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Sequencing-based assays (Page 135)
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GSE117965: KLF4 as a rheostat of osteolysis and osteogenesis in prostate tumors in the bone
We previously found that KLF4, a gene highly expressed in adult prostate stem cells, blocks the prog...
GSE115976: Potent anti-tumor efficacy of palbociclib in H3K27M-mutant diffuse intrinsic pontine glioma
Diffuse intrinsic pontine glioma (DIPG) is a rare and fatal pediatric brain cancer without cure. DIP...
GSE117192: A generally conserved response to hypoxia in iPSC-derived cardiomyocytes from humans and chimpanzees
Despite anatomical similarities, there are differences in susceptibility to cardiovascular disease (...
GSE132044 (human): Systematic comparative analysis of single cell RNA-sequencing methods
A multitude of single-cell RNA sequencing methods have been developed in recent years, with dramatic...
GSE117970: Human Tumor-Associated Macrophage and Monocyte Transcriptional Landscapes Reveal Cancer-Specific Reprogramming, Biomarkers, and Therapeutic Targets
The roles of tumor-associated macrophages (TAMs) and circulating monocytes in human cancer are poorl...
GSE115650: MRI-informed muscle biopsies correlate MRI with pathology and DUX4 target gene expression in FSHD
Facioscapulohumeral muscular dystrophy (FSHD) is a common, dominantly inherited disease caused by th...
GSE116277: Generation of FOXO3 engineered human stem cells with enhanced efficacy and safety
FOXO3 is an evolutionally conserved transcription factor that has been linked to longevity. Here we ...
GSE142385: A long noncoding RNA, LOC157273, is the effector transcript at the chromosome 8p23.1-PPP1R3B metabolic traits and type 2 diabetes risk locus
Genome wide association studies (GWAS) identified a chromosome 8 locus associated with fasting gluco...
GSE115821: Robust prediction of response to immune checkpoint blockade therapy in metastatic melanoma
Immune checkpoint blockade (ICB) therapy provides remarkable clinical gains, where melanoma is at th...
GSE134591: Effect of HDL enriched with Serum Amyloid A1 (HDL+SAA1) on Gene Expression by Classical CD14+/CD16- Human Peripheral Blood Monocytes from Asthmatics
IL-6 and PTGS2 were the most highly expressed mRNA transcripts in Classical CD14+/CD16- Monocytes fr...
GSE121428: Disruption of the TFAP2A regulatory domain causes Branchio-Oculo-Facial Syndrome (BOFS) and illuminates pathomechanisms for other human neurocristopathies [RNA-seq data set 2]
BOFS is a rare congenital syndrome that arises due to defects during neural crest (NC) development a...
GSE115988: Specific inhibition of DPY30 activity by peptides suppresses blood cancer cell growth
Epigenetic modulators are being recognized as attractive targets for potential cancer treatment. SET...
GSE115257: Single-cell RNA sequencing enables transcriptomic analysis of iPSC-derived beta-cells in a model of neonatal diabetes caused by insulin mutations.
Insulin gene mutations are a leading cause of neonatal diabetes. They can lead to proinsulin misfold...
GSE118075 (human): Dynamics and Topology of Human Transcribed Cis-regulatory Elements
Promoters and enhancers are key cis-regulatory elements, but how they orchestrate to generate cell-t...
GSE118302: Combined Experimental and System-Level Analyses Reveal the Complex Regulatory Network of miR-124 during Human Neurogenesis [AGO2-RIP-Seq -miRNAs]
Non-coding RNAs regulate many biological processes including neurogenesis. The brain-enriched miR-12...
GSE117994: AML subtype is a major determinant of the association between prognostic gene expression signatures and their clinical significance.
Relapse in acute myeloid leukemia (AML) may result from variable genetic origins or convergence on c...
GSE142833: Global gene expression analysis of breast cancer cell line responses to Topsentinol L Trisulfate or DMSO as the vehicle control
We generated a signature for topsentinol L trisulfate in breast cancer cells to predict drug sensiti...
GSE118077: The long non-coding RNA LINC00941 and SPRR5 are novel regulators of human epidermal homeostasis
Several long non-coding RNAs (lncRNAs) act as regulators of cellular homeostasis; however, few of th...
GSE120720: GREB1 amplifies androgen receptor output in prostate cancer and contributes to antiandrogen resistance
Genomic amplification of the androgen receptor (AR) is an established mechanism of antiandrogen resi...
GSE116129: Chromosomal deletion and chromatin remodeling Drive ABT-199 Resistance in B-cell Lymphomas [RNA-seq]
Drug-tolerant persister cells underlie the emergence of drug-resistant clones and allow residual tum...
GSE118088: Mechanism suppressing H3K9 trimethylation in pluripotent stem cells and its demise by polyQ-expanded huntingtin mutations [RNA-seq]
We find that HTT binds ATF7IP, a regulator of the histone H3 methyltransferase SETDB1. HTT inhibits ...
GSE115763: KLF6-dependent transcription in renal cancer cells
The PDGF and mTOR pathways are clinically relevant therapeutic targets in clear cell renal cell carc...
GSE116166: Chemical Screen Identifies a Geroprotective Role of Quercetin in Premature and Physiological Aging
Aging increases the vulnerability to various diseases. The main goal of aging research is to find th...
GSE118148: RNA-seq analysis of AKTi MK2206 resistant BT474 and T47D cells
BRD4 assembles transcriptional machinery at gene super-enhancer regions and governs the expression o...
GSE116815: Generation of trichogenic adipose-derived stem cells by expression of three factors
Background: Previous studies demonstrated that adipose-derived stem cells (ASCs) can promote hair gr...
GSE116142: Fibroblasts in cholesteatoma activate osteoclasts.
Cholesteatoma arises from a tympanic membrane and expands in the middle ear. It erodes the surroundi...
GSE122848: Cistromic re-programming by truncating GATA3 mutations promotes mesenchymal transformation in vitro, but not mammary tumour formation in mice [RNA-seq]
Heterozygous mutations in the transcription factor GATA3 are identified in 10-15% of all breast canc...
GSE121351: A non-canonical GLTSCR1L-containing BAF complex mediates H3K27ac-dependent enhancer activities
H3K27ac is known to associate with regulatory active enhancers, but its exact role in enhancer funct...
GSE116324: RNA-Seq of newly diagnosed patients in the PADIMAC study leads to a bortezomib/lenalidomide decision signature
Improving outcomes in multiple myeloma will not only involve development of new therapies, but bette...
GSE116862: Chromatin structure dynamics during human cardiomyocyte differention reveals a role of HERV-H in demarcating TAD boundaries.
The three-dimensional chromatin architecture plays a critical role in the establishment of cell-type...
GSE116178: Human bone marrow resident natural killer cells have a unique transcriptional profile and resemble resident memory CD8+ T cells
Human lymphoid tissues harbor, in addition to CD56bright and CD56dim natural killer (NK) cells, a th...
GSE115643: EVI1 carboxy-terminal phosphorylation is ATM-mediated and sustains transcriptional modulation and self-renewal via enhanced CtBP1 association
The transcriptional regulator EVI1 has an essential role in early hematopoiesis and development. How...
GSE119324: Unique Properties of a Subset of Human Pluripotent Stem Cells With High Capacity for Self-Renewal [RNA-Seq]
Archetypal human pluripotent stem cells (hPSC) are widely considered to be equivalent in development...
GSE118947: Enhanced hemato-endothelial specification during human embryonic development through developmental cooperation between AF4-MLL and MLL-AF4 fusions
The t(4;11)(q21;q23) translocation is associated with high-risk infant pro-B-cell acute lymphoblasti...
GSE130067: Transcriptomic response of LSD1-UTX inhibitor on human breast cancer MCF7 cells
In many human cancers, including breast and prostate cancers, LSD1 and other lysine demethylases (KD...
GSE125602: RNA-sequencing of fibrolamellar carcinoma (FLC) cell line treated with miR-375 mimic
Fibrolamellar carcinoma (FLC) is a rare liver cancer. Expression of miR-375 is significantly lost in...
GSE121637: Single-cell sequencing of peripheral blood and tumor-infiltrating immune cells in renal clear cell carcinoma [VDJ sequencing]
In order to investigate heterogeneity and dynamics of cancer-associated immune cells, we performed s...
GSE116284 (human): NF-B p65 dimerization and DNA-binding is important for inflammatory gene expression
Increasing evidence shows that many transcription factors execute important biologic functions indep...
GSE121995: H1609088 Human RNA-Sequencing
Transcriptome profiling of KYSE30 cells after intracellular invasion by Porphyromonas gingivalis Pu...
GSE118157: Effects of rFVIIIFc on human macrophages
Immune responses in hemophilia A patients to replacement factor VIII can be either tolerogenic or im...
GSE118127: Single-cell analysis of adult human ovary using 10X genomics
The ovary is perhaps the most dynamic organ in the human body, only rivaled by the uterus. The molec...
GSE119584: Precise Gene Editing Preserves Hematopoietic Stem Cell Function Following Transient p53-Mediate DNA Damage Response [bulk RNA-seq]
We evaluated transcriptional changes elicited by targeting AAVS1 and IL2RG genes and we found that t...
GSE117264: SHQ1 regulation of RNA splicing is required for T-lymphoblastic leukemia cell survival
T-acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy with complicated hete...
GSE116927: Effects of HSP90 inhibitors on airway goblet cell metaplasia
Goblet cell metaplasia and mucus hypersecretion are disabling hallmarks of chronic lung diseases for...
GSE123892: Stranded RNA-seq were performed on total RNA following ribosomal RNAs depletion (Ribo-zero removal kit, illumina) for 3 brain , 8 IDHwt and 5 IDHmut glioma samples.
Aberrant DNA methylation is a well-defined feature of cancer cells that is commonly associated to tr...
GSE117305 (human): N-Myc-mediated epigenetic reprogramming drives lineage plasticity in advanced prostate cancer [RNA-seq]
Despite recent advances in highly effective androgen receptor (AR)-directed therapies for the treatm...
GSE117480: Acquisition of a side population fraction through downregulation of MSL3, ZNF691, VPS45, ITGB3BP, TLE2, and ZNF498 augments malignant phenotype in ovarian cancer.
Side population (SP) cells harbor malignant phenotypes, such as sphere forming capacity, single cell...
GSE117489: Leading edge airway epithelial cell responses to in vitro wounding
The airway epithelium of asthmatics is characterized by intrinsically abnormal wound repair that may...
GSE117446: Pervasive H3K27 acetylation leads to ERV expression and a therapeutic vulnerability in H3K27M gliomas [RNA-Seq]
Epigenetic alterations are recurrently observed in cancer and are the subject of active therapeutic ...
GSE118843: Activity-by-Contact model of enhancer specificity from thousands of CRISPR perturbations [RNA-Seq human]
Mammalian genomes harbor millions of noncoding elements called enhancers that quantitatively regulat...
GSE119744: Enhancer profiling of chronic lymphocytic leukemia cells
Enhancer profiling has emerged as a powerful approach for discovering the cis-regulatory elements t...
GSE121472: O-GlcNAc transferase fine-tunes MYC-dependent transcription to promote cell cycle [RNA-seq]
O-GlcNAc transferase (OGT) is overexpressed in aggressive prostate cancer. Here, we employed ChIP-se...
GSE121680: ZEB1 insufficiency causes corneal endothelial cell state transition and altered cellular processing
The zinc finger e-box binding homeobox 1 (ZEB1) transcription factor is a master regulator of the ep...
GSE120766: Genome-wide expression analysis of human hTert immortalized fibroblasts after downregulation of MCM2
Minichromosome maintenance (MCM) proteins facilitate replication by licensing origins and unwinding ...
GSE118933: Immune Checkpoint Regulation of Pulmonary Fibrosis [bulk RNA-seq]
Fibroblasts from idiopathic pulmonary fibrosis (IPF) patients acquire an invasive phenotype that is ...
GSE118900: Molecular Signatures of Multiple Myeloma Progression through Single Cell RNA-Seq
Multiple myeloma (MM) is a malignant plasma cell disorder with well-defined clonal genetic/cytogenet...
GSE118761: RNA-sequencing of ex vivo nasal and tracheal epithelial cells from a paediatric cohort including non-atopic non-wheezers, atopic non-wheezers, atopic wheezers, and non-atopic wheezers
Rationale: Emerging evidence suggests that disease vulnerability is expressed throughout the airways...
GSE135992: Identification and elimination of the platelet-derived transcripts contamination in circulating tumor cell single-cell RNA-seq study
Single-cell RNA sequencing (scRNA-seq) holds great potential to revolutionize our understanding of c...
GSE121627: Analysis of HPV16 E2 host gene expression using TERT immortalized keratinocytes (NOKs) cell lines and RNA-sequencing
HPV must reprogram host gene expression to promote infection, and HPV proteins E6 and E7 contribute ...
GSE125692: PRRX2 and HEY2 double knock-down facilitates ASCL1-induced neuron conversion in human dermal fibroblasts.
Forced expression of ASCL1, Nurr1, Lmx1a, miRNA-124 and p53shRNA (ANLmp) in fibroblasts reprograms f...
GSE120226: 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...
GSE124451: Integrative analysis identifies lincRNAs up- and downstream of neuroblastoma driver genes (PHOX2B)
Long intergenic non-coding RNAs (lincRNAs) are emerging as integral components of signaling pathways...
GSE121476: Poly(ADP-ribose) polymerase 1 is necessary for coactivating hypoxia-inducible factor-1-dependent gene expression by Epstein-Barr virus latent membrane protein 1
Latent membrane protein 1 (LMP1) is the major transforming protein of Epstein-Barr virus (EBV) and i...
GSE122791 (human): The Type I interferon response impairs differentiation potential of pluripotent stem cells [seq]
Upon virus infection,pluripotent stem cells neither induce nor respond to canonical Type I interfero...
GSE124411: Cell-specific expression and function patterns of microRNA-150-5p in liver fibrogenesis
MicroRNAs (miRNAs) are endogenous and small non-coding RNA molecules that mediate post-transcription...
GSE119834: CHROMATIN LANDSCAPES REVEAL DEVELOPMENTALLY ENCODED TRANSCRIPTIONAL STATES THAT DEFINE GLIOBLASTOMA [RNA-Seq]
Glioblastoma is an incurable brain cancer characterized by high genetic and pathological heterogenei...
GSE119102: Deep sequencing and automated histochemistry of human tissue slice cultures improve their usability as preclinical model for cancer research
Cancer research requires models closely resembling the tumor in the patient. Human tissue cultures c...
GSE121477: Recapitulating and Deciphering Tumor-stroma Microenvironment by Using a LEGO like 3D printed microfluidic device
The tumor-stroma microenvironment is extremely important on tumor progression, metastasis and angiog...
GSE120756: TET2 coactivates gene expression through demethylation of enhancers
The tet methylcytosine dioxygenase 2 (TET2) enzyme catalyzes the conversion of the modified DNA base...
GSE122897: RNA Sequencing Analysis of Intracranial Aneurysm Walls Reveals Involvement of Lysosomes and Immunoglobulins in Rupture
Background and PurposeAnalyzing genes involved in development and rupture of intracranial aneurysms ...
GSE123631: BRCA2 abrogation triggers innate immune responses potentiated by treatment with PARP inhibitors
Heterozygous germline mutations in BRCA2 predispose to breast and ovarian cancer. Contrary to non-ca...
GSE124472: Single Cell RNA-Seq profiling of human embryonic kidney outer and inner cortical cells and kidney organoid cells
To study the developmental process of human podocytes and compare to the in vitro counterpart, we di...
GSE121309: Single cell analysis reveals dynamics of transposable element expression following epigenetic de-repression
De-repression of transposable elements (TEs) occurs concomitantly with the progressive loss of DNA m...
GSE120203: NRDE2 negatively regulates nuclear exosome functions II
To examine whether NRDE2 can impact the competition between hMTR4 and ALYREF, we performed stranded ...
GSE120836: Genomic Reorganization of Lamin-Associated Domains in Cardiac Myocytes is Associated with Differential Gene Expression and DNA Methylation in Human Dilated Cardiomyopathy [RNA-Seq]
Mutations in the LMNA gene causes set of disorders collectively referred to as laminopathies that i...
GSE119317: Prolonging culture of primary human keratinocytes isolated from suction blisters with the Rho kinase inhibitor Y-27632
Keratinocytes are the most abundant cell type in the epidermis. They prevent desiccation and provide...
GSE121629: Hemolysis in the spleen facilitates erythrocyte turnover
Red pulp macrophages of the spleen mediate daily turnover of billions of senescent erythrocytes. How...
GSE121667: Transcriptome-wide off-target RNA editing induced by CRISPR-guided DNA base editors [Modifications - validation]
Base Editing has been touted the most intelligent and precise application of the CRISPR platform so ...
GSE120178: Pharmacodynamic Biomarkers and Differential Effects of TNF- and GM-CSF-Targeting Biologics in Rheumatoid Arthritis
A major unmet need in rheumatoid arthritis (RA) is the choice of treatment options for patients with...
GSE125109: TGFR and Hh signalling regulate prognostic matrisome molecules in ovarian cancer
We previously identified a matrisome gene expression signature with prognostic significance in high-...
GSE133751: Comprehensive analyses of function and molecular interaction of differentiallyexpressed non-coding RNAs and mRNA in Hantaan virus infection
Hantaan virus (HTNV), the prevalent prototype of the hantavirus in Asia, causes hemorrhagic fever wi...
GSE124706: Species-specific maturation profiles of human, chimpanzee and bonobo neural cells
Understanding the evolutionary mechanisms underlying expansion and reorganization of the human brain...
GSE120210: Inhibition of histone H3K27 demethylases inactivates brachyury (TBXT) and promotes chordoma cell death [RNA-Seq II]
The expression of transcription factor brachyury (TBXT) is normally restricted to embryonic developm...
GSE126319: Variant and cell-context specific H3K27M reprogramming results in distinct enhancer architecture and oncogenic states
Diffuse intrinsic pontine glioma (DIPG) is a fatal malignancy of the childhood pons characterized by...
GSE122002: Dioxin and AHR impairs mesoderm gene expression and cardiac differentiation in human embryonic stem cells (RNA-Seq)
Dioxin and dioxin-related polychlorinated biphenyls are potent toxicants with association with devel...
GSE124494: Single-cell survey of human lymphatics unveils marked endothelial cell heterogeneity and mechanisms of homing for neutrophils
Lymphatic vessels form a critical component in the regulation of human health and disease. While the...
GSE127938 (human): Transcriptome profiling of organoids from the human and murine gastrointestinal tract
The epithelial layer of the gastrointestinal tract is the bodys first line of defense against gut pa...
GSE129779: ARID1A and PI3-Kinase pathway mutations in the endometrium drive epithelial transdifferentiation and collective invasion [12Z_1A_PI3K_RNA-seq]
ARID1A and PI3-Kinase (PI3K) pathway alterations are common in neoplasms originating from the uterin...
GSE124500: Modeling CADASIL vascular pathologies with patient-derived induced pluripotent stem cells
Cerebral autosomal dominant arteriopathy with subcortical infarcts and leukoencephalopathy (CADASIL)...
GSE124582: Bromodomain inhibition of the co-activators CBP/EP300 facilitates reprogramming (RNA-seq fibroblasts)
Silencing of the somatic cell-type specific gene expression programs is a critical yet poorly unders...
GSE120521: RNA-seq of stable and unstable section of human atherosclerotic plaques
Atherosclerosis is a serious and very common condition where plaque builds up inside arteries and th...
GSE119954: The Genetic Landscape of Diamond-Blackfan Anemia
Diamond-Blackfan anemia (DBA) is a rare bone marrow failure disorder that affects 7 out of 1,000,000...
GSE119978: Cisplatin induces inefficiently translated short transcripts in long genes
We explored the regulation of intronic polyadenylation (IPA) by cisplatin, and its impact on the tra...
GSE120328: Global Long Terminal Repeat activation participates in establishing the unique gene expression program of classical Hodgkin Lymphoma [Primary RNA-Seq]
Long terminal repeat (LTR) elements are wide-spread in the human genome and have the potential to ac...
GSE122654: Telomere-Dependent and Telomere-Independent Roles of RAP1 in Regulating Human Stem Cell Homeostasis
RAP1 is well known as a telomere-binding protein; yet its functions in human stem cells remain uncle...
GSE121699: Transcriptomes in healthy and CHB fetal hearts
Given that diseases associated with anti-SSA/Ro autoantibodies such as systemic lupus erythematosus ...
GSE119345: Inhibition of the integrin alpha-V beta-3 reverts the paradoxical effect of levothyroxine replacement during bexarotene therapy in cutaneous T-cell lymphoma
Bexarotene is a specific RXR agonist that has been used for the treatment of cutaneous T-cell lympho...
GSE122198: 3'-TARGET-seq: a novel method for high-sensitivity single-cell mutational analysis and parallel high throughput RNA-sequencing [Figures 5 and 6, Figure S7]
We developed 3'-TARGET-seq, a single-cell genotyping and RNA-seq method, which allows accurate detec...
GSE123055: Formative transition of human nave pluripotent stem cells
Human nave pluripotent stem cells (PSC) share features with pre-implantation epiblast. They thus pro...
GSE120957: The EN1 transcription factor drives neural features and brain metastases in triple negative breats cancer (TNBC)
To define transcriptional dependencies of TNBCs, we identified transcription factors highly and spec...