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Sequencing-based assays (Page 125)
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GSE73565: Complementary Post Transcriptional Regulatory Information is Detected by PUNCH-P and Ribosome Profiling
Two novel approaches were recently suggested for genome-wide identification of protein aspects synth...
GSE79666: Transcriptome sequencing reveals aberrant alternative splicing in Huntington's disease
Huntingtons disease (HD) is an autosomal dominant neurodegenerative disorder caused by a CAG expansi...
GSE75489: Determination of a comprehensive alternative splicing regulatory network and the combinatorial regulation by key factors during Epithelial-to-Mesenchymal Transition [ESRP KD]
Epithelial specific splicing regulatory protein 1 and 2 (ESRP1 and ESRP2) are important regulators o...
GSE73696: Effects of NSD2 depletion on gene expression and H3K36me2 in a lung cancer cell line
The histone methyltransferase NSD2/WHSC1/MMSET is overexpressed in a number of solid tumors but its ...
GSE82110: Acriflavine inhibits the epithelial-to-mesenchymal transition in vitro in liver and pancreatic cancer cells (part of study on HepG2)
Background: Epithelial-to-mesenchymal transition (EMT) is considered an important driving mechanism ...
GSE81498: Multiple mechanisms disrupt let-7 miRNA biogenesis and function in neuroblastoma [longRNA]
The let-7 microRNA families are tumor suppressors often deregulated in cancer, yet the underlying me...
GSE72696: Integrative fine-mapping of regulatory variants and mechanisms at coronary artery disease loci
Coronary artery disease (CAD) is the leading cause of mortality and morbidity driven by both genetic...
GSE73784: Three-dimensional disorganisation of the cancer genome occurs coincident with long range genetic and epigenetic alterations [RNA-seq]
A three-dimensional chromatin state underpins the structural and functional basis of the genome by b...
GSE71858: Fixed single-cell transcriptomic characterization of human radial glial diversity
The human neocortex is created from diverse progenitors that are intermixed with multiple cell types...
GSE77784 (human): MOF acetyl transferase regulates transcription and respiration in mitochondria
Histone acetylation is sensitive to metabolic cues, however interplay between histone acetyl transfe...
GSE73941: Reversible and Dynamic m1A Methylation in the Human Transcriptome
N1-methyladenosine (m1A) is an abundant post-transcriptional RNA modification, yet little is known a...
GSE73929: Genome-wide MAF1-dependent regulation of RNA polymerase III transcription [RNA-Seq]
In higher eukaryotes, an important mechanism to tune translation in different tissues and conditions...
GSE74324: BRD4 connects enhancer remodeling to senescence immune surveillance (RNA-seq)
Cellular senescence is a homeostatic program associated with tumor suppression, wound healing, and c...
GSE71972: Histamine footprint on the human exercise transcriptome
Transcriptome wide analysis of the skeletal muscle response to exercise in humans. Subjects performe...
GSE73471: The bromodomain protein BRD4 regulates splicing during heat shock
During heat stress cyto-protective genes including heat shock proteins are transcriptionally up-regu...
GSE74246: Unstranded RNA sequencing data
A single hematopoietic stem cell can give rise to all blood cells with remarkable fidelity. Here, we...
GSE73663: Development of Pathway Preferential Estrogens Affording Beneficial Metabolic and Vascular Actions without Reproductive Tissue Stimulation in Mice
There is great medical need for estrogens having favorable pharmacological profiles, supporting desi...
GSE73708: Gene expression analysis of human hepatocellular cancers
Gene expression profiling was carried out in 4 matched human hepatocellular cancer samples/normal li...
GSE72820: Gene expression analysis of human adenomas.
Gene expression profiling was carried out in 7 matched colon adenoma samples and normal mucosa to ch...
GSE81513: Splicing towards noncoding isoforms in colorectal carcinoma is associated with tumor hypoxia and the DNA damage response
Tumor hypoxia is associated with poor patient outcome and resistance to therapy. It is associated wi...
GSE75299: Expression changes in Melanomas pre MAPKi treatment vs. on MAPKi treatment (RNA-seq)
Treatment of advanced V600BRAF mutant melanoma using a BRAF inhibitor (BRAFi) or its combination wit...
GSE148978: An Integrated Epigenomic and Transcriptomic Map of Mouse and Human ab T Cell Development (Human scRNAseq)
ab lineage T cells, most of which are CD4+ or CD8+ and recognize MHC I or MHC II-presented antigens,...
GSE73999: P120-catenin dependent glioma-cell networks drive growth and diffuse brain infiltration
The poor prognosis of diffuse gliomas is the consequence of adaptive growth and survival programs co...
GSE74053: RNA-seq transcriptional profiling in human primary fetal and adult CD34+ hematopoietic stem/progenitor cells (HSPCs) erythroid progenitor cells (ProEs)
Advances in sequencing-based genomic profiling present a new challenge of explaining how changes in ...
GSE72713: Transcriptome analysis of eosinophilic and noneosinophilic chronic rhinosinusitis with nasal polyps reveals distinct lncRNA expression profiles
Background: The pathogenesis of chronic rhinosinusitis with nasal polyps (CRSwNP) remains unclear. L...
GSE75643: Massive reshaping of genome - nuclear lamina interactions during oncogene induced senescence (RNA-seq)
Cellular senescence is a mechanism that virtually irreversibly suppresses the proliferative capacity...
GSE72483: ROR- drives androgen-receptor expression and represents a therapeutic target in castration-resistant prostate cancer
The androgen receptor (AR) is overexpressed and hyperactivated in human castration-resistant prostat...
GSE74220: Transcriptome response to 4h IL-1b stimulation of primary chondrocytes
Using RNA sequencing (Illumina Hi-Seq 2000 sequencer) we report the transcriptome profile of primary...
GSE76081: Mesenchymal Stromal Cells undergo major changes during therapeutic application
Mesenchymal stromal cells (MSC) are increasingly used as an investigative therapeutic product for im...
GSE73213: Promoter H3K4 methylation reveals the dynamic reinforcement of activation-induced pathways in human CD4 T cells with differential kinetics in nave and memory cells (RNA-Seq)
The epigenetic determinants driving the rapid responses of memory CD4 T cells to antigen are current...
GSE72821: High-throughput RNA-sequencing of human macrophages infected with Mycobacterium abscessus Smooth and Rough variants
Mycobacterium abscessus is an emerging pathogen causing pulmonary infections in those with inflammat...
GSE75440: Gene expression profiles in NORAD knockout and PUMILIO overexpressing cells
Purpose: PUMILIO proteins are known to repress target genes by specifically binding to PUMILIO respo...
GSE72956: Transcriptomic and Epigenetic analysis of cell line derivatives from H2087 and HCC1954 cell lines
We profiled the transcriptomes of latency-competent cells derived from the human cancer cell lines H...
GSE74383: Targets of ROR2 overexpression in MCF-7 cells revealed a differentially regulated module of non-canonical WNT signaling pathway
RNA-Seq profiling of estrogen-receptor-positive MCF-7 cell lines with different perturbations of non...
GSE74289: Improved LCL to iPSC reprogramming: RNA Analysis of LCLs, reprogrammed iPSCs, and differentiated NSCs reveal potential regulatory and functional processes involved in these cellular transitions.
Purpose: There exists a rich bio-resource of numerous lymphoblastoid cell line (LCL) repositories ge...
GSE103843: Genome-wide profiling of siRNA targeting EWS-FLI1 in TC32 Ewing sarcoma cell line
Identification of genes and pathways that were influenced by knock-down EWS-FLI1 in TC32 Ewing sarco...
GSE75859: Activation of Wnt/beta-catenin in Ewing sarcoma cells antagonizes EWS/ETS function and promotes phenotypic transition to more metastatic cell states
Ewing sarcomas are characterized by the presence of EWS/ETS fusion genes in the absence of other rec...
GSE74450: Direct Isolation and Characterization of Human Nephron Progenitors.
Mature nephrons originate from a small population of uninduced nephrogenic progenitor cells (NPs) wi...
GSE74516: RNA-seq Profiles in Transcription elongation factors are in vivo-specific cancer dependencies in glioma
Glioblastoma ranks as one of the most lethal human cancers, with no effective therapies. To discove...
GSE83547: Lipid catabolism inhibition sensitizes prostate cancer cells to antiandrogen blockade
Prostate cancer (PCa) is the most common malignancy among western men and the second leading-cause o...
GSE74557: Adaptive chromatin remodeling in glioblastoma stem cell plasticity and drug tolerance
Many cancers are postulated to harbor developmental hierarchies in which cells display variability i...
GSE75935: Combined Genome and Transcriptome Sequencing to Identify Allelic Selection in Epithelial Ovarian Cancer
Identifying genes where a variant allele is preferentially expressed in tumors could lead to a bette...
GSE75711: Generation of nephronal cells from human pluripotent stem cells via renal-vesicle formation
Human pluripotent stem cells (hPSC) provide a possible source for generation of kidney cells and org...
GSE73211: Comparing isogenic pairs of hESC and hiPSC lines reveals genetic background and reprogramming method as primary sources of transcriptional variation
The equivalency of human induced pluripotent stem cells (hiPSCs) with human embryonic stem cells (hE...
GSE74620: ATRX is necessary for cellular senescence and represses HRAS to drive cells from quiescence into senescence [RNA-Seq]
Senescence is a state of stable cell cycle exit that has important implications for development, phy...
GSE75035: Lipid degradation promotes prostate cancer cell survival
Prostate cancer is the most common male cancer and androgen receptor (AR) is the major driver of the...
GSE75515: Gene expression analysis of human haploid cells (HAP1) depleted of SMARCB1 and SMARCA4
The aim of this study is to analyze the change in genome wide expression levels in HAP1 cells upon l...
GSE74698: Developing a Novel Two-Dimensional Culture System to Enrich Human Prostate Luminal Progenitors That Can Function as a Cell of Origin for Prostate Cancer
Elucidating the cell of origin of cancer has great significance in stratifying patients into appropr...
GSE76129: ZNF599 and DNMT3A coordinately control nuclear envelope organization by repression of SUN4 expression
Human-specific KRAB-ZF proteins are putative transcription factors and correlate with human cognitiv...
GSE75906: Small molecules modulate chromatin accessibility to promote NEUROG2-mediated fibroblast-to-neuron reprogramming [RNA-seq]
Pro-neural transcription factors and small molecules can induce the transdifferentiation of fibrobla...
GSE75530: Human RNase L Tunes Gene Expression by Selectively Destabilizing the MicroRNA-Regulated Transcriptome
Purpose: The goal of this study was to map the pathway of mRNA decay by human RNase L; ; Methods: To...
GSE74927: Subtypes of HPV-positive head and neck cancers are associated with HPV characteristics, copy number variations, PIK3CA mutation, and pathway signatures. [RNA-Seq]
Purpose: There is substantial heterogeneity within the human papillomavirus (HPV) positive head and ...
GSE81507: Post-transcriptional manipulation of TERC reverses molecular hallmarks of telomere disease
The telomerase RNA component (TERC) is a critical determinant of cellular self renewal. Poly(A)-spec...
GSE80727: Utilizing single-cell variations to reveal environment-dependent tuning of network connectivity in human macrophages (RNA-Seq, CAGE and ChIP-Seq)
Through analysis of gene expression and chromatin state, this study examines human monocyte-derived ...
GSE71519: Synergistic gene expression signature observed in TK6 cells upon co-exposure to UVC-irradiation and protein kinase C-activating tumor promoters, a time course study (study 1/2)
The purpose of this study, including this time course series and another dosage series, was to estab...
GSE102860: Next Generation Sequencing of Lung Primary Fibroblast Responding to Eosinophil-Degranulation Products
Methods: Two human lung primary fibroblast (HLF) lines were activated for 24 h with eosinophil condi...
GSE81062: Targeting MTHFD2 in Acute Myeloid Leukemia
Purpose: Identify new targets in acute myeloid leukemia (AML).; Methods: MOLM-14 cells were transd...
GSE77913: Cajal bodies are linked to genome conformation [RNA-Seq]
The mechanisms underlying nuclear body (NB) formation and their contribution to genome function are ...
GSE76947: A novel compound that blocks HIV-1 replication inhibits the splicing regulatory function of SRSF10
Purpose: We have identified a new compound (1C8) that inhibits HIV-1 replication and that displays v...
GSE76098: Connexin 32-mediated cell-cell communication is essential for hepatic differentiation from human embryonic stem cells
Gap junction-mediated cell-cell interactions are highly conserved and play essential roles in cell s...
GSE77538: Genome-wide expression profile in FH-deficient (UOK262) vs FH-competent (UOK262pFH) human cells derived from metastatsis to the mediastinum of a HLRCC patient
Comparison of the transcriptome of human kideny cancer cells either wild-type for FH or FH-deficient...
GSE76421: JAG1 Mediated Notch Signaling Regulates Secretory Cell Differentiation of the Human Airway Epithelium
Background: Basal cells (BC) are the stem/progenitor cells of the human airway epithelium capable of...
GSE77938: Transcriptome profiling of human keratoconus corneas through RNA sequencing identifies collagen synthesis disruption and downregulation of core elements of TGF-, Hippo, and Wnt pathways
To understand better the factors contributing to keratoconus (KTCN), we used RNA sequencing to perfo...
GSE81233: Single Cell DNA Methylome Sequencing of Human Preimplantation Embryos
Although the DNA methylome of human early embryos has been analyzed, some of the key features have n...
GSE76683: RNA-seq expression data from FL-HSPCs after HOXA7 knockdown
HOXA7 regulates FL-HSPC self-renewal in vitro and in vivo. We profiled FL-HSPCs after HOXA7 knockdo...
GSE76661: RPA interacts with HIRA and regulates H3.3 deposition at gene regulatory elements in mammalian cells
The incorporation of histone variant H3.3 has been implicated in the formation and maintenance of sp...
GSE76173: Comparative transcriptomic analysis of human and Drosophila extracellular vesicles reveals extensive conservation
Extracellular vesicles (EVs) are membrane-enclosed nanoparticles containing specific repertoires of ...
GSE96860: Enhancer Transcription Reveals Subtype-Specific Transcription Programs Controlling Breast Cancer Pathogenesis [RNA-Seq]
Noncoding transcription is a defining feature of active enhancers, linking transcription factor (TF)...
GSE80153: Enhancer invasion shapes MYCN dependent transcriptional amplification in neuroblastoma [RNA-seq]
In neuroblastoma, amplification of the oncogenic basic helix-loop-helix (bHLH) transcription factor ...
GSE101353: Exaggerated BMP4 signalling alters human airway basal progenitor cell differentiation to cigarette smoking-related phenotypes [RNA-Seq]
Airway remodelling in chronic obstructive pulmonary disease (COPD) originates, in part, from smoking...
GSE77382: Arnica montana stimulates extracellular matrix gene expression in human macrophages differentiated to wound-healing phenotype.
Arnica m. effects were associated with a purported anti-inflammatory and tissue healing actions afte...
GSE76240: DNA breaks and chromatin structural changes enhance the transcription of Autoimmune Regulator target genes [RNA-Seq]
The Autoimmune Regulator (AIRE) protein is the key factor in thymic negative selection of autoreacti...
GSE77992: Next Generation Sequencing Facilitates Quantitative Analysis of HCC cells transfected with NCsiRNA or CDCA8siRNA
We hypothesized if targeting of CDCA8 with small interfering (si) RNA could inhibit HCC progression....
GSE76998: Transcriptomic Dynamics during Differentiation Process of Human Pluripotent Cells into Hepatocyte-like Cells
Examine characteristics of hESCs and hiPSCs during directed in-vitro differentiation into HLCs. SOUR...
GSE76743: Implication of Long noncoding RNAs in the endothelial cell response to hypoxia revealed by RNA-sequencing.
Long noncoding RNAs (lncRNAs) are non-protein coding RNAs regulating gene expression. Although for s...
GSE78195: Next Generation Sequencing Facilitates Quantitative Analysis of colorectal cancer cells transfected with NC siRNA or RPL9 siRNA
Ribosomal protein L9 (RPL9), a component of the 60S subunit, is up-regulated in human colorectal can...
GSE76326: Role of OSGIN1 in Mediating Smoking-induced Autophagy in the Human Airway Epithelium [RNA-Seq]
Enhanced autophagy is recognized as a component of the pathogenesis of smoking-induced airway diseas...
GSE80136: Whole transcriptome splicing analysis in isogenic lung epithelial and adenocarcinoma cell lines with or without a recurrent splicing factor mutation, U2AF1 (S34F)
The splicing factor gene, U2AF1, is recurrently mutated in a variety of human cancers, including lun...
GSE79272: Stimulation of isolated plasmacytoid dendritic cells (pDCs) with TLR9 agonist CpG C (CpG) and TLR7 agonist imiquimod (IMQ)
The purpose of this experiment was to assess the genes upregulated when pDCs were stimulated with TL...
GSE76572: Coordinated control of senescence by lncRNA UCA1 and a novel CAPER/TBX3 co-repressor
Coordination of a complex series of transcriptional, structural and signaling events culminates in c...
GSE77307: Transcriptome analysis reveals malignant and hypoxic signature of glioblastoma
Purpose:Glioblastoma (GBM) is the most common primary brain tumor in adults with poor prognosis and ...
GSE78236: Comparison of HCC cell lines and primary HCCs-RNAseq data
There are concerns about whether cancer cell lines could faithfully represent the matched primary ca...
GSE77039: Distinct gene regulatory programs define the inhibitory effects of LXRs and PPARG on cancer cell proliferation
The liver x receptor (LXR) and peroxisome proliferator-activated receptor gamma (PPARG) nuclear rece...
GSE78853: Tricyclic Antidepressants Induce Inactivation of Hepatic Stellate Cell (HSC) Myofibroblasts
Hepatic stellate cells (HSCs) are the primary cell type responsible for liver fibrosis, the final co...
GSE81620: Next Generation Sequencing Facilitates Quantitative Analysis of miR-29b-1 and miR-29a targets in tamoxifen-sensitive and tamoxifen-resistant human breast cancer cells
The goal of this experiment was to identify the putative mRNA targets of miR-29b-1 and miR-29a in LC...
GSE77072: Spliced synthetic genes as internal controls in RNA sequencing experiments.
RNA sequencing (RNAseq) can be used to assemble spliced isoforms, quantify expressed genes and provi...
GSE85121: Dysregulation of Lung Biology of Healthy Never Smokers Following Acute Inhalation of E-Cigarette Vapors
Little is known about the health risks to humans associated with smoking or vaping electronic cigare...
GSE76491 (human): Coordination of neuron production in mouse and human cerebral cortex by the homolog of Drosophila Mastermind protein
The coordination of progenitor self-renewal, neuronal production and migration is essential to the n...
GSE78220: mRNA expressions in pre-treatment melanomas undergoing anti-PD-1 checkpoint inhibition therapy
PD-1 immune checkpoint blockade provides significant clinical benefits for cancer patients. However,...
GSE77509: RNA-seq analysis of hepatocellular carcinoma with portal vein tumor thrombosis
Portal vein tumor thrombosis is a strong poor indication of HCC. Characterizing the molecular altera...
GSE76453: The Chromatin-Looping Factor ZNF143 Engages at Looping Promoters to Favor the Estrogen Response in Breast Cancer (RNA-seq)
Estrogen signaling in breast cancer cells relies on long-range chromatin interactions connecting dis...
GSE81671: Genome models integrating chromatin contacts and nuclear lamin-genome interactions reveal implications of laminopathy-causing lamin mutations on genome architecture
Processes shaping the 3-dimensional (3D) human genome remain elusive. We present Chrom3D, a user-fri...
GSE76490: Transcriptomic analysis of human iPS cells derived from fragile X syndrome patients during neural differentiation
Fragile X syndrome (FXS) is one of the most prevalent inherited intellectual disabilities. The patie...
GSE77085: Deep RNA sequencing of the human placental transcriptome
The goal of this study was to conduct an in-depth analysis of the human placental transcriptome. RNA...
GSE78285: Modeling the ESR1 tyrosine 537 mutation with CRISPR-Cas9 for mechanistic studies and evaluation of therapeutic approaches for metastatic breast cancer [RNA-Seq]
Estrogen receptor- (ER) is an important driver of breast cancer and is the target for hormonal thera...
GSE77108: HDAC inhibitor SAHA reverses inflammatory gene expression in diabetic endothelial cells
While histone deacetylase (HDAC) inhibitors are thought to regulate gene expression by post-translat...
GSE79842: RNAseq from disomic and trisomic fibroblasts and lymphoblastoids
RNA was sequenced from individuals Disomic and Trisomic for chromosome 21 to identify consistent cha...
GSE81322: DNMT and HDAC inhibitors globally induce cryptic TSSs encoded in long terminal repeats
By mapping global transcription start site (TSS) and chromatin dynamics, we observed the activation ...
GSE76586: The control of rRNA synthesis during the directed differentiation of human embryonic stem cells precedes heterochromatin formation.
It has become increasingly clear that proper cellular control of pluripotency and differentiation is...
GSE81637: Transcriptome analysis of virus infected tissues
We report the application of RNA sequencing for transcriptome analysis of virus infected tissues, en...