repurposing of promoters and enhancers during mammalian evolution
The spatiotemporal control of gene expression exerted by promoters and enhancers is central for orga...
GSE112007: Next Generation Sequencing Facilitates Quantitative of Transcriptomes in Various Cells Treated with or without LD100 and siRNA of SOD1
Purpose: mRNA-sequencing has revolutionized systems-based analysis of cellular pathways. The goals o...
GSE113585: Profiling of colorectal tumor-infiltrating CD8 T cells according to their expression status of CD39
Human tumors are infiltrated by various immune cells, including CD8 T cells. CD8 T cells express uni...
GSE113195: Sex differences in transcriptomic profiles in aged kidney cells of renin lineage
Renin expressing cells in the kidneys juxta-glomeruluar compartment likely also serve as progenitors...
GSE116464: Human-iPSC-Derived Cardiac Stromal Cells Enhance Maturation in 3D Cardiac Microtissues and Reveal Non-cardiomyocyte Contributions to Heart Disease
Cardiomyocytes (CMs) from human induced pluripotent stem cells (hiPSCs) are functionally immature, b...
GSE117836: ARID3a Gene Profiles are Strongly Associated with Human Interferon Alpha Production
Percentages of ARID3a-expressing low density neutrophils in SLE patients correlate with lupus diseas...
GSE116650: RIG-I and MDA5 fRIP during KSHV lytic reactivation
The RIG-I like receptors (RLRs) RIG-I and MDA5 are cytosolic RNA helicases best characterized as res...
GSE129071: Oxaliplatin resistance is enhanced by saracatinib via upregulation of ABCG1 and Wnt/-catenin signaling in hepatocellular carcinoma
Background:Oxaliplatin-resistant hepatocellular carcinoma (HCC) is associated with increased insulin...
GSE111819: Reactivation of Human Herpesvirus 6 (HHV-6) in Diverticulitis
Background: Diverticular disease is a significant healthcare burden in the United States. Younger di...
GSE113210: Acute viral bronchiolitis (PBMC)
Background: A subset of infants are hyper-susceptible to severe/acute viral bronchiolitis (AVB), for...
GSE113046: Identification of two distinct pathways of human myelopoiesis.
The myeloid innate immune system plays key roles in the defence against parasites and bacteria, and ...
GSE121536: TFAP2C signalling in human fibroblasts
Our work has shown that the transcription factor TFAP2C is upregulated in fibroblasts that generate ...
GSE111881: Transcriptome analysis of total RNA in human osteosarcoma cell line U2OS before and after inhibition of zinc finger protein ZNF768
Inhibition of ZNF768 function was achieved by conditional over expression expression of the C-termin...
GSE117875: Transcriptomic profile of intestinal epithelial cells obtained from ileal endoscopic biopsies from newly-diagnosed, pediatric Crohn's disease patients and healthy controls.
Purpose: To uncover differentially-regulated transcripts and pathways/biological processes in newly-...
GSE114796: RNA transcriptome sequencing analysis of AGS cells transfected with MFAP2 shRNA or control shRNA
An RNA transcriptome sequencing analysis was performed in AGS cells that were transfected with MFAP2...
GSE113685: Metabolic adaptations underlie epigenetic vulnerabilities in chemoresistant breast cancer. [RNA-Seq2]
Purpose:Assess the difference in gene expression of taxol-resistant TNBC cells relative to parental ...
GSE119378: Transcriptional landscape changes during human embryonic stem cell derivation
Currently, there is only minimal information elucidating the transcriptional changes occurring durin...
GSE114961: Cell-specific proteome analyses of human bone marrow reveal molecular features of age-dependent functional decline [single cells]
Diminishing potential to replace damaged tissues is a hallmark for ageing of somatic stem cells, but...
GSE119654: Proline 152 mutation in p53 abolishes cognate DNA binding, induces gain of function tumorigenesis
We have identified a relatively rare mutation in p53 in an Indian oral cancer patient sample at the ...
GSE114273: Gene expression profilings for prostate cancer cells after inhibition of PARP1 or PARP2 using pharmaceutical or siRNA-based approaches
Androgen receptor (AR) signaling is a key driver of prostate cancer (PCa) growth and progression. Un...
GSE114510: GM604 regulates developmental neurogenesis pathways and the expression of genes associated with amyotrophic lateral sclerosis
Background: Amyotrophic lateral sclerosis (ALS) is currently an incurable disease without highly eff...
GSE112013: The Human Testis Cell Atlas via Single-cell RNA-seq (Healthy men scRNA-seq data set)
Human adult spermatogenesis involves a balance of spermatogonial stem cell self renewal and differen...
GSE114922: RNA sequencing of bone marrow CD34+ hematopoietic stem and progenitor cells from patients with myelodysplastic syndrome and healthy controls
SF3B1, SRSF2 and U2AF1 are the most frequently mutated splicing factor genes in MDS. We have perform...
GSE143373: RNAseq analysis of a genome-wide loss-of-function CRISPR/Cas9 library in haploid human embryonic stem cells (hESCs) differentiated into three germ layers
Pluripotentstemcells can differentiate into all embryonic germ layers, a process that is orchestrate...
GSE117824: RNA-seq of Single-Cell Genotyping of Transcriptomes
Somatic cancer driver mutations may result in distinctly diverging phenotypic outputs. Thus, a commo...
GSE114159: Next Generation Sequencing Analysis of human hematopoietic stem/progenitor cells (HSPCs) differentiated from pluripotent stem cells
Purpose: global gene expression profiling of H1 and iPSC derived HSPCs.; Methods: SMART-seq2 amplifi...
GSE113005: Transcriptomics-based drug repurposing approach identifies novel drugs against sorafenib-resistant hepatocellular carcinoma
Hepatocellular carcinoma (HCC) is frequently diagnosed in patients with late-stage disease who are i...
GSE114558: Targeting an RNA-binding Protein Splicing Network in Acute Myeloid Leukemia
RNA-binding proteins (RBPs) are essential modulators of transcription and translation and are often ...
GSE113117: Stabilizing Heterochromatin by DGCR8 Alleviates Senescence and Osteoarthritis
DiGeorge syndrome critical region 8 (DGCR8) is a critical component of the canonical microprocessor ...
GSE113120: RNA-Seq with and without RNase treatment in PCa cell lines
Standard RNA analyses using microarrays and low-coverage polyadenylation enriched RNA-Sequencing (RN...