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Sequencing-based assays (Page 138)
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GSE128365: Sequencing of metabolically labeled transcripts in single cells from RPE1-FUCCI cells and murine intestinal organoids.
Measurements of metabolically labeled transcripts in single cells for estimation of mRNA synthesis a...
GSE124393: LARP7 is a substrate of BRCA1 that regulats genome instability and tumorigenesis
Impaired DNA repair leads to cancer, aging and many genetic diseases. However, understanding of the ...
GSE128268: A Unique Epigenomic Landscape Defines Human Erythropoiesis (RNA-seq)
Mammalian erythropoiesis yields a highly specialized cell type, the mature erythrocyte, evolved to m...
GSE125119: CD73 Immune Checkpoint Defines Inducible Regulatory NK cells in the Tumor Microenvironment
High levels of ecto-5'-nucleotidase (CD73) have been implicated in immune suppression and tumor prog...
GSE128804: Serine racemase is required for colorectal tumor growth and a potential therapeutic target.
Serine racemase (SRR) is an enzyme that catalyzes two reactions, the racemization and the dehydratio...
GSE128967: The Wnt/-catenin and RAS-ERK Pathways were Activated in Tissues of Chemotherapy-Resistant Gastric Cancer PDX Tumor
Chemotherapy resistance and disease recurrence remains major causes of gastric cancer patient mortal...
GSE126486: Genome-wide CRISPR-Cas9 screen identifies druggable synthetic lethality between LSD1 and MTORC1 in MLL-translocated AML
Lysine Specific Demethylase 1 (LSD1 or KDM1A) is one of a number of epigenetic regulators which have...
GSE126520: endogenous mRNA decay in 293t, hela, RPE cell line
mRNA endogenous decay profiles approach in 293T, HeLa and RPE cells.; mRNA translation decodes nucle...
GSE127903: Protein Tyrosine Phosphatase Non-receptor 3 Acts as a Tumor Suppressor and Boosts TGF-b Signaling Independent of its Phosphatase Activity
Transforming Growth Factor b (TGF-b) controls a variety of cellular functions during development. A...
GSE131696: Sexually dimorphic crosstalk at the maternal-fetal interface
The first trimester is a critical window of maternal-fetal communication for pregnancy. Using single...
GSE128253: Transcriptome of human neck-derived immortalized white preadipocyte cell lines
White adipose tissue is a major site of energy storage and plays a noteworthy role in physiological ...
GSE128416: RNA sequencing on HT29 colorectal cancer cell line
We report the single cell RNA sequencing on HT29 colorectal cancer line with 100 nM dasatinib treatm...
GSE131592: Transcriptional consequences of wild-type and missense mutant p53 in isogenic human acute myeloid leukemia (AML) cell lines
TP53, encoding for the tumor suppressor p53, is the most frequently mutated gene in human cancer. Th...
GSE128469: Synchronized HES7 Oscillation In Human Embryonic Stem Cell-Derived Presomitic Mesoderm
Little is known about human segmentation clock during somitogenesis. Human embryonic stem (ES) cell ...
GSE128257: RNA-seq of RKO cells with cTAZ KO or putback
RKO cells with cTAZ KO or putback were subjected to RNA isolation and RNA-seq analyses were generate...
GSE128405: Characterization of prostate cancer cell expression profile upon treatment with extracellular vesicles derived from senescent stromal cells in the tumor microenvironment
Recent advances in next generation sequencing (NGS) has revolutionized system-based analysis of geno...
GSE125259: Transcriptomic and barrier responses of human airway epithelial cells exposed to cannabis smoke with and without LABA/GC intervention
Purpose: Globally, many jurisdictions are legalizing or decriminalizing cannabis, creating a potenti...
GSE126504: Next Generation Sequencing Facilitates Quantitative Analysis of SW480 cells and HPSE-knockdown SW480 cells Transcriptomes
Heparanase (HPSE), the only known mammalian endoglycosidase responsible for heparan sulfate cleavage...
GSE125218: An Improved Human smORF Annotation Workflow Combining De Novo Transcriptome Assembly and Ribo-Seq
Protein-coding smallopen reading frames (smORFs) are emerging as an important class of genes, howeve...
GSE132195: Persistence of inflammatory phenotype in residual psoriasic plaques in patients on effective biologic therapy
The goal of our study is to elucidate mechanisms of plaque persistence despite overall good drug res...
GSE135505: Transcriptome sequencing of HELZ-null HEK293T human cell line generated by CRISPR/Cas9 gene editing
Eukaryotic SF1 helicases have been implicated in various aspects of RNA metabolism, including transc...
GSE128328: Gene expression profile in endometrial organoids cultured in normal follicular phase vs PCOS-like hormone profile
We generated scaffold-free endometrial organoids from human primary endometrial tissues. These organ...
GSE128950: RNA-seq analysis of AML cells in response to ASLAN003
We aim to gain insight into the changes of gene expression induced by ASLAN003, a novel, potent Dihy...
GSE130534: Identification of drivers and therapeutic vulnerabilities in anti-androgen resistant prostate cancer cells
Inhibition of the androgen receptor (AR) by anti-androgens is the standard treatment for castration ...
GSE131660: Allosteric Antagonist Modulation of TRPV2 by Piperlongumine Impairs Glioblastoma Progression
Using machine learning to identify biological targets for natural products with anticancer propertie...
GSE133941: Three-dimensional Oxabicycloheptene sulfonate targets the homologous recombination and repair programs through estrogen receptor antagonism
Selective Estrogen Receptor Modulators (SERMs) are a class of structurally diverse compounds possess...
GSE130236: Disrupting -catenin dependent Wnt signaling activates an invasive gene program predictive of colon cancer progression
The recent classification of colon cancer into molecular subtypes revealed that patients with the po...
GSE129457: RNA sequencing, chromatin accesibility and ChIP seq analysis of BAP1 -/- human liver organoids
Liver organoids were engineered by CRISPR/Cas9 to introduce mutation in the BAP1 gene and profiled f...
GSE126530: Next Generation Sequencing of isolated EGFR+ and HLA-G+ first trimester human trophoblasts
The aim of this study was to identify differentially expressed signatures of non-invasive (EGFR+) an...
GSE128477: A predictable conserved DNA base composition signature defines human core DNA replication origins
Here, we identify DNA replication initiation sites from 19 human samples, representing three untrans...
GSE140437: Bronchial Epithelial cells gene expression profiles in response to Mycobacterium abscessus
Bronchial Epithelial cells were exposed to microparticles generated frommycobacterium abscessusMAB c...
GSE125370: Nucleotide excision repair capacity increases during differentiation of human embryonic carcinoma cells into neurons and muscle cells
Embryonic stem cells can self-renew and differentiate, holding great promise for regenerative medici...
GSE128392: CD8+ T cells regulate tumor ferroptosis during cancer immunotherapy
CD8+ T cells activated by cancer immunotherapy execute tumor clearance mainly by inducing cell death...
GSE126542: Loss of Nuclear TDP-43 Is Associated with Decondensation of LINE Retrotransposons [RNA-Seq]
Loss of the nuclear RNA binding protein TAR DNA binding protein-43 (TDP-43) into cytoplasmic aggrega...
GSE128367: Transcriptomic analysis of ATP6V1A knock-down and amyloid beta-treated neurons
ATP6V1A plays a unique role in synapse function in neurons and we found decreased neuronal activity ...
GSE145069: Differential gene expression and pathway analysis by RNA sequencing in human OPTN(E50K) retinal ganglion cells
Retinal ganglion cells (RGCs) serve as the essential connection between the eye and the brain, with ...
GSE128805: Cancer-Causing Mutations in SF3B1 Alter Splicing by Disrupting Interaction with SUGP1
SF3B1, which encodes an essential spliceosomal protein, is frequently mutated in myelodysplastic syn...
GSE126797: Reducing the structure bias of RNA-Seq reveals a large number of non-annotated non-coding RNA
The study of RNA expression is the fastest growing area of genomic research. However, despite the dr...
GSE129111: Spatial control of oxygen delivery to 3D cultures alters cancer cell growth and gene expression
Commonly used monolayer cell cultures lack the capacity to provide a physiologically relevant enviro...
GSE126564: RNA sequencing from FOXM1 knockout HEK293T cells reconstituted with FOXM1 isoforms a, b and c.
To study the transcriptional programs of FOXM1 isoforms, we generated a FOXM1 HEK293T cell line then...
GSE135510: Gene expression analysis following depletion of LOXL2 in esophgeal cancer cells
Esophageal cancer is the sixth most common cause of cancer death globally, of which esophageal squam...
GSE125437: Functional diversity of inhibitors tackling the differentiation arrest of MLL-rearranged leukemia
Purpose: The chromosomal rearrangements of the mixed-lineage leukemia (MLL) gene have been extensive...
GSE125421: A comprehensive gene expression analysis identifies novel immune signatures in cesarean-born infants
The rate of cesarean delivery (CD) in China has risen sharply and the high rate was reported to be a...
GSE135487: PT2385 HIF2A inhibitor treatment of patient derived orthotopic xenograft neuroblastoma cells in the presence or absence of hypoxia
neuroblastoma cells derived from PDOX models were treated with the HIF2A inhibitor in normoxic and h...
GSE130793: Human Thoracic Duct Lymph Contains Circulatory Intermediates T Follicular Helper Cells [RNA-Seq]
T follicular helper CD4 T cells (Tfh) provide requisite help to B cells in the germinal centers (GC)...
GSE126569: Genome-wide fetalization of enhancer architecture in heart disease [RNA-Seq]
Heart disease is associated with re-expression of key transcription factors normally active only dur...
GSE128406: PHF19 Promotes Cell Growth and Confers Drug Resistance through EZH2 Phosphorylation in Multiple Myeloma
To determine the effect of overexpression PHF19 in ARP1 myeloma cells; Drug resistance is a major r...
GSE128385: BI-3406, a potent and selective SOS1::KRAS interaction inhibitor, is effective in KRAS-driven cancers through combined MEK inhibition
KRAS is the most frequently mutated driver of pancreatic, colorectal, and non-small cell lung cancer...
GSE137687: Polyunsaturated Fatty Acids from Astrocytes Activates PPAR Gamma Signaling in Cancer Cells to Promote Brain Metastasis
Brain metastasis, the most ominous form of melanoma and carcinoma, is the consequence of favorable i...
GSE126821: Transcriptomic analysis of Fusobacterium nucleatum-stimulated Human gingival-derived mesenchymal stem cells
To better understand the global responses of GMSCs to F. nucleatum infection along the time sequence...
GSE130174: Biomarkers of Cavernous Angioma with Symptomatic Hemorrhage (CASH) [RNA-seq]
Background: Cerebral cavernous angiomas with a symptomatic hemorrhage (CASH) have a high-risk of rec...
GSE132215: The secretome of skin cancer cells activates the mTOR/MYC pathway in healthy keratinocytes and converts them into tumorigenic cells
Cutaneous squamous cell carcinoma (cSCC) is the most aggressive tumor among non-melanoma skin cancer...
GSE131697: A fully defined protocol for differentiation of human pluripotent stem cells into forebrain neural progenitors
Human embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs) were differentiated int...
GSE128590: Role of Histone H3 Lysine 27 Crotonylation in Gene Transcriptional Repression
Histone lysine acetylation and methylation regulate gene transcription through coordination of chrom...
GSE127186: CDK8/19 small molecule inhibition promotes nave features in human and mouse pluripotent stem cells
Pluripotent stem cells (PSCs) can transition between cell states in vitro, closely reflecting develo...
GSE127478: Mitochondrial 3243A>G mutation confers pro-atherogenic and pro-inflammatory properties in MELAS iPS derived endothelial cells
We obtained three independent sets of endothelial cells differentiated from iPSCs derived from a Mit...
GSE130873: Total RNA-seq of siRNA-mediated WTAP and TPR knockdown
To identify changes in splicing patterns following WTAP and TPR knockdown, RNA-sequencing was perfor...
GSE131182: Expression profile of circular RNAs in oral squamous cell carcinoma
We analyzed the circRNA expression profile in 6 pairs of samples of OSCC and normal oral mucosa tiss...
GSE125511: -Caryophyllene Enhances the Transcriptional Upregulation of SREBP-dependent Lipid Biosynthesis in Breast Cancer Cells
-caryophyllene (BCP) exhibits anti-proliferative properties in cancer cells. Here, we examine the h...
GSE127223: CPSF controls PAS selection and epidermal differentiation
Alternative polyadenylation (APA) is a regulatory mechanism that controls gene expression level and ...
GSE125534: The Human Integrator Complex Facilitates Transcriptional Elongation by Endonucleolytic Cleavage of Nascent Transcripts
Transcription by RNA polymerase II (RNAPII) is pervasive in the human genome. However, the mechanism...
GSE127165: Whole transcriptome sequencing of57 laryngeal squamous cell carcinoma and paired adjacent normal tissues
Laryngealsquamous cell carcinoma (LSCC) is a common form of head and neckcancerwith poor prognosis. ...
GSE126840: RNA-sequencing of Wnt-dependent and Wnt-independent of Glioblastoma stem cell cultures
Four Wnt-dependent and four Wnt-independent GSC cultures were grown in stem cell media and RNA expre...
GSE131203: Identification of a Midkine-associated gene expression profile in melanoma cells
We performed gain-of-function (GoF) and loss-of-function (LoF) analyses of Midkine in melanoma cells...
GSE128771: CBF-SMMHC affects genome-wide Polycomb Repressive Complex 1 activity in Acute Myeloid Leukemia
Polycomb activity is frequently altered in acute leukaemia through mutation or deletion of Polycomb ...
GSE142430: PRMT5 promotes cancer cell migration and invasion through the E2F pathway
We identified distinct sets of genes under the control of PRMT5 and E2F1. Some of the most highly re...
GSE128515: Therapeutic targeting of splicing in aggressive prostate cancer
Androgen deprivation therapy (ADT) is the main therapeutic regimen for patients with advanced prosta...
GSE129009: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type (WT), AAG-/-, and ELP1-/- Transcriptomes
mRNA profiles of HEK293T wild type (WT), AAG-/-, and ELP1-/- cells were generated by deep sequencing...
GSE125583: RNA Expression in fusiform gyrus of AD and Control subjects
RNA was purified from frozen fusiform gyrus tissue sections of autopsy-confirmed Alzheimer's cases a...
GSE128458: Coordinated Enhancer Reprogramming by GATA3 and AP1 Promotes Cellular Plasticity to Achieve Breast Cancer Endocrine Resistance [RNA-Seq]
Cellular plasticity has emerged as an important mechanism of therapy resistance in cancers, yet the ...
GSE125638: Distinct Pathological Signatures in Human Cellular Models of Myotonic Dystrophy Subtypes
Myotonic dystrophy (DM) is the most common autosomal dominant muscular dystrophy and encompasses bot...
GSE129014: Automated High Frequency Sampling of Stem Cell Differentiation Reveals Early Stage Divergence of Human and Mouse Gene Expression Kinetics
We performed whole transcriptome RNA sequencing experiments of neural differentiation time courses s...
GSE131631: Next Generation Sequencing and differential expression analysis in stem-like vs. non-stem breast cancer cells in response to HDAC1 and HDAC7 knockdown
Purpose: We performed RNA-seq differential expression analysis after 72h HDAC1 and HDAC7 knockdown i...
GSE126562: Heterozygous and homozygous knock-in of PIK3CA-H1047R into human iPSCs
We used CRISPR/Cas9 to knock in the cancer "hotspot" mutation PIK3CA-H1047R into one or both alleles...
GSE128994: The human methyltransferase ZCCHC4 catalyses N6-methyladenosine modification of 28S ribosomal RNA
RNA methylations are essential both for RNA structure and function, and are introduced by a number o...
GSE126635: The structural basis for cohesin/CTCF anchored loops [RNA-seq]
Cohesin catalyses the folding of the genome into loops that are anchored by CTCF. The molecular mech...
GSE125905: Reassessment of Exosome Composition
RNA-Seq of cellular and extracellular samples from DKO-1 and Gli36 cell lines. The distribution of e...
GSE125838: Silencing Trisomy 21 with XIST in Neural Stem Cells Promotes Neuronal Differentiation (single cells)
Although Down Syndrome (DS) is the leading genetic cause of intellectual disability in children, the...
GSE128554: Transcriptome Dynamics of Long Non-Coding RNAs and Transcription Factors Demarcate Human Neonatal, Adult, and MSC-derived Engineered Cartilage
Characterization of the transcriptional differences between human bone marrow MSC-derived cartilage,...
GSE135437: Mapping microglia diversity in the human brain through the integration of high-dimensional techniques
Microglia are tissue-resident macrophages of the central nervous system (CNS) that orchestrate local...
GSE127468: Alterations of redox and iron metabolism accompany development of HIV latency
Metabolic alterations, such as oxidative stress, are hallmarks of HIV-1 infection. However, their in...
GSE127506: A novel Menin-MLL inhibitor induces specific chromatin changes and eradicates disease in models of MLL-rearranged leukemia [RNA-seq]
Cells carrying MLL-rearrangements are sensitive to treatment with VTP-50469 with IC50 in 20-60 nM. W...
GSE133942: The effect of slow and rapid H2S production on the levels of LPS-induced proinflammatory mediators and transcription in different human cell cultures
In this study we investigated the effect of two different agents producing hydrogen sulfide (H2S) on...
GSE125686: Transcriptomic profiling of peripheral blood NK cells of chronic HBV, HCV and HIV patients
Background: NK cells during chronic viral infection have been well studied over the last decade. We ...
GSE131705: Transcriptomic Signature of Celiac show induced epithelial proliferation coupled with suppressed metabolic functions
Background and aims: Celiac disease is provoked by gluten exposure, but the resultant pathogenic pro...
GSE126068: Heterogeneity and evolution in acute myeloid leukemia initiating cells
Little is currently known about the heterogeneity of leukemic initiating cells and how they evolve d...
GSE128627: Prediction of bacterial infection outcome using single cell RNA-seq analysis of human immune cells [WB/PBMCs bulk RNA-seq]
During host-pathogen encounters, the complex interactions between different immune cell-types can de...
GSE137675: Analysis of gene expression, motif and pattern of m6A modified region and m6A enrichment level in Ocular melanoma and Melanocyte cell lines. Gene expressin analysis of METTL3 knock down in PIG1, ALKBH5 knock down and HINT2 over expression in OCM1.
Dynamic N6-methyladenosine (m6A) RNA modification installed and erased by N6-methyltransferases and ...
GSE143148: The histone demethylase JMJD2B regulates endothelial-to-mesenchymal transition [HTS]
Endothelial cells play an important role in maintenance of the vascular system and the repair after ...
GSE125775: BRD9 defines a novel SWI/SNF sub-complex and constitutes a specific vulnerability in malignant rhabdoid tumors [RNA-seq 2]
Bromodomain-containing protein 9 (BRD9) was recently identified to be associated with the chromatin ...
GSE125848: Chromatin remodeling mediated by ARID1A is indispensable for normal hematopoiesis in mice (human RNA-Seq)
ARID1A is a component of the mammalian SWI/SNF complex involved in chromatin remodeling. A functiona...
GSE130226: Inactivation of CFTR by CRISPR/Cas9 alters transcriptional regulation of inflammatory pathways and other networks
Individuals with cystic fibrosis (CF) experience elevated inflammation in multiple organs, but wheth...
GSE126895: Drivers of topoisomerase II poisoning mimic and complement cytotoxicity in AML cells
Recently approved cancer drugs remain out-of-reach to most patients due to prohibitive costs and onl...
GSE129241: Directly Reprogrammed Human Neurons Identify a Pathogenic Mechanism of Valproic Acid at Early Developmental Stages
Human pluripotent stem cells can be rapidly converted into functional neurons by ectopic expression ...
GSE130234: Gene expression profile in Caco-2 cells upon co-treatment with lovastatin and selective AHR ligands
We report high-throughput profiling of gene expression from human colon adenocarcinoma Caco-2 line. ...
GSE133624: Transcriptomics analysis of gene expression in human urothelial carcinoma of the bladder (UCB) and adjacent normal tissues.
36 cases of UCB and 29 adjacent normal bladder tissues (22 pairs) were derived from patients diagnos...
GSE133976: GREB1, a novel target of Wnt signaling, promotes development of hepatoblastoma by suppressing TGF signaling
The -catenin mutation is frequently observed in hepatoblastoma (HB), but the underlying mechanism by...
GSE135291: Transcriptomic analysis of freshly purified human CD226- and CD226+ CD8+ T cell subsets isolated from the peripheral blood of healthy donors.
We recently found that loss of the activating receptor CD226 (DNAM-1) was a critical mechanism affec...
GSE127268: Gene expression profiling of neural crest progenitor cultures derived from human embryonic stem cells carrying nonsense mutations in the Polycomb gene ASXL1 [HET]
We observed impaired neural crest cell differentiation from human embryonic stem cells that harbor n...
GSE135452: RNA sequencing of CD4+ and CD8+ subsets of human engineered regulatory T cell lines expressing FOXP3, FOXP+Helios-FL, FOXP3+Helios-3b
We report RNA sequencing data for three human engineered regulatory T cell lines expressing FOXP3, F...