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Sequencing-based assays (Page 54)
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GSE89296: Role of liquid sugar in regulating the hepatic transcriptome in a high fat Western diet model of NAFLD
Purpose: The goals of this study are to use hepatic transcriptome profiling (RNA-seq) to examine th...
GSE100918: Mechanisms of the innate defense regulator peptide 1002 anti-inflammatory activity in a sterile inflammation mouse model
Innate defense regulator (IDR) peptide-1002 is a synthetic host defense peptide derivative with stro...
GSE93007: Exhaustion-associated regulatory regions in CD8+ tumor-infiltrating T cells (anti-PD-L1 vs Control IgG RNA-seq)
T cell exhaustion is a progressive loss of effector function and memory potential due to persistent ...
GSE100035: Sex differences in peripheral not central immune responses to pain-inducing injury
Women suffer chronic pain more frequently than men. It is not clear whether this is due to differenc...
GSE100805: Decreased expression of a subset of TLR-dependent genes by heme-inducible Spi-C
To determine the functions of Spi-C in innate immune responses, we investigated the overall gene exp...
GSE99078: Induced pluripotent stem cell-derived primitive macrophages as a cellular platform to model tissue-resident macrophage differentiation and function
Specialized tissue macrophages arise during embryogenesis from yolk-sac (YS) progenitors that migrat...
GSE89848: Id proteins suppress E2A-driven iNKT cell development prior to TCR selection [RNA-seq]
Id proteins have been shown to promote the differentiation of conventional and T cells, and to supp...
GSE98875: LSD1 inhibition induces neurodegeneration and provides a common link to Alzheimer's disease and Frontotemporal dementia
Alzheimers disease (AD) and Frontotemporal dementia (FTD) are the two most common forms of dementia ...
GSE102368: RNA-seq of MMTV-Neu AXL KO tumors
AXL is activated by its ligand GAS6 and is expressed in triple-negative breast cancer cells. We repo...
GSE99086: Retinoic Acid Related Receptor Orphan Receptor a (RORa) expressing T regulatory cells thwart type-2 cutaneous allergic inflammation
We used RNA-sequencing to profile gene expression differences between Tregs from skin and LNs of Fox...
GSE102491: c-Maf-dependent transcripts in effector Tregs from Peyer's patches
We identify c-Maf as an essential factor regulating adoption of RORgamma t+ and T follicular regulat...
GSE100587: Dynamics of Proteo-Transcriptomic Response to HIV-1 Infection
Throughout HIV-1 replication cycle, a complex interplay of host-pathogen interactions takes place in...
GSE102448: Genome-wide transcriptome in the mouse seminal vesicles (SVs) and uterus (U) following neonatal DES exposure [RNA-seq]
DES is a synthetic estrogen that is associated with adverse effects on reproductive organs. Our grou...
GSE99028: Expression profiling of etoposide-induced senescent cells
We report here the RNA-seq data of proliferating IMR90 cells and etoposide-induced senescent cells w...
GSE100982: hMTR4 plays a central role in creating balanced nuclear RNA pools for degradation and export VI
To examine whether the competition between hMTR4 with ALYREF is important for the specific exosome r...
GSE105045: Cerebellar gene expression from Mecp2-null and WT mice [RNA-Seq data set]
Several recent studies have suggested that genes that are longer than 100 kb are more likely to be m...
GSE102419: Expression data from liver sinusoidal endothelial cells in Wild Type and NICeCA
The Notch pathway plays a critical role in regulating the proliferation and differentiation of endot...
GSE99771: Transcriptome analysis of gene expression and single-nucleotide-resolution m6A sites in normal and mettl3 cKO testis samples (RNA-Seq)
RNA was isolated from control and Mettl3 cKO mouse testes using the TRIzol (Invitrogen) reagent by f...
GSE135824: RNA-seq study of HUVEC/MSC cell growth on micropatterned Si-TiB2 substrates
Analysis of transcriptome changes in human umbilical vein cells (HUVEC) and mesenchymal stem cells (...
GSE106835: Novel Principles of Cellular Reprogramming Revealed by Prospective Isolation and Characterization of Rare Intermediates Poised to Generate iPSCs [RNA-seq 1]
Cellular reprogramming converts differentiated cells into induced pluripotent stem cells (iPSCs). Ho...
GSE99975: Thiol-linked alkylation for the metabolic sequencing of RNA [Transcriptional inhibition by Actinomycin D]
Gene expression profiling by high-throughput sequencing reveals qualitative and quantitative changes...
GSE98400: Polycomb repressive complex 1 regulates the nucleosome landscape but not accessibility at target genes [RNA-seq]
Polycomb repressive complexes 1 and 2 (PRC1/2) act to limit transcriptional activity at gene promote...
GSE98579: RNAseq for Tfam knock under NKX2.5 promoter
Tfam inactivation by Nkx2.5Cre caused embryonic lethal myocardial hypoplasia. Tfam inactivation was ...
GSE99791: Astrocyte-enriched pan-brain aging transcriptome
Normal brain aging is marked by a cognitive decline, spurred by changes in cellular metabolism and h...
GSE106969: RNA-seq of Injured Nerve in Schwann cell conditional knockout of Eed
The goal of the experiment was to determine the role of the polycomb repressive complex 2 in the ner...
GSE98850: Ribosomal Oxygenase 2 Constrains A Latent Anthelmintic Pathway In Intestinal Epithelial Cells
Expulsion of parasitic gastrointestinal nematodes requires diverse effector mechanisms coordinated b...
GSE90625: Blimp1 induces transient metastatic heterogeneity in pancreatic cancer [688M_RNA-seq]
Purpose: Due to its high metastatic proclivity, pancreatic ductal adenocarcinoma (PDAC) is one of th...
GSE93431: Two independent modes of chromosome organization are revealed by cohesin removal
The three-dimensional organization of chromosomes is tightly related to their biological function. B...
GSE95127: PCGF5 is required for neural differentiation of embryonic stem cells [RNA-seq]
Polycomb-group proteins are key regulators of the transcriptional programs that maintain stem cell i...
GSE134818: Comparative analysis of mRNA distribution in heavy and light polysomes in wild type and Dicer1 knockout cells
To gain a global view of translational inhibition by microRNA (miRNA), we isolated polysomes from wi...
GSE99015: Synergistic activity and heterogeneous acquired resistance of combined MDM2 and MEK inhibition in KRAS mutant cancers
There are currently no effective targeted therapies for KRAS mutant cancers. Therapeutic strategies ...
GSE98900: TIMP3, a CLOCK-controlled gene, determines cell susceptibility to UV-induced expression of inflammatory factors in human keratinocytes.
To search for CLOCK-controlled genes in human keratinocytes, we introduced siRNAs against CLOCK and ...
GSE93027: Chromatin Open/Close Logic in Cellular Reprogramming [RNA-Seq]
The reprogramming of fibroblasts into pluripotent stem cells by Oct4, Sox2, Myc and Klf4 represents ...
GSE121569: ALS implicated protein TDP-43 sustains levels of STMN2 a mediator of motor neuron growth and repair
The discovery that TDP-43 mutations cause familial ALS and that many patients display pathological T...
GSE137096: Endothelial mutagenesis screen identifies genetic risk factors in the development vascular anomalies [muscle]
mRNA transcriptional comparison between two pieces of tissue from three SBxVEC-Cre+ animals and thre...
GSE99839 (mouse): Inhibitors of the histone methyltransferases EZH2/1 induce a potent antiviral state and suppress infection by diverse viral pathogens [RNA-Seq]
Epigenetic regulation is based upon a network of complexes that modulate the chromatin character and...
GSE100411: Signaling strength determines proapoptotic functions of STING
T cells exhibit an intensified STING response, which leads to the expression of a distinct set of ge...
GSE100882: SAMHD1 is recurrently mutated in T-cell prolymphocytic leukemia [RNA-seq]
We identified novel recurrent genetic lesions in T-PLL affecting genes involved in JAK/STAT signalin...
GSE97702: A UTXMLL4p300 Transcriptional Regulatory Network Coordinately Shapes Active Enhancer Landscapes for Eliciting Transcription (RNA-Seq)
Enhancer activation is a critical step for gene activation. Here we report a novel epigenetic crosst...
GSE103958: Transcript dynamics in classically and alternatively activated macrophages
Using RNA-seq, we have reported that signaling crosstalk among IFN- and LPS is integrated at the lev...
GSE107007: Aged Hematopoietic Stem Cells Drive Aging-Associated Immune Remodeling
Phenotypic and functional changes seen in the aged adaptive immune system are primarily driven by ag...
GSE100888: Transcriptional effects of motor neuron autophagy inhibition
To investigate the role of motor neuron autophagy in ALS, we generated mice in which the critical au...
GSE100943: Microsatellite expansion RNA visualization, elimination, and reversal of molecular pathology by RNA-targeting Cas9
In this Study, we used RNA-targeting Cas9 (RCas9) to reverse characteristic Myotonic Dystrophy (DM1)...
GSE103956: Migratory CD11b+ conventional dendritic cells induce T follicular helper cell dependent antibody responses
T follicular helper (Tfh) cells are a subset of CD4+ T cells that promote antibody production during...
GSE100969: The RNA binding protein PTBP1 is necessary for B cell selection in germinal centres
Antibody affinity maturation occurs in germinal centres (GC) where B cells cycle between the light z...
GSE100581: Loss of c-Jun NH2-Terminal Kinase in Mammary Epithelial Cells is Sufficient for Adenosquamous Tumor Formation
The JNK pathway has been implicated in breast cancer, both from human tumor sequencing studies and f...
GSE95835: Transcriptome of choroid endothelial cells from P5 and P30 mice.
Purpose: The outer blood-retina barrier is established through the coordinated terminal maturation o...
GSE105452: Full-length TARGET-seq resolves molecular signatures of distinct genetic subclones in MPN patients [full length TARGET-seq patient samples; Figures 3,4]
We developed TARGET-seq, a single-cell genotyping and RNA-seq method, which allows accurate detectio...
GSE101824: Intron retention induced by microsatellite expansions as a disease biomarker.
Microsatellite expansions often occur in non-coding regions of the genome. In this study, we test th...
GSE96638: Single-cell RNA sequencing of Zfp36l2 knock-out and floxed GV mouse oocytes.
Global transcriptional silencing is a highly conserved evolutionary event central to the transition ...
GSE101818: Transcriptomes of normal liver and spontaneous hepatocellular carcinoma in C3HeB/FeJ male mice
The goal of this study was to identify and analyze differential gene expression between normal liver...
GSE112985: RNA-seq analysis of A2780 and OVCAR3 human ovarian cancer cell lines after overexpression of collagen type XI alpha 1 (COL11A1)
Collagen type XI alpha 1 (COL11A1) is identified as one of the most upregulated genes in cisplatin-r...
GSE101061: Oncogenic Serine-Threonine Kinase Receptor Associated Protein Supports Hepatocellular Carcinoma Cell Growth by Enhancing Wnt/-catenin Signaling
Serine-threonine kinase receptor-associated protein (STRAP) is upregulated in breast, colorectal and...
GSE99818: Lhx2 controls changes in chromatin accessibility in retinal progenitor cells during developmental competence transitions.
We profiled retinal progenitor cells by integrating next generation sequencing methods and interroga...
GSE100225: Integrative analysis of behavioral, syaptic, and genomic plasticity in the hippocampus
We examined the the effects of cognitive training on behavior, synaptic physiology, and gene express...
GSE106594: Sorted Mouse Phagocytes RNAseq
RNAseq of murine CD11b+ CD103+ DCs and CD11b+ CX3CR1+ Mononuclear Phagocyes SOURCE: Irina LeonardiLA...
GSE100678: A cell competition-based drug screen identifies a novel compound that targets c-Myc addiction of leukemia cells
Purpose: BCR-ABL-positive acute lymphoid leukemia (ALL) has a dire prognosis. Despite improved disea...
GSE141089: Zileuton Liver Toxicity Study in DO Mice
In this study, female DO mice were administered zileuton or vehicle i.g. daily for seven days, and a...
GSE96674: COX-2 mediates tumor-stromal Prolactin signaling to initiate tumorigenesis [single cells]
Tumor-stromal communication within the microenvironment contributes to initiation of metastasis and ...
GSE102534: Comparative gene expression profiling of MHH-CALL4 cells subject to pharmacological JAK2 inhibitor treatment (ruxolitinib or CHZ868) or shRNA-mediated JAK2 depletion in vitro
Gene expression profiling was performed to characterise transcriptional programs associated with res...
GSE100464: Epigenomic analysis of Atrx deficiency in murine glioma cells of orgin [RNA-seq]
The chromatin regulator ATRX is inactivated in large subsets of adult and pediatric glioma. Whether...
GSE101144: The effect of genetic background on cognitive and pathological traits: AD-BXD
Female C57BL/6J mice hemizygous for the 5XFAD transgene (MMRRC Stock No #34848-JAX) were bred to ma...
GSE100886: PARP14 controls the nuclear accumulation of a subset of type I Interferon-inducible proteins [RNA-seq1]
The enzymes of the poly-ADP-ribose polymerase (PARP) super-family control many relevant cellular pro...
GSE94324: A family of double-homeodomain transcription factors promotes zygotic genome activation in placental mammals [RNA-seq]
In metazoans, the fertilized embryo is transcriptionally mostly silent for a few cell divisions, unt...
GSE93655: Store operated Ca2+ entry (SOCE) controls ameloblast cell function and enamel development
Abstarct:Mutations in the endoplasmic reticulum (ER) Ca2+ sensor stromal interaction molecule 1 (STI...
GSE129573: RNA-Seq analysis of inguinal white adipose tissue (iWAT) from control and high fat diet mice treated with THCA and THCA+T007
Medicinal cannabis has garnered worldwide attention in recent years but has been hampered by the psy...
GSE103885: Gene expression profiling of mouse liver with hepatocyte-specific knockout of STAT5a/STAT5b genes (STAT5ab-KO)
rRNA-depleted RNA isolated from livers of control male and female mice and from male mice with hepat...
GSE99703: Increased Susceptibility to AKI in a Mouse Model of Presymptomatic Cardiomyopathy
The early events that signal renal dysfunction in presymptomatic heart failure are unclear. To evalu...
GSE96107: Multi-scale 3D genome rewiring during mouse neural development
Chromosome conformation capture technologies have revealed important insights into genome folding. Y...
GSE102460: BACH2 in human plasma cell fate decision
We report here the broad transcriptomic program regulated by BACH2 transcription factor. We used a...
GSE93539: Protein O-GlcNAcylation Silences Methylated Promoters in Mammalian Genomes
Methylated mammalian promoters are transcriptionally silenced even in the presence of all the factor...
GSE100094: Fluctuations in sex hormones affect ex vivo HIV infection in cervical mucosa and mucosal immunity
There is an ongoing debate whether sex hormones impact risk of HIV transmission. This study evaluate...
GSE100260: Transcriptomic Characterization of LIPA+/+ and LIPA-/- iPSC-derived Macrophages
Using RNA-Seq, we examined the transcriptome profiles of human iPSC-derived macrophage (IPSDM) with ...
GSE114853: Human enteroendocrine cell transcriptomic profiling
We purified two populations of human jejunal enteroendocrine cells (GLP1+ and GLP1-) by FACS and ide...
GSE99938: LMO2 Is Required for TAL1 DNA Binding Activity and Initiation of Definitive Haematopoiesis at the Haemangioblast Stage
We differentiated WT, LMO2KO or TAL1 KO mouse ES cell lines into Flk-1+ haemangioblasts and/or Tie2...
GSE101091: LCM-seq of resident NG2 glia reprogrammed to neurons in vivo using the transcription factors Ascl1, Lmx1a and Nurr1 (ALN)
Reprogramming resident glia into functional and subtype-specific neurons in vivo by delivering repro...
GSE101878: Transcriptional changes during naturally-acquired ZIKA Virus infection render dendritic cells highly conducive to viral replication
Although dendritic cells (DCs) are among the human cell population best equipped for cell-intrinsic ...
GSE90821: ESRP1 mutations cause hearing loss due to defects in alternative splicing that disrupt cochlear development
Alternative splicing contributes to gene expression dynamics in many tissues, yet its role in audito...
GSE101853: Dpy30 regulates Myc binding to targets and Myc-driven tumorigenesis (ChIP-seq, RNA-seq)
It remains unclear how epigenetic modulators impact the tumorigenic potential of Myc. Here we show t...
GSE100175: Molecular characterisation of sorted populations of DRG and TG ganglia neurons
Sensory neurons were extracted from the dorsal root or trigeminal ganglia of AdvGFP transgenic mice ...
GSE93566: Regulation of the transition from mitosis to meiosis by the conserved RNA-helicase YTHDC2/BGCN [RNA-Seq]
In the germline stem cell lineage, proliferating gonial cells switch from mitotic proliferation to m...
GSE102566: Transcriptional profiling of a mouse model of Uromodulin Associated Kidney Disease (UAKD)
Uromodulin (UMOD) is a secreted glycoprotein exclusively expressed by the cells lining the thick asc...
GSE106636: Neonatally imprinted mesenteric lymph node stromal cell subsets induce tolerogenic dendritic cells [Tx FSC]
Gut-draining mesenteric lymph nodes (mLNs) play a key role in peripheral tolerance towards food and ...
GSE101826: Alternative RNA Splicing in the Endothelium Mediated in Part by Rbfox2 Regulates the Arterial Response to Low Flow
Low and disturbed blood flow drives the progression of arterial diseases including atherosclerosis a...
GSE102073: Molecular analysis of high-grade serous ovarian carcinoma with and without associated serous tubal intra-epithelial carcinoma [RNA-Seq]
Many high-grade serous carcinomas (HGSCs) of the pelvis are thought to originate in the distal porti...
GSE114969: Transcriptome of liver tissue in 2 week old and E17.5 Stabilin-1 knock-out mice
Stabilin-1/CLEVER-1 is a multidomain protein present in lymphatic and vascular endothelial cells and...
GSE99768: B-cell activating factor (BAFF) stimulation of Burkitt Lymphoma cell line [RNA-Seq]
RNA-Seq profiling of Burkitt Lymphoma cell line (BL2) with B-cell activating factor (BAFF) for 24 hr...
GSE100081: Mining the stiffness-sensitive transcriptome in human vascular smooth muscle cells identifies long non-coding RNA stiffness regulators
Vascular extracellular matrix (ECM) stiffening is a risk factor for aortic and coronary artery disea...
GSE135309: RNA-Seq analysis of Tcf7-deficient and -sufficient lung CD8+ TRM cells after influenza infection
T cell factor 1 (Tcf1, encoded by Tcf7) promotes the central memory CD8+ T cell (TCM) differentiatio...
GSE90736: Transcriptome analysis of microglia in a mouse model of Rett Syndrome: differential expression of genes associated with microglia/macrophage activation and cellular stress
Rett Syndrome (RTT) is a severe, neurodevelopmental disorder primarily affecting girls, characterize...
GSE101485: Pseudouridylation of tRNA-derived fragments steers translation control in stem cells [Polysome-Seq]
Pseudouridylation (pseudouridine) is the most abundant and widespread type of RNA epigenetic modific...
GSE106874: Combinatory RNA sequencing analyses reveal RNA editing-dependent and -independent gene regulation by ADAR1 in gastric cancer
To investigate the role of ADAR1 in gastric carcinogenesis, RNA sequencing and small RNA sequencing ...
GSE95145: NF45 and NF90/NF110 coordinately regulate ESC pluripotency and differentiation
While years of investigation have elucidated many aspects of embryonic stem cell (ESC) regulation, t...
GSE99811: Transcriptomic analysis of the role of the RasGEF1B circular RNA in the TLR4/LPS pathway
Circular RNAs (circRNAs) have recently emerged as a large class of novel non-coding RNA species. How...
GSE113053: Hemeatopoietic stem cells but not multipotent progenitors drive erythropoiesis during chronic erythroid stress in EPO transgenic mice
The hematopoietic stem cell (HSC) compartment consists of a small pool of cells capable of replenish...
GSE98563: TREM2 is a global regulator of microglia energetic and biosynthetic metabolism during steady state and in Alzheimers disease
The most common form of senile dementia, Alzheimers disease (AD), is characterized by A plaques and...
GSE100100: A data mining paradigm for identifying key factors in biological processes using gene expression data
RNA-Seq was performed on the mouse keratinocyte cultures with Sbsn knockeddown to study the role of ...
GSE101859: The RhoJ-BAD Signaling Network: An Achilles Heel for BRAF Mutant Melanomas
Genes and pathways that allow cells to cope with oncogene-induced stress represent selective cancer ...
GSE100039: Learning and age-related changes in genome-wide H2A.Z binding in the hippocampus
We characterize histone H2A.Z binding and RNA expression in the hippocampus of young (2.5 months) an...
GSE101497: Genome-wide RNA deep sequencing of CAL-101 or AKTi primed human T cells in comparison to traditionally expanded T cells
Differential expression patterns of total mRNA in traditionally expanded T cells (vehicle) compared ...