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Sequencing-based assays (Page 121)
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GSE154428: Different effects of constitutive and induced microbiota modulation on microglia in a mouse model of Alzheimers disease
It was recently revealed that gut microbiota promote amyloid-beta (A) burden in mouse models of Alzh...
GSE156271: Core transcription regulatory circuitry orchestrates stratified epithelial homeostasis (RNA-seq)
Adult stem cell identity, plasticity, and homeostasis are precisely orchestrated by lineage-restrict...
GSE157056: Mechanical control of MSC adipogenesis does not require Lamin A/C
Mesenchymal stem cells (MSC) maintain the musculoskeletal system by differentiating into multiple ce...
GSE65485: Next Generation Sequencing Identification of HBV-MLL4 integration and its molecular basis in Chinese hepatocellular carcinoma
Purpose: To gain molecular insights of HBV integration that may contribute to HCC tumorigenesis, we ...
GSE153662: Next Generation Sequencing of Wild Type and Zeb1-/- CLP
Zeb1, a zinc finger E-box binding homeobox epithelial-mesenchymal (EMT) transcription factor, confer...
GSE154468: RNA-Seq of MADM induced UPDs of Chr. 7, 11, 12 (QuantSeq)
In mammalian genomes a subset of genes is regulated by genomic imprinting resulting in silencing of ...
GSE153751: RNA-sequencing of FACS-sorted Prominin1+ radial glial cells of E12.5 SmadNes mutant embryos (Smad1wt/fl;Smad5wt/fl;Nestin:Cre+/0) and control littermates (Smad1wt/fl;Smad5wt/fl;Nestin:Cre0/0)
We report the transcriptomes of mouse E12.5 cortical radial glial cells and the changes caused by in...
GSE157069: Transcriptome analysis of the circadian clock gene BMAL1 deletion with opposite carcinogenic effects
We have previously reported that the deletion of BMAL1 gene has opposite effects in respect to its c...
GSE157110: High throughput RNA-sequencing identifies Differentially Expressed Genes (DGS) of control and shATXN7L3 HCCLM3 cells
Purpose: High throughput RNA-seq has provided an efficient and convenient access to screening substa...
GSE156450: RNA sequencing of livers from Per2-/- and WT mice following MC38 cancer cells injection reveals transcriptional differences as early as 7 days post injection
The circadian clock regulates diverse physiological processes by maintaining a 24-hour gene expressi...
GSE154355: Nfil3, a target of the NACA transcriptional coregulator, affects osteoblast and osteocyte gene expression differentially.
Purpose: Identify PTH-responsive genes in MC3T3-E1 cells. The aim of the study is to identify novel ...
GSE154398: Zfp281 functions as a barrier in embryonic stem cells to extraembryonic endoderm stem cells differentiation [RNA-seq]
Cell-fate decisions and lineage commitment in early embryonic development are governed by comprehens...
GSE156119: RNA-seq of WT ileum with DEX, Zn and untreated controls
The cytokine TNF drives inflammatory diseases, e.g. Crohn disease. In a mouse model of TNF-induced s...
GSE154368: Increased transcriptome variation and localised DNA methylation changes in oocytes from aged mice revealed by parallel single-cell analysis [scRNA-seq]
Advancing maternal age causes a progressive reduction in fertility. The decline in developmental com...
GSE157185: Comparative transcriptional profiling of motor neuron disorder-associated genes in various human cell culture models
Disease modelling requires appropriate cellular models that best mimic the underlying pathophysiolog...
GSE156071: Transcriptome reprogramming of CD11b+ bone marrow cells by pancreatic cancer extracellular vesicles
Pancreatic cancers (PC) are highly metastatic with poor prognosis, mainly due to delayed detection. ...
GSE156135: M. tuberculosis reprograms HSCs to limit myelopoiesis and impair trained immunity via a type I IFN/iron axis [AERO_SERIES_2]
A greater understanding of hematopoietic stem cell (HSC) regulation is required for dissecting prote...
GSE151698: Microglial responses to CSF1 overexpression do not promote expansion of other glial lineages
CSF1 expression in the central nervous system (CNS) increases in response to a variety of stimuli, a...
GSE131568: Differential expression of circular RNA in oral leukoplakia: novel potential biomarkers exploration for diagnosis and prognosis of precancer
6 pairs of OLK tissues and normal oral mucusal (NOM) tissues were obtained to detect circRNAs expres...
GSE151691: Essential role for CD30-Transglutaminase 2 axis in memory Th1 and Th17 cell generation.
Memory helper T (Th) cells are crucial for secondary immune responses against infectious microorgani...
GSE151829: Absence of central tolerance in Aire-deficient mice synergizes with immune-checkpoint inhibition to enhance antitumor responses
Therapeutic targeting of immune checkpoint pathways, that are exploited by tumors to evade the immun...
GSE151822: RUNX2 is a dependency factor in immature and KMT2A-rearranged T-cell acute lymphoblastic leukemia [KMT2A-MLLT1_ Runx2 ko RNA-seq]
T-cell acute lymphoblastic leukemia (T-ALL) is an aggressive hematologic malignancy with a high inci...
GSE154495: A CTCF binding element regulates RA-induced early ESCs differentiation through orchestrating long-range chromatin interactions between its adjacent enhancers and HoxA
Proper Homeobox A (HoxA) cluster genes expression is essential for embryonic stem cells (ESCs) diffe...
GSE151830: Absence of central tolerance in Aire-deficient mice synergizes with immune-checkpoint inhibition to enhance antitumor responses
Therapeutic targeting of immune checkpoint pathways, that are exploited by tumors to evade the immun...
GSE153898: Alteration in the transcriptome of lung resident fibroblast isolated from fibrotic lungs of TGFalpha mice upon genetic knockdown of Aurora Kinase B
Pulmonary fibrosis (PF) is associated with many chronic lung diseases including Systemic sclerosis (...
GSE157234: Microglia RNA profiling in steady state and post-LPS chellenge in the absence of IL-10R, or both IL-10R and TNF, in microglia.
We used the CX3CR1CreER system to generate mice in which the microglia are IL-10R-deficient, or both...
GSE153909: Next Generation Sequencing Facilitates Quantitative Analysis of the effects of PD-1 deficiency on sorted mouse pulmonary ILC2 Transcriptomes
Allergic asthma is a leading chronic disease associated with airway hyperreactivity (AHR). Type-2 in...
GSE156126: Temporal analysis of Brd4 displacement in the role of B cell survival, proliferation and differentiation
JQ1 is a BET-bromodomain inhibitor that has immunomodulatory effects. However, the precise molecular...
GSE154573: Lack of desmin in mice causes structural and functional disorders of neuromuscular junctions
Desmin, the major intermediate filament (IF) protein in muscle cells, interlinks neighboring myofibr...
GSE154417: The precursor of PI(3,4,5)P3 alleviates aging by activating daf-18(Pten) and independent of daf-16
Aging is characterized by the loss of homeostasis and the general decline of physiological functions...
GSE156134: M. tuberculosis reprograms HSCs to limit myelopoiesis and impair trained immunity via a type I IFN/iron axis [Bulk_SERIES_1]
A greater understanding of hematopoietic stem cell (HSC) regulation is required for dissecting prote...
GSE156338: Circulation of gut pre-activated nave CD8+ T cells enhances anti-tumor immunity in B cell defective mice
The gut microbiome has garnered attention as an effective target to boost immunity and improve cance...
GSE29282: A biochemical basis for toggling enhancers from the active to poised state in B cells
BCL6 is crucial for B-cell activation and lymphomagenesis. We used integrative genomics to explore B...
GSE156918: FLCN Gene Ablation Reduces Fibrosis and Inflammation in a Diet-Induced NASH Model
Non-alcoholic steatohepatitis (NASH) represents a major economic burden and is characterized by trig...
GSE156136: M. tuberculosis reprograms HSCs to limit myelopoiesis and impair trained immunity via a type I IFN/iron axis [EG_SERIES_3]
A greater understanding of hematopoietic stem cell (HSC) regulation is required for dissecting prote...
GSE154516: Transforming growth factor beta signaling and decidual development in mice
Transforming growth factor (TGF) signaling regulates multifaceted reproductive processes via its tr...
GSE154622: Different mutant RUNX1 oncoprotein classes program alternate hematopoietic differentiation trajectories [RNA-Seq]
Mutations of the hematopoietic master regulator RUNX1 cause acute myeloid leukaemia, familial platel...
GSE156202: Modifying macrophages at the periphery has the capacity to change microglial reactivity and increase ALS survival
Microglia and peripheral macrophages, combined, have been implicated in the motor neuron disease Amy...
GSE155088: Enhancer priming by H3K4 methylation safeguards germline competence [scRNA-seq]
Germline specification in mammals occurs through an inductive process whereby competent cells in the...
GSE157562: FoxO maintains a genuine quiescent muscle stem-cell state until geriatric age (RNA-seq)
We identify two quiescent stem-cell states through relative CD34 expression: CD34High, with stemness...
GSE156506: Disturbed mitochondrial dynamics in CD8+ TIL reinforce epigenetic programming linked with T cell exhaustion [RNA-Seq]
The metabolic challenges present in tumors attenuate the metabolic fitness and anti-tumor activity o...
GSE155120: IFN-I and CD8 T cells increase intestinal barrier permeability after chronic viral infection
Intestinal barrier leakage constitutes a potential therapeutic target for many inflammatory diseases...
GSE154615: Next Generation Sequencing of LSK EpCAM+ and EpCAM- of Zeb1-/-
Zeb1, a zinc finger E-box binding homeobox epithelial-mesenchymal (EMT) transcription factor, confer...
GSE156667: Effect of SWELL1 (LRRC8a) gene deletion on gene expression in differentiated myotubes
Maintenance of skeletal muscle is beneficial in obesity and Type 2 diabetes. Mechanical stimulation ...
GSE157434: Quantitative RNAseq Analysis of Treatment Outcomes with Talazoparib, Romidepsin or Combination in MBL2 cell line
To explore the molecular mechanisms by which romidepsin potentiates the effect of talazoparib, RNA s...
GSE154654: Autophagy Promotes Growth of High Tumor Mutational Burden Tumors by Inhibiting a T Cell Immune Response
Autophagy degrades and recycles intracellular components to sustain metabolism and survival during s...
GSE155182: Single cell RNA seq of hepatic and renal p16 positive cells
We performed the single cell RNA sequencing of mouse normal kidney, normal liver, and NASH-induced l...
GSE154680: Foxp3 imparts regulatory T cell epigenetic identity through a transcription factor relay
RNA-seq, ATAC-seq, and CUT&RUN analysis in Foxp3+ regulatory T cells, Foxp3- conventional CD4 T cell...
GSE157507: Lymphatic endothelial cells contribute to blood vessel formation in tumours
Using multicolor lineage tracing, in vivo time-lapse imaging and single cell transcriptional profili...
GSE154659: Transcriptional reprogramming of distinct peripheral sensory neuron subtypes after axonal injury
Primary somatosensory neurons specialize in transmitting distinct types of sensory information throu...
GSE154543: An epigenetic program established by gene environment interactions initiates pancreatic carcinogenesis [Set3]
Damaged tissues have increased risk of cancer development through poorly understood mechanisms. In t...
GSE156230: Gene therapy with secreted acid alpha-glucosidase rescues Pompe disease in a novel mouse model with early-onset spinal cord and respiratory defects
Pompe disease (PD) is a neuromuscular disorder caused by deficiency of acid-alpha-glucosidase (GAA),...
GSE155217: CHD8 dosage regulates transcription in pluripotency and early murine neural differentiation [RNA-seq]
The chromatin remodeler CHD8 is among the most frequently mutated genes in autism spectrum disorder ...
GSE156235: Next-generation sequencing facilitates quantitative analysis of control and Lhx6-/- molar transcriptomes
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular path...
GSE156505: DIS3 ribonuclease is required for the maintenance of spermatogenic lineage in mice
Spermatogonial stem cells (SSCs) self-renewal and differentiation are the foundation for continious ...
GSE156605: Changes of gene expression patterns of mouse lung epithelial cells in response to IL-15 whether or not they have MCMV-memory CD8 T cells [mouse in vivo]
We report the differences of gene expression pattern of 4 different groups of mouse lung epithelial ...
GSE157215: Brain RNA-seq in the LXS RI strains: Saline and ethanol treatment
Purpose: To investigate the effect that acute ethanol tretament (5 g/kg) has on the brain transcript...
GSE157667: Effect of maternal iron deficiency on placental transcriptome in mouse
the goal of this study is to use high-throughput RNA-Sequencing technology to identify genes that ar...
GSE156242: RNA-seq of GR WT and GR DIM ileum/IEC with DEX, Zn and untreated controls
The cytokine TNF drives inflammatory diseases, e.g. Crohn disease. In a mouse model of TNF-induced s...
GSE156234: Single-Cell RNA Sequencing Uncovers Heterogenous Transcriptional Signatures in Macrophages during Efferocytosis
Efferocytosis triggers cellular reprogramming, including the induction of mRNA transcripts which enc...
GSE155291: Amelioration of autism-like social deficits by targeting histone methyltransferases EHMT1/2 in Shank3-deficient mice
Many of the genes disrupted in autism are identified as histone-modifying enzymes and chromatin remo...
GSE156543: Suppression of DDX39B sensitizes ovarian cancer cells to DNA-damaging chemotherapeutic agents via destabilizing BRCA1 mRNA
Multiple RNA processing events including transcription, mRNA splicing and export are delicately coor...
GSE156749: Upregulation of 5-terminal oligopyrimidine mRNA translation upon loss of the tumor suppressor ARF
Tumor cells require nominal increases in protein synthesis in order to maintain high proliferation r...
GSE156542: Loss of TDP-43 in astrocytes leads to motor deficits by triggering A1-like reactive phenotype and tri-glial dysfunctions
The majority of patients with amyotrophic lateral sclerosis (ALS) have abnormal TDP-43 aggregates in...
GSE156267: The microRNA, miR-133b, functions to slow Duchenne muscular dystrophy pathogenesis
Duchenne muscular dystrophy (DMD) is characterized by progressive skeletal muscle degeneration. No t...
GSE156533: Transcriptomic profiling in 3-month-old P23H Retinitis Pigmentosa mouse retinas
Neuronal plasticity of the inner retina has been observed in response to photoreceptor degeneration....
GSE156936: RNA-Seq analysis of E4FAD mouse brain cortex to evaluate the impact of omega-6 fatty acid docosapentaenoic acid on neuroinflammation
Purpose: In this study, we report on an effective anti-inflammatory lipid, linoleic acid (LA) metabo...
GSE156307: Gene Expression in the developing hindstomach and forestomach of wild type and GATA4 conditional knock out and knock in embryonic mice
Gene expression was compared between wild type forestomach and hindstomach epithelial cells at embry...
GSE157156: Liver Epithelial Focal Adhesion Kinase Modulates Fibrogenesis and Hedgehog Signaling
Focal adhesion kinase (FAK) is an important mediator of extracellular matrix-integrin mechano-signal...
GSE157244: Type I interferon responses to ischemic injury begin in the bone marrow of mice and humans and depend on Tet2, Nrf2, and Irf3
Sterile tissue injury is thought to locally activate innate immune responses via damage associated m...
GSE157270: Crtc1 deficiency aggravates fat accumulation in the white adipose tissue
Obesity is described as excessive fat accumulation that drives the development of glucose and lipid ...
GSE157233: Comparative gene expression profiling in livers of A1cf-transgenic, A1cf-knockout, and wild-type mice
Rationale: RNA binding protein Apobec1 Complementation Factor (A1CF) regulates posttranscriptional A...
GSE157375: The inner nuclear membrane protein LEMD2 and the chromatin organizer SATB2 regulate overlapping gene-sets in primary cortical neurons
SATB2, encoding a nuclear chromosomal scaffolding protein, is a schizophrenia risk gene and genetica...
GSE157602: RNA-seq analysis of PD-1 treatment outcomes in IL-34 expressing or not expressing CT26 cell line
Interleukin-34 (IL-34) is an alternative ligand to colony-stimulating factor-1 (CSF-1) for the CSF-1...
GSE157460: Interleukin-6 (IL-6) deficiency enhances intramembranous osteogenesis following stress fracture in mice
Interleukin-6 (IL-6) is highly upregulated in response to skeletal injury, suggesting it plays a rol...
GSE157635: TREM2 Alzheimers variant R47H causes similar transcriptional dysregulation to knockout, yet only subtle functional phenotypes in human iPSC-derived macrophages
TREM2 is a microglial cell surface receptor, with risk mutations linked to Alzheimers disease (AD), ...
GSE37686: Identification of miRNA signatures during the differentiation of hESCs into retinal pigment epithelial cells
Retinal pigment epithelium (RPE) cells can be obtained through in vitro differentiation of both embr...
GSE38234: Genistein and bisphenol A exposure cause estrogen receptor 1 to bind thousands of binding sites in a cell type-specific manner
To obtain an integrated view of gene regulation in response to environmental and endogenous estrogen...
GSE39878: RNA-DNA DIFFERENCES IN NASCENT RNA
RNA sequences are expected to be identical to their corresponding DNA sequences. Advances in techno...
GSE41716: Somatic copy-number mosaicism in human skin revealed by induced pluripotent stem cells (sequencing)
Reprogramming human somatic cells into induced pluripotent stem cells (iPSC) has been suspected of c...
GSE42420: CFIm25 links alternative polyadenylation to glioblastoma tumour suppression
Purpose: To identify all of the APA targets of CFIm25 on a global scale and develop an algorithm tha...
GSE44718: Multiple roles for Grainyheadlike transcription factors in the establishment and maintenance of human mucociliary airway epithelium
The airways of the human lung are lined by an epithelium made up of ciliated and secretory luminal c...
GSE39748: Argonaute proteins couple chromatin silencing to alternative splicing (RNA IP-Seq)
While Argonaute (AGO) proteins play a major role in transcriptional gene silencing (TGS) in many org...
GSE52834: Analysis of pre-mRNA splicing trans-regulation in human lymphoblastoid cell lines
To understand the role of trans factors in the regulation of splicing and alternative splicing, we k...
GSE50580: Binding motif analysis of METTL3WTAP in METTL3WTAP overexpressed Human 293T cells
label the cells overexpressed Myc tagged METTL3 and Flag tagged WTAP with 4-SU, the RNA bound by MET...
GSE85011: CRISPRi-based genome-scale identification of functional long non-coding RNA loci in human cells
The human genome produces thousands of long non-coding RNAs (lncRNAs) transcripts >200 nucleotides ...
GSE40705: Comprehensive comparative analysis of RNA sequencing methods for degraded or low input samples
RNA-Seq is an effective method to study the transcriptome, but can be difficult to apply to scarce o...
GSE56691: Characterizing the contrasting roles of JMJD3 and UTX histone demethylases in T cell acute lymphoblastic leukemia [GSKJ4_RNA-seq]
T-cell acute lymphoblastic leukemia (T-ALL) is an immature hematopoietic malignancy driven mainly by...
GSE46876: The ABRF Next-Generation Sequencing Study (ABRF-NGS): Multi-platform and cross-methodological reproducibility of transcriptome profiling by RNA-seq.
Next-generation sequencing (NGS) technology applications like RNA-sequencing (RNA-seq) have dramatic...
GSE55008: Transcriptome profiling of omental adipose tissues in human obesity by RNA-Seq
Purpose: To profile the transcriptomes of omental adipose tissues from obese and lean humans.; Metho...
GSE40710: aSyn polyA-RNAseq in PD and unaffected cortical brain samples
We sought to more precisely characterize the different alpha-synuclein (aSyn) 3UTR mRNA species in n...
GSE47058: Differential gene expression by suppression of either SOX2 or TP63 in KYSE70 human esophageal squamous carcinoma cell line.
SOX2 is a transcription factor essential for pluripotent stem cells, and development and maintenance...
GSE55536: Functional and Transcriptomic Characterization of iPSC-derived Macrophages and their Application in Modeling Mendelian Disease
Using RNA-Seq, we reported novel findings in the comparison of transcriptome profiles of isogenic HM...
GSE45669: RNA-sequencing of the human milk fat layer during colostrum, transitional, and mature stages of lactation
Human milk fat globules, by enveloping cell contents during their secretion into milk, are a rich so...
GSE65000 (human): Human-specific gene ARHGAP11B promotes basal progenitor amplification and neocortex expansion
The evolutionary expansion of the human neocortex reflects increased amplification of basal progenit...
GSE41009: Divergent transcription of lncRNA/mRNA gene pairs in embryonic stem cells
Many long non-coding RNA (lncRNA) species have been identified in mammalian cells, but the genomic o...
GSE46056: RNAseq of PRMT4KD in human cord blood derived CD34+ cells
Defining the role of epigenetic regulators in normal hematopoiesis has become critically important, ...
GSE49155: Profiling premalignant lesions in lung squamous cell carcinomas identifies mechanisms involved in stepwise carcinogenesis
Lung squamous cell carcinoma (SCC) is thought to arise from premalignant lesions in the airway epith...
GSE43550: Small RNA Solexa sequencing of colorectal tumor and adjancent normal tissues
A pair of stage III colorectal cancer (CRC) tumor and adjacent normal tissue were collected from a p...
GSE47114: RNA-Guided Human Gene Activation by Cas9/CRISPR-Based Engineered Transcription Factors
Synthetic transcription factors can be applied in many areas of biotechnology, medicine, and basic r...