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Sequencing-based assays (Page 129)
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GSE147333: RNA-seq of Histamine stimulated HUVECs infected with shNT or shH1R
To investigate the mechanism of histamine H1 receptor (H1R)- mediated proliferation and angiogenesis...
GSE95304: Systematic Functional Perturbations Uncover a Prognostic Genetic Network Driving Human Breast Cancer [RNA-Seq]
Gene-expression patterns of primary breast cancers aid clinicians in predicting the risk of metastat...
GSE96613: Neuronal brain region-specific DNA methylation and chromatin accessibility are associated with neuropsychiatric trait heritability [RNA-Seq]
We analyzed differential methylation (via WGBS) between four distinct human brain regions (NAcc-nucl...
GSE94270: RNA-Seq analysis of cSCC cells followed by siRNA-induced gene knockdown of AIM2.
Keratinocyte-derived cutaneous squamous cell carcinoma (cSCC) is the most common metastatic skin can...
GSE94277: Cancer-specific retargeting of BAF complexes by a prion-like domain [RNA-Seq]
Alterations in the function of transcriptional regulators can orchestrate oncogenic programs that ar...
GSE94374: Epigenetic mechanisms underlie the crosstalk between growth factors and a steroid hormone [HCT RNA-Seq]
Growth factors (GFs) suppression by steroid hormones recurs in embryology and is co-opted in pathol...
GSE95372: N6-methyladenosine mRNA marking promotes selective translation of regulons required for human erythropoiesis [RNA-Seq]
Many of the regulatory features governing erythrocyte specification, maturation, and associated diso...
GSE94330: Tyrosine-1 of RNAPII CTD controls global termination of gene transcription in mammals
The carboxy-terminal domain (CTD) of RNA polymerase (Pol) II is composed of a repetition of YSPTSPS ...
GSE100709: RNA-seq comparison of gene induction in RIG-I stimulated old and young human monocytes
Goal: The goal of this study was to compare gene induction in old and young human monocytes upon sti...
GSE96637: Knock-down of Ror1 in MDA-MB-231 cell line decreases cell invasiveness
RNA-Seq profiling of triple-negative MDA-MB-231 cell line with know-down of non-canonical WNT signal...
GSE112104: Gene expression profiling identifies a gene signature that predicts progression to active tuberculosis several years before disease onset
We evaluated the predictive ability of various gene signatures in baseline peripheral blood mononucl...
GSE95389: Global mRNA expression profile in cardiac progenitor cells generated by ISX-9
We developed a strategy to generate cardiac progenitor cells from human induced pluripotent stem cel...
GSE106545: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and AXL-/- astrocytes Transcriptomes
Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular pathways. The...
GSE95375: Global transcriptome profiling of triple-negative breast cancer cell lines treated with small-molecules targeting Bromodomain and Extra Terminal (BET) proteins
Triple negative breast cancer (TNBC) represents the most clinically challenging subtypes of breast c...
GSE95374: Selective silencing of euchromatic L1s revealed by genome-wide screens for L1 regulators
Transposable elements (TEs) are now recognized not only as parasitic DNA, whose spread in the genome...
GSE97084: Enhanced Protein Translation Underlies Improved Metabolic and Physical Adaptations to Different Exercise Training Modes in Young and Old Humans
The molecular transducers of benefits from different exercise modalities remain incompletely defined...
GSE94464: Gene expression of thyroid cancer cell lines
Purpose: The primary goal of this study was to identify gene-expression profiles of anaplastic thyr...
GSE102004: ATF6 safeguards organelle homeostasis and cellular aging in human mesenchymal stem cells
Loss of organelle homeostasis is a hallmark of aging. However, it remains elusive how this occurs at...
GSE94461: The effect of PPARG inhibition on human angiomyolipoma cells
Angiomyolipoma (AML), the most common benign renal tumor, can result in severe morbidity from hemorr...
GSE97003: Altered Hydroxymethylation is seen at regulatory regions in pancreatic cancer and regulates oncogenic pathways [RNA-seq]
Transcriptional deregulation of oncogenic pathways is a hallmark of cancer, and can be due to epigen...
GSE97265: High-efficiency RNA-based reprogramming of human primary fibroblasts
Induced pluripotent stem cells (iPSCs) hold great promise for regenerative medicine; however, their ...
GSE96975: Integrated target discovery screens identify IL11 as novel therapeutic target for fibrosis [human]
Cardiac fibrosis is the final common pathology in heart disease. Here we establish an integrated ima...
GSE109761 (human): Neutrophils Escort Circulating Tumor Cells to Enable Cell Cycle Progression
Circulating tumor cells (CTCs) are precursors of metastasis in several cancer types, and are occasio...
GSE94502: A novel role for the EWS portion of EWS/FLI in binding GGAA-microsatellites required for oncogenic transformation in Ewing sarcoma [RNA-Seq]
Ewing sarcoma usually expresses the EWS/FLI fusion transcription factor oncoprotein. EWS/FLI regulat...
GSE97262: Major hnRNP proteins act as general TDP-43 functional modifiers both in Drosophila and human neuronal cells.
Nuclear factor TDP-43 is known to play an important role in several neurodegenerative pathologies. I...
GSE97384: mTORC1 balances cellular amino acid supply with demand for protein synthesis through post-transcriptional control of ATF4
The mammalian target of rapamycin complex 1 (mTORC1) is a master regulator of cell growth that is co...
GSE98289: Post-transcriptional remodelling is temporally deregulated during motor neurogenesis in human ALS models
Mutations causing amyotrophic lateral sclerosis (ALS) strongly implicate regulators of RNA-processin...
GSE98088: An integrative analysis of non-coding regulatory DNA variations associated with autism
A number of genetic studies have identified rare protein-coding DNA variations associated with autis...
GSE95446: Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease [2]
Intestinal health is sustained by cooperation between diverse cell types, including epithelial cells...
GSE94488: Harnessing BET inhibitor sensitivity reveals AMIGO2 as a melanoma survival gene.
We utilize the transcriptional effects of BETi in melanoma and identify AMIGO2 as a direct target ge...
GSE94396: Time-course RNA-sequencing of human induced regulatory T cell (iTreg) differentiation
Regulatory T cells (Tregs) expressing the transcription factor FOXP3 are crucial mediators of self-t...
GSE94555: Single Cell RNA-Sequencing Identifies Diverse Roles of Epithelial Cells in Idiopathic Pulmonary Fibrosis
Idiopathic pulmonary fibrosis (IPF) is a lethal interstitial lung disease causing alveolar remodelin...
GSE95450: Structural Remodeling of the Human Colonic Mesenchyme in Inflammatory Bowel Disease [3]
Intestinal health is sustained by cooperation between diverse cell types, including epithelial cells...
GSE98624: Human RELA haploinsufficiency results in autosomal dominant chronic mucocutaneous ulceration: the transcriptional profile of RelA haploinsufficient patients
The treatment of chronic mucocutaneous ulceration is challenging and only some patients respond sele...
GSE94874: Alternative classification of glioblastoma based on BUB1B-inhibition sensitivity
We created a computational framework with which to predict BUB1B-GLEBS sensitivity based on gene exp...
GSE97038: Identification of a Cell-of-Origin for Fibroblasts Comprising the Fibrotic Reticulum in Idiopathic Pulmonary Fibrosis
Idiopathic pulmonary fibrosis (IPF) is a progressive disease of the middle aged and elderly with a p...
GSE98645: Analysis of gene expression changes in whole blood samples from young men after acute or short-term intake of probiotic yoghurt compared to acidified milk
Fermented dairy milks have been associated with many health benefits including the regulation of met...
GSE102947: SETDB2 links E2A-PBX1 to cell cycle dysregulation in acute leukemia through CDKN2C repression
Acute lymphoblastic leukemia (ALL) is associated with significant morbidity and mortality necessitat...
GSE112305: Post-transcriptional regulation of the epithelial cell response to colitis
Aim: RNA binding proteins (RBPs) are emerging as critical regulators of gut homeostasis via post-tra...
GSE95561: Lineage specific differentiation is influenced by state of human pluripotency [RNA-seq]
Human pluripotent stem cells (hPSCs) have been reported in nave and primed states. However, the abil...
GSE97326: Resetting the Epigenetic Balance of Polycomb/COMPASS Function at Enhancers for Cancer Therapy
MLL3/KMT2C is a COMPASS family member and tumor suppressor that functions as a histone H3K4 mono-met...
GSE108693: Luminal lncRNAs Regulation by ER-controlled Enhancers in a Ligand-independent Manner in Breast Cancer Cells
Estrogen receptor- (ER) is a ligand-inducible protein which mediates estrogenic hormones signaling a...
GSE139833: Transcriptional profiles of human mature B cells from tonsil tissue
Mature B cells leave the bone marrow as nave B cells and migrate to the secondary lymphoid organs w...
GSE97679: Rare cell variability and drug-induced reprogramming as a mode of cancer drug resistance [RNA-seq]
Therapies targeting signaling molecules mutated in cancers can often have striking short-term effect...
GSE99963: Transcriptomic and epigenetic responses to short-term nutrient-exercise stress in humans [RNA-seq]
High fat feeding is deleterious for skeletal muscle metabolism, while exercise has well documented b...
GSE95573: Whole transcriptome analysis of PBMCs stimulated with either a P. aeruginosa phage PNM lysate or with its bacterial host P. aeruginosa
The ability of bacteriophages to kill bacteria is well known, as is their potential use as alternati...
GSE129412: The effects of TBBPA/TBBPS/TCBPA on human hepatic development
We evaluated the hepatic developmental toxicity of TBBPA/TBBPS/TCBPA with a human embryonic stem cel...
GSE98208: RNA-sequencing in immortalized human mammary epithelial cells
The epithelial-to-mesenchymal transition (EMT) contributes to tumor heterogeneity and has been impli...
GSE109947: Lymphocyte-specific chromatin accessibility pre-determines glucocorticoid resistance in acute lymphoblastic leukemia [RNA-seq]
Semi-synthetic glucocorticoids are used to treat a broad range of medical conditions including infla...
GSE94660: RNA sequencing (RNA-SEQ) of 21 HBV-HCC patients with non-neoplastic liver and tumor tissues
Purpose: Chronic Hepatitis B virus (HBV) infection leads to liver fibrosis which is a major risk fac...
GSE98370: A gene expression study of the developing human eye
There is a vast range of tools with which to study the cells and tissues of the human body, however ...
GSE99626: Combinatorial Reprogramming of Estrogen Signaling by the Nuclear Receptor Family 3C
Progesterone, glucocorticoid, androgen and mineralocorticoid receptors (PR, GR, AR and MR) appropria...
GSE94728: pSILAC mass spectrometry reveals ZFP91 as novel IMiD dependent substrate of the CRL4CRBN ligase
Thalidomide and its derivatives lenalidomide and pomalidomide (IMiDs) are effective treatments of he...
GSE98483: p63 controls the enhancer landscape during keratinocyte differentiation
Here we characterized the transcriptome and epigenome of control keratinocytes during differentiatio...
GSE99356: The role of FAM46C in myeloma cells [sequencing]
FAM46C is one of the most recurrently mutated genes in multiple myeloma (MM), however its role in di...
GSE115112: Estrogen responsive transcriptome of estrogen receptor positive normal human breast cells in 3D cultures
Understanding how differentiation, microenvironment, and hormonal milieu influence human breast cell...
GSE97080: Epigenetic and transcriptional analysis of mesoderm progenitor cells identifies HOPX as a novel regulator of hemogenic endothelium
We analyzed chromatin dynamics and transcriptional activity of human embryonic stem cell (hESC)-deri...
GSE131575: Differential gene expression upon shRNA-mediated silencing of APC in HT-29 colorectal cancer cells
Wnt signaling plays a pivotal role in colorectal cancer. Intrinsic activation of Wnt by mutational e...
GSE95605: SLC25A25-AS1 knockdown data of two colorectal carcinoma cell lines (HT29 and SW480)
We identified that SLC25A25-AS1 was a lncRNA influencing radiation response. Therefore, we aimed to ...
GSE96777: ZBTB48 is both a vertebrate telomere-binding protein and a transcriptional activator [RNA-seq]
Here we show that ZBTB48 binds directly both to telomeric as well as to subtelomeric variant repeat ...
GSE96811: Single-cell epigenomics maps the continuous regulatory landscape of human hematopoietic differentiation [bulk RNA-Seq]
Normal human hematopoiesis involves cellular differentiation of multipotent cells into progressively...
GSE97053: Regeneration of the pulmonary gas exchange niche by an evolutionarily conserved alveolar epithelial progenitor [human RNA-seq]
The lung alveolus is the primary site of gas exchange in mammals. Within the alveolus, the alveolar ...
GSE125780: DART-seq: an antibody-free method for global m6A detection
m6A is a widespread modificaiton which plays important roles in the regulation of gene expression. M...
GSE112339: Regional differences in mRNA and lncRNA expression patterns in the non-failing human heart
Background: Although chamber specialization is critical for proper cardiac function, a comprehensive...
GSE100451: Function of HNRNPC in breast cancer cells by controlling the dsRNA-induced interferon response
Elevated expression of RNA binding protein HNRNPC has been reported in cancer cells, while the essen...
GSE94897: B cells expressing the IgA receptor FcRL4 participate in the autoimmune response in patients with rheumatoid arthritis
The clinical efficacy of B cell targeting therapies highlights the pathogenic potential of B cells i...
GSE95352: Novel SF3B1 Deletion Mutations Result in Aberrant RNA Splicing in CLL Patients
Recurrent mutations in RNA splicing factors SF3B1, U2AF1, and SRSF2 have been reported in hematologi...
GSE99552: Gene Expression Analysis of Melanoma Cells Treated with 6-Thio-dG In Vitro
Telomerase promoter mutations are highly prevalent in human tumors including melanoma. Telomere tran...
GSE97919: Self-organized cerebral organoids with human specific features predict effective drugs to combat Zika virus infection [RNA-seq]
The human cerebral cortex possess distinct structural and functional features that are not found in ...
GSE94957: Mitochondrial dsRNA triggers antiviral signalling in humans
Mitochondria as descendants of endosymbiotic bacteria retain essential prokaryotic features such as ...
GSE97156: RNA-seq of overgrown interscapular adipose tissue with biallelic MFN2 mutations
Mitofusin 2 (MFN2) mutations previously associated with axonal neuropathy have recently been found i...
GSE94928: Transcriptome analysis of IMR90 fibroblasts expressing OSKM or control vector and OSKM-induced senescent IMR90 fibroblasts upon p21CIP or mTOR knockdown
Ectopic expression of the transcription factors Oct4, Sox2, Klf4 and c-Myc (OSKM) can reprogram soma...
GSE102943: Transcriptomal changes during differentiation of human iPS cells to PGC-like cells
Pluripotent stem cell-derived human primordial germ cell (PGC)-like cells (hPGCLCs) may provide impo...
GSE98394: Transcriptional dissection of melanoma identifies a high-risk subtype underlying TP53 family genes and epigenome deregulation
We set out to identify molecular underpinnings of high-risk melanomas, those that are likely to prog...
GSE97681: Gene expression signature of vemurafenib resistance in WM989 and WM983B melanoma cells
Therapies targeting signaling molecules mutated in cancers can often have striking short-term effect...
GSE124218: Human Bacille Calmette-Gurin vaccination elicits trained immunity via the hematopoietic progenitor compartment [bone marrow]
Induction of trained immunity by human Bacille-Calmette-Gurin (BCG) vaccination is implicated in the...
GSE135936: Human plasma-like medium improves T lymphocyte activation
T lymphocytes are critical effectors of the immune system and the ability to study their behavior in...
GSE97590: Next Generation Sequencing RNA Seq data from UKE Phase I rVSV ZEBOV vaccine clinical trial, from full blood samples on Days 0,1,3,7
10 adult participants of dose group 3x10^6 pfu, and 10 participants of dose group 20x10^6 pfu. Reads...
GSE101661: Expression profiles of the four human major ectodermal lineages
Here we report a chemically defined strategy to derive the entire human ectoderm from pluripotent st...
GSE97655: Single-cell transcriptomics of East-Asian pancreatic islets cells
Single-cell RNA-seq (scRNA-seq) of pancreatic islets have reported on - and -cell gene expression in...
GSE98454: Pluripotent stem cell models of Blau syndrome reveal an IFN-<gamma>-dependent inflammatory response in macrophages
Background: Blau syndrome, or early-onset sarcoidosis, is a juvenile-onset systemic granulomatosis a...
GSE99986: Low and High Dose Progestins Elicit Distinct Breast Cancer Biology
An incomplete understanding of dose-dependent progesterone receptor (PR) biology has led to the subo...
GSE98785: Therapeutic targeting of KDM1A/LSD1 in Ewing sarcoma engages the ER-stress response I
The purpose of this study was to define biomarkers of sensitivty and mechanisms of resistance to th...
GSE97928: Enhancer profiling in metastatic cancer [RNA-Seq]
Metastases cause the majority of cancer-related deaths. Yet, the origins of metastatic cancer phenot...
GSE97806 (human): Disrupted prenatal RNA processing and myogenesis in congenital myotonic dystrophy
Myotonic dystrophy type 1 (DM1) is a CTG microsatellite expansion (CTGexp) disorder caused by expres...
GSE97881: Medial Ganglionic Eminence and Cortical Organoids Model Human Brain Development and Interneuron Migration [RNA-seq]
Organoid techniques provide unique platforms to model brain development and neurological disorders. ...
GSE109985: Genome-wide transcriptional profiles for the GSK3 selective inhibitor BRD0507 and for the GSK3/ dual inhibitor BRD0320
Exploiting an Asp-Glu switch in glycogen synthase kinase 3 to design paralog selective inhibitors fo...
GSE97668: Rhinovirus infection results in stronger and more persistent genomic dysregulation: evidence for altered innate immune response in asthmatics at baseline, early in infection, and during convalescence
Background: Rhinovirus (HRV) is associated with the large majority of virus-induced asthma exacerbat...
GSE132363: Gene expression profiling of human DLD-1 cells after instant depletion of basket nucleoporins
We used RNA-seq approach to distinguish roles of basket nucleoporins Nup153, Nup50, and Tpr in trans...
GSE98104: CRISPR/Cas9-mediated ASXL1 mutation in U937 cells perturbs myeloid differentiation
Purpose: Recurrent ASXL1 mutations are frequently observed in all spectrums of myeloid malignancies ...
GSE98126: Mapping the chemotherapy-induced RNA interactome in Glioblastoma [RNA-Seq]
Long non-coding RNAs (lncRNAs) are increasingly recognized as important players in transcription and...
GSE103305: Thyroid State Regulates Gene Expression in Human Whole Blood Cells
Context: Despite the well-recognized clinical features due to insufficient or excessive thyroid horm...
GSE102652: Transcription Factor Activating Protein 4 is synthetically lethal and a master regulator of MYCN-amplified neuroblastoma
Despite the identification of MYCN amplification as an adverse prognostic marker in neuroblastoma, M...
GSE98183: Chromosomal instability promotes metastasis through a cytosolic DNA response
Chromosomal instability (CIN) is a hallmark of cancer, and it results from ongoing errors in chromos...
GSE108763: The translation termination factor GSPT1 is a phenotypically relevant off-target of heterobifunctional phthalimide degraders
Protein degradation is an emerging therapeutic strategy with a unique molecular pharmacology that en...
GSE98201: Medial Ganglionic Eminence and Cortical Organoids Model Human Brain Development and Interneuron Migration [RNA-seq2]
Organoid techniques provide unique platforms to model brain development and neurological disorders. ...
GSE106564: Super-enhancer-driven CCAT1 is co-activated by SOX2 and TP63 and promotes squamous cancer from esophagus, head and neck and lung [RNA-seq]
Squamous cell carcinomas (SCCs) are aggressive malignancies. Previous report demonstrated that the t...
GSE100530: Mutational landscape of splicing genes and functional consequences across 33 cancer types
Hotspot mutations in the spliceosome component genes have been recently reported at high frequency i...
GSE99680: Estrogen signaling is functionally reprogrammed in breast tumorigenesis
Background: The estrogen receptor (ER) is expressed in approximately 70% of sporadic breast cancers ...
GSE102033: Transcriptome profiling at day 30 of microRNA-mediated neuronal reprogramming [RNA-seq d30]
Neuronal microRNAs, miR-9/9* and miR-124 (miR-9/9*-124), exert reprogramming activities to direct ce...