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Sequencing-based assays (Page 77)
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GSE111172: Genome-wide identification of distinct target loci for de novo DNA methylation by DNMT3A and DNMT3B during mammalian development
DNA methylation plays essential roles in mammalian development. During post-implantation development...
GSE123380: Overexpression of Claspin and Timeless protects cancer cells from replication stress in a checkpoint-independent manner
RNA-seq analysis of BJ cells overexpressing RasV12 and escaping senescence SOURCE: romain forey (rom...
GSE123045: In search for materials able to be colonized by a normal endothelium: haracterization and NGS gene expression profiling of human primary endotheliocytes cultivated on electrospun 3D matrices
Endothelization of the luminal surface of vascular grafts is required for their long-term functionin...
GSE116374: Inactivation of Irf1 causes susceptibility to colitis-associated colorectal cancer
The incidence of colorectal cancer (CRC) is increased in patients afflicted by inflammatory bowel di...
GSE136022: Genome-wide view of the impact of Spt5-Pol II inhibitors (SPIs) on mRNA levels [RNA-Seq 2h]
We identified the first Spt5-Pol II inhibitors (SPIs). SPIs faithfully reproduced Spt5 knockdown eff...
GSE123943: SOX11 knockdown in B-ALL cell lines
Acute lymphoblastic leukemia is marked by aberrant transcriptional features that alter cell differen...
GSE122653: Optimal-transport analysis of single-cell gene expression identifies developmental trajectories in reprogramming III
We collected triplicate samples at day 15 under serum condition, generated single cell suspensions a...
GSE137512: Heterogeneity of Brain Metastasis-associated Microglia and Macrophages
Brain metastasis (BrM) represents a challenging clinical issue. The most common treatment options ar...
GSE123127: Transcriptional profiling of dendritic cells in a mouse model of food-antigen induced anaphylaxis using RNA-Seq
We used RNA sequencing to study gene expression in lymph node derived DCs from anaphylactic mice sen...
GSE121883: Essential and non-overlapping IL-2R-dependent signaling for thymic development and peripheral homeostasis of regulatory T cells
IL-2R signaling is essential for regulatory T cell (Treg) function. However, the precise contributio...
GSE125092: Transcriptome Effects of the knockout of Intraflagellar Transport 88 gene in mitral leaflets and in mitral leaflets with mutations in Dzip1
The genes Ift88 and Dzip1 are critical for primary cilium biogenesis, the objective this study was t...
GSE122663: Microglial microRNAs mediate sex-specific responses to tau pathology
Sex is a key modifier of neurological disease outcomes. Microglia are implicated in neurological dis...
GSE125217: RNA-seq of iPSC-ECs treated e-cig liquids with and without nicotine
Two healthy iPSC lines (78 and 273) were differentiated into ECs. iPSC-ECs were then treated with e-...
GSE136071: RNA-expression profiling of LMP1 expressing mouse B cells before and after transformation in vivo
Non-transformed LMP1 expressing mouse B cells or mouse LMP1 lymphomas were analysed by RNA-sequenci...
GSE121857: Identification of Sin3B regulated genes during quiescence
We report differences in gene expression between WT and Sin3B KO T98G cells throughout the cell cycl...
GSE116391 (mouse): Mutations in splicing factor SF3B1 promote transformation through MYC stabilization
Although mutations in the RNA splicing factor SF3B1 are frequently observed in multiple human cancer...
GSE123070: Small Sample-Big Data: Integrative Indexed Systems Biology Reveals Dramatic Molecular Ontogeny over the First Week of Human Life in Papua New Guinea
This study examines the global transcriptomic profiles in peripheral blood of Papua New Guinea newbo...
GSE123779: RNAseq data of WT and Pparg-ablated mouse urothelium under homeostasis and during regneration
Peroxisome Proliferator-Activated Receptor-gamma (PPARG) is a nuclear hormone receptor that was orig...
GSE121966: HuR controls apoptosis and activation response without effects on cytokine 3 UTRs
RNA binding proteins (RBPs) regulate gene expression through several post-transcriptional mechanisms...
GSE112769: Lymphoid Biased Hematopoietic Stem Cells are Maintained with Age and Retain Normal Developmental Potential in the Absence of Inflammatory Stimuli
The hematopoietic stem cell (HSC) compartment includes lymphoid biased (Ly-HSCs) and myeloid biased ...
GSE123134: Linking cell dynamics with coexpression networks to characterize key events in chronic virus infections
The host immune response against an infection requires the coordinated action of many diverse cell s...
GSE121858: Linking YAP to Mller glia quiescence exit in the degenerative retina
Contrasting with fish or amphibian, retinal regeneration from Mller glial cells is largely limited i...
GSE123761: Calorie restriction regulates translation to regulate metabolism in mouse liver
Using next generation sequencing, we report transcripts that are differentially associated in the mo...
GSE125272: Characterization of estrogen and the endocrine-disrupting chemical-induced mouse mammary gland reorganization via single-cell RNA-sequencing
Exposure to estrogen and its mimics during menopausal transition is thought to modify the structure ...
GSE122055: DEGs in the bone marrow of Esr1Nkx2-1Cre females
Disrupting central estrogen signaling exposes a powerful sex-dependent brain-to-bone axis in female ...
GSE115931: Defining multistep cell fate decision pathways during pancreatic development at single-cell resolution
The generation of terminally differentiated cell lineages during organogenesis requires multiple, co...
GSE123044: Quantitative Analysis of Wild Type and Lztr1 +/- Transcriptomes in MEFs (murine embryonic fibroblasts)
The goals of this study are to compare MEFs transcriptome profiling (RNA-seq) from Lztr1 +/+ and +/...
GSE139907: Genome wide gene expression profiling and methylation profiling of directly reprogrammed osteoblasts from mouse fibroblasts
We identified four transcriptional factors, Runx2, Osx, Dlx5, and ATF4, that rapidly and efficiently...
GSE123951: RNA Seq to identify novel transcripts originating from orphan CGIs
To identify novel transcripts originating from orphan CGIs we isolated RNA from undifferentiated emb...
GSE123774: Therapeutic targeting of RNA splicing catalysis through inhibition of protein arginine methylation
RNAseq of samples to identify changes in gene expression upon SRSF2 mutation SOURCE: Diana,HP,Low (d...
GSE112232: Engineering a haematopoietic stem cell niche by reprogramming mesenchymal stromal cells (RNA-Seq)
Haematopoietic stem cells (HSCs) reside in bone marrow (BM) niches where they are maintained to repl...
GSE123039: mRNA expression profile in MHCC-97H-SH-NC And MHCC-97H-SH-UCK2 liver cancer cells
To study the mRNA modulating network and different expressed mRNA lists in MHCC-97H-SH-UCK2 cells, w...
GSE123942: Epigenetic regulation of unique genes and repetitive elements by KRAB zinc finger protein ZFP57 in embryonic stem cells
KRAB-zinc finger proteins (KZFPs) represent one of the largest families of DNA binding proteins in v...
GSE118283: Placenta and uterus transcriptomes from transgenic mice expressing human corticotropin-releasing hormone in placenta
Purpose: Parturition is delayed by approximately 12 hours in transgenic mice expressing human corti...
GSE125324: Embryoid Body-based RNA-seq Analyses Reveal a Potential TBPPA Multifaceted Developmental Toxicity
In this study, we differentiated mouse ESCs via 3D aggregates called embryoid bodies in presence of ...
GSE112176: A Foxp3 mutation drives Th2 effector function in regulatory T cells
Regulatory T (Treg) cells maintain immune tolerance through the action of the master regulator FOXP...
GSE125994: Compare transcriptional profile of AXL knockdown cell and AXL wild type cell
We report the comparative investigation of gene expression profiles between genetic inactivation AXL...
GSE122069: Premature polyadenylation-mediated loss of stathmin-2 is a hallmark of TDP-43-dependent neurodegeneration
Amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) are associated with loss of nu...
GSE111264: A non-canonical BRD9-containing BAF chromatin remodeling complex regulates nave pluripotency in mouse embryonic stem cells
The mammalian BRG1-associated factors (BAF) complex is a multi-subunit chromatin remodeling complex ...
GSE124538: Induction and Therapeutic Targeting of Human NPM1c+ Myeloid Leukemia in the Presence of Autologous Immune System in Mice
Purpose: To understand the molecular mechanisms underlying NPM1c-mediated tumorigenesis by comparing...
GSE122200: PRMT1-Mdm4-p53 pathway controls epicardial invasion and cell fate transition
Epicardial cells are progenitors giving rise to the majority of cardiac fibroblasts, coronary smooth...
GSE122309: Aging-associated patterns in the expression of human endogenous retroviruses
Human endogenous retroviruses (HERV) are relics of ancient retroviral infections in our genome. Most...
GSE113689: Single cell RNAseq of Wild Type and IL27ra KO Tumor infiltrating lymphocytes isolated from B16F10 melanoma batch 3
Expression of co-inhibitory receptors, such as CTLA-4 and PD-1, on effector T cells is a key mechani...
GSE126001: Skeletal muscle transcriptional response to endurance exercise in Il13-deficent mice
RNA-seq analysis of gastrocnemius of control and Il13-deficient mice after 5-weeks of endurance exer...
GSE123773: Hoxb1 LoF RNA-seq
Transcriptomic profiling of second heart field progenitor cells deficient for Hoxb1 in mouse embryos...
GSE136153: RNA-sequencing study on DSS-induced ulcerative colitis in mice of wild type and intestinal epithelial cell-sepific NCoR1 deletion.
Purpose: The goal of this study is to investigate the role of NCoR1 in protecting colon from ulcerat...
GSE121904: Dynamic transcriptome profiles within spermatogonial and spermatocyte populations during postnatal testis maturation revealed by single-cell sequencing
This analysis represents the first comprehensive sampling of germ cells in the developing testis ove...
GSE122635: LRP5 and LRP6 are required for maintaining self-renewal and differentiation of hematopoietic stem cells
The canonical Wnt signaling pathway has been demonstrated as a critical role in the self-renewal, pr...
GSE112842: A system of checks and balances: an ERK-dependent feedback mechanism prevents hematopoietic stem cell exhaustion
Hematopoietic stem cells (HSC) sustain hematopoiesis throughout life, exiting dormancy to replenish ...
GSE111997: Increased lactate dehydrogenase activity is dispensable in squamous carcinoma cells of origin
We sought to determine whether Ldh activity in SCC tumors is a marker of the cell type from which th...
GSE112755: The placental transcriptome in late gestational hypoxia resulting in murine intrauterine growth restriction predicts adult cardiometabolic disease
Intrauterine growth restriction (IUGR) affects up to 10% of pregnancies and often results in short- ...
GSE126332: The transcriptional repressor SNAI2 impairs neuroblastoma differentiation and inhibits response to retinoic acid therapy
Analyses of the effect of CRISPR/CAS9 mediated knock out of the EMT-transcription factor SNAI2 on th...
GSE122033: RNA-Seq analysis identifies pancreatic lncRNAs
Aim: Identification of long noncoding RNAs using transcriptional analysis of e15.5 mouse embryonic p...
GSE122628: CD146+CD45-CD31- pericyte RNA sequencing following an acute bout of electrical stimulation
The objective of this study was to understand the mechanisms by which electrical stimulation in vivo...
GSE129791: Transcriptome profiling of brown adipocytes treated with BML-260, DMSO or ISO for revealing the BML-260 mechanism
To explore BML-260 how to increase thermogenesis, we treated brown adipocytes with BML-260 and DMSO ...
GSE126021: RNAseq Suv39h1 injected single embryo
Suv39h1wt or mut mRNA was injected into the zygote and cultured for the indicated timepoints SOURCE:...
GSE119633: Fibroblast activation protein restrains adipogenic differentiation and regulates matrix-mediated mTOR signaling
Obesity is a risk factor for multiple diseases, including diabetes, cardiovascular disease, and canc...
GSE131122: RNA sequencing analysis of wildtye and Acc2 iKO mice heart in chow and HFD
Here, we show that short term HFD feeding did not change the cardiac function in normal (Con) and in...
GSE122113: Genome-wide analysis of astrocyte XBP1 activation and regulation of transcriptional programs in CNS cells during EAE.
We report XBP1 activation and regulation of pro-inflammatory signaling in astrocytes, microglia, and...
GSE127482: Activin A impacts on the allocation of the epiblast stem cells to the ectoderm lineage
The modulation of TGFb activity is critical for the specification of mesendoderm tissue progenitors ...
GSE122701: Transcriptome analysis of small molecule-mediated astrocyte-to-neuron reprogramming
Human astrocytes can be efficiently reprogrammed into functional neurons in culture by the addition ...
GSE123067: Single-cell RNA-seq of murine thymic Treg cell progenitors and mature Treg cells
We use single-cell RNA-seq to determine distinct selection phenotypes of 2 rare thymic Treg cell pro...
GSE129766: Transcriptome sequencing analysis of LncMyod-knockdown satellite cells by RNA-seq
To understand the effect of LncMyod knockdown on cultured satellite cells, we isolated satellite cel...
GSE123116: Gene expression profile in Liver of 10mo old MANFHet mice
Transcriptome analysis comparing livers of 10 month old MANFHet mice and WT littermates revealed the...
GSE111318: Ribonucleotide excision repair prevents intestinal tumorigenesis
Insufficient repair of DNA lesions results in the acquisition of somatic mutations and displays the ...
GSE121862: A single-nucleus RNA-sequencing pipeline to decipher the molecular anatomy and pathophysiology of human kidneys
Defining cellular and molecular identities within the kidney is necessary to understand its organiza...
GSE122367: Gene expression profiling of basal and luminal epithelial cells from young adult and old mouse prostates
We set out to determine if prostate epithelial cell-types exhibited age-related differences in their...
GSE129818: Next Generation Sequencing Facilitates Quantitative Analysis of Wild Type and FMCD mice Translatomics
We performed rigorous ribosome profiling in FMCD mouse models with human MTOR point mutations. By ob...
GSE121908: RNA-sequencing on Nrn1-/- and Nrn1+/- OTII cells recovered from OVA-peptide induced anergy TCRa-/- host mice
Nrn1-/- and Nrn1+/- Thy1.1+ OTII cells were cotransferred with wt Treg cell into TCRa-/- hosts and s...
GSE116413: Unfolding the inactive X chromosome
The inactive X chromosome (Xi) is folded in a stepwise process into a compartment-less structure. He...
GSE131143: RNAseq of prostate from mice submitted to diets containing different fatty acids profile (pork fat, linseed oil and soybean oil)
To perform mRNA expression analysis through deep sequencing, RNA was isolated from prostate mice tre...
GSE123952: RNA-Sequencing Quantitative Analysis of Mice Wild Type and Tg-ACE (ACE overexpression) Macrophages
In this study we compared transcriptome profiling (RNA-seq) in wild type vs. ACE overexpressiong Tg-...
GSE122271: RNA sequencing of PND55 mammary glands of mice fed 20% ISP, 1% ISP, 20% casein or Teklad 2018
Epidemiologic studies demonstrate that women from cultures that consume high levels of dietary soy h...
GSE122291: Estrogen Signaling in Arcuate Kiss1 Neurons Suppresses a Sex-Dependent Circuit That Promotes Dense Strong Bones in Female Mice
Purpose: To characterize the estrogen receptor (ESR1)-dependent transcriptome of neurons in the arc...
GSE126044: Gene expression features of response to anti-PD-1 immunotherapy in non-small cell lung cancer [RNA-seq]
The purpose of this study is to compare transcriptional profiles of non-small-cell lung cancer betwe...
GSE123372: Chromosome topology shapes neuronal non-CG DNA methylation to influence MeCP2-mediated enhancer repression (RNA-Seq)
The genomes of mammalian neurons contain uniquely high levels of non-CG DNA methylation that can be ...
GSE122067: RNA-seq of Mus musculus: WT and MTCH2 KO Nave & Primed mouse embryonic stem cells
The role of mitochondria dynamics and its molecular regulators remains largely unknown during nave-t...
GSE111301 (mouse): mRNA sequencing of the mouse and human Hep-Orgs, Chol-Orgs and primary hepatocytes
The mammalian liver possesses a remarkable regenerative ability. 1) The 'oval cell' response emanate...
GSE125932 (mouse): Transcriptome analysis of mouse and human sinoatrial node cells reveals a conserved genetic program
Expression analysis of mouse sinoatrial nodes and working cardiomyocytes SOURCE: Vincent,M.,Christof...
GSE127927: Induction of Pluripotency by Alternative Factors (RNA-Seq)
Reprogramming somatic cells to pluripotency represents a paradigm for cell fate determination. A bin...
GSE122303: PolyA-sequencing in Kelly and Kelly E9R neuroblastoma cells treated with THZ531 or DMSO
We performed RNA-seq analsysis of polA transcripts in Kelly and Kelly E9 resistant (E9R) cells treat...
GSE122120: Examination of Glis3 binding and affects on gene expression in mouse pancreas
RNA sequencing of mouse islets from mice containing a pancreas-specific deletion of Glis3, and contr...
GSE74085: N6-methyladenosine Recruits HNRNPG for Alternative Splicing Regulation
Understanding how RNA-binding proteins interact with RNA transcripts for splicing regulation is fund...
GSE112853: Next generation sequencing profiling experimental circulating tumor cells-derived metastatic variants [micro-environment]
Hematogenous metastasis is initiated by a subset of circulating tumor cells (CTCs) shed from primary...
GSE124051: Transcriptome profiling of caspase-2 deficient lymphomas from EMyc and neuroblastomas from Th-MycN mice
The project used next generation sequencing for RNA-seq analysis, to identify transcriptome changes ...
GSE127929: Transcriptional analysis of skeletal muscles from wild type and mdx/mTR mice
We report RNA sequencing data from tibialis anterior muscles of 4 month old male wild type C57Bl/6 m...
GSE122100: Neuronal subtype expression profiles from adult mouse cortex
Neurons were dissociated and purified from adult (~3 months) mouse brains. We used four strains with...
GSE114631: Tumor-resident memory-like CD8 T cells represent an essential cellular target for cancer immunotherapy
Persistent exposure to high levels of antigen results in the progressive exhaustion of T cells and h...
GSE124963: Suppression of oncogenic super enhancers in MYC-dependent AMLs by NR4A Nuclear Receptors
NR4A nuclear receptors are tumor suppressors of acute myeloid leukemia (AML) that are silenced in AM...
GSE111385: Transcriptomes of Tgfbr2 Knockout Microglia and Macrophages
The cytokine transforming growth factor-B (TGF-B) regulates development and homeostasis of several t...
GSE112724: Contrasting stage-dependent requirements during AML evolution identify EZH2 as a therapeutic target in AML
Epigenetic regulators are commonly mutated in cancer. Activating mutations and overexpression of the...
GSE129784: ARID1A and PI3-Kinase pathway mutations in the endometrium drive epithelial transdifferentiation and collective invasion [Mouse_RNA-seq]
ARID1A and PI3-Kinase (PI3K) pathway alterations are common in neoplasms originating from the uterin...
GSE130842: Identification of tissue regulatory T cell precursors in lymphoid organs [bulk RNA-Seq]
Regulatory T (Treg) cells maintain self-tolerance in lymphoid tissues, and specialized Treg cells ac...
GSE123387: A Preformed Chromatin Architecture Ensures Robust Shh Transcription during Limb Development [RNA-Seq]
During embryogenesis, enhancer-promoter interactions control gene transcriptional activation. These ...
GSE121246: RNA-seq data from wildtype, STAT5A-knockout and STAT5B-knockout BCR/ABLp185+ transformed mouse bone marrow cell lines
RNA-Seq of immortalized Stat5a-/-, Stat5b-/-, and wildtype BCR/ABLp185+ cell lines was used to ident...
GSE73458: The whole transcriptome analysis in a replicative senescence model.
RNA-Seq was performed to screen transcripts in whole lyastes or mitoplast fraction prepared from you...
GSE125990: Gene expression profiling of fibroblasts in a family with LMNA-related cardiomyopathy reveals molecular pathways implicated in disease pathogenesis
LMNA mutation caused reduced expression of IGFBP5 in patient samples SOURCE: Trina,M.,Norden-Krichma...
GSE123071: Neural cell adhesion molecule 1 (NCAM1; CD56) promotes leukemogenesis and confers drug resistance in acute myeloid leukemia.
Neural cell adhesion molecule 1 (NCAM1; also known as CD56) is expressed in up to 20% of acute myelo...
GSE120413: RNAseq in protected BAP1 mESc
Malignancies arising from mutation of tumor suppressor genes display an unexplained tissue proclivit...
GSE111394: Oligogenic inheritance of congenital heart disease involving a NKX2-5 modifier [mouse]
Complex genetic inheritance is thought to underlie many human diseases, yet experimental proof of th...