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Sequencing-based assays page 99
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GSE129424: Impact of genome architecture upon the functional activation and repression of Hox regulatory landscapes [RNA-seq]
The spatial organization of the mammalian genome is complex and relies upon the formation of chromat...
GSE141227: Myc-mediated SDHA Acetylation Triggers Epigenetic Regulation of Gene Expression and Tumorigenesis.
Trimethylated H3K4 (H3K4me3), which is often found surrounding the transcriptional start site of act...
GSE140900: Dual blockade of IL-4 and IL-13 with dupilumab, an IL-4Ra antibody, is required to broadly inhibit type 2 inflammation
Background: Dupilumab, a fully human monoclonal antibody that binds IL-4Ra and inhibits signaling of...
GSE152222: Transcriptional changes during astrocyte maturation in vivo at single cell resolution
Analysis of gene expression during striatal astrocyte maturation in vivo in mouse by scRNA-Seq SOURC...
GSE143867: c-Maf restrains T-bet-driven programming of CCR6-negative group 3 innate lymphoid cells
We performed RNA-Seq analysis of small intestinal lamina propria ILC3s of Rorc.Cre Maf.flox and Maf....
GSE140110: Effect of SHP2 inhibition on hepatic stellate cell transcriptome.
Hepatic stellate cell autophagy inhibits extracellular vesicle release to attenuate liver fibrosis.;...
GSE157525: SMARCB1 loss interacts with neuronal differentiation state to block maturation in an organoid model
We conducted 10X single-cell RNA sequencing of control organoids and organoids differentiated with S...
GSE140230: Tacrolimus- and sirolimus-induced human b cell dysfunction is reversible and preventable
We used RNA-seq to investigate transcriptional changes in human islet grafts that were treated in vi...
GSE152167: Integrated Analysis of mRNA-seq and miRNA-seq to Identify c-MYC, YAP1 and miR-3960 as Major Players in the Anticancer Effects of Caffeic Acid Phenethyl ester in Human Small Cell Lung Cancer Cell Line
Small-cell lung cancer H446 cells were treated with CAPE. The regulation mediated by miR-3960 after ...
GSE139092: VE-Cadherin-Mediated Epigenetic Regulation of Endothelial Gene Expression
Rationale: The mechanistic foundation of vascular maturation is still largely unknown. Several human...
GSE141160: Transcriptome profiling of purified red blood cells from Nxf1 mutant and control mice [Erythrocytes]
Purpose: Nxf1 is thought to be an essential nuclear exporter of messenger RNA (mRNA) in eukaryotic c...
GSE137918: Mouse Klf14matKO Placenta mRNA-seq
Bulk, paired-end mRNA seq from matKO and control 17.5dpc placentas SOURCE: Erik Koppes (koppesea@upm...
GSE139119: MicroRNA-431 promotes metastasis of pancreatic neuroendocrine tumors by targeting DAB2IP, a RasGAP tumor suppressor
Analysis of pathways regulated by miR-431 at the mRNA expression levels in pancreatic neuroendocrin...
GSE152183: Single Cell Sequencing Reveals Artifactual Gene Expression in Microglia in Response to Tissue Dissociation
Single Cell Sequencing of FACS purified microglia/myeloid cells isolated with different dissociation...
GSE140201: Integrated transcriptomic analyses identify altered nerve triglycerides in mouse models of prediabetes and type 2 diabetes
We employed high-fat diet (HFD)-induced prediabetes and HFD/streptozotocin (STZ)-induced type 2 diab...
GSE142772: p53 activates the long noncoding RNA Pvt1b to inhibit Myc and suppress tumorigenesis
The tumor suppressor p53 transcriptionally activates target genes to suppress cellular proliferation...
GSE155313: Cocaine induces paradigm-specific changes to the transcriptome within the Ventral Tegmental Area
We found that cocaine alters distinct sets of VTA genes within each exposure paradigm. Using behavio...
GSE140350: Role of CD133 in human embryonic stem cell proliferation and teratoma formation
We knocked out CD133 by CRISPR/Cas9 to analyze the role of CD133 in human embryonic stem cells. SOUR...
GSE138838: Single cell analysis reveals humancytomegalovirusdrives latently infected cells towards an anergic-like monocyte state
Human cytomegalovirus (HCMV) causes a lifelong infection through establishment of latency. Although ...
GSE155379: CRL5-dependent regulation of the small GTPAses ARL4C and ARF6 controls hippocampal morphogenesis
Purpose: Understanding the role of RBX2 during hippocampla development, pyramidal neuron migration a...
GSE140172: High-Throughput Kinetic Analysis of Fractional Killing
Anti-cancer drugs and other lethal agents can induce heterogeneous cell death responses in a populat...
GSE134636: Developmental Dieldrin Exposure Alters DNA Methylation at Genes Related to Dopaminergic Neuron Development and Parkinsons Disease in Mouse Midbrain
Human and animal studies have shown that exposure to the organochlorine pesticide dieldrin is associ...
GSE140922: The identification of differentially expressed genes in granulosa cell specific Cbfb and Runx2 double knockout mice
The removal of RUNX1/2 and CBFb affects the expression of many genes involved in ovulation and CL fo...
GSE140306: RNA sequencing analysis of Purkinje cells differentiating from human pluripotent stem cells
To model human cerebellar disease, we developed a novel, reproducible method to generate cerebellar ...
GSE140385: Transcriptomic analysis of CD34+ progenior cells from normal bone marrow controls and chronic phase chronic myeloid leukemia
Using RNA-sequencing, we report the differences in gene expression between healthy bone marrow and c...
GSE132029: Regulation of enhancer transcription by Spt5 directly couples enhancer activation with enhancer function
Transcription is a ubiquitous feature of active enhancers, yet the regulatory role of enhancer trans...
GSE149031 (human): Che-1/AATF-induced transcriptionally active chromatin promotes cell proliferation in Multiple Myeloma
We have strong evidence on the essential role of Che-1 protein in promoting the proliferation of MM ...
GSE138858: RNA sequencing of BT142 and TS603 cell lines
We report the levels of the transcripts arising from the RNA sequencing analysis of IDH1-mutant cell...
GSE140308: GH induces IL-17A in human podocytes
The growth hormone plays a significant role in normal renal function and overactive growth hormone s...
GSE140936: Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress [RNA-seq_CHK1i]
Schlafen 11 (SLFN11) has recently arisen as a novel cellular restriction factor against replication ...
GSE133187: Comparison of gene expression profiles between wild-type and Kdm7a mutan embryos
Temporal and spatial colinear expression of Hox genes determines the specification of positional ide...
GSE138122: Specific chromatin landscapes and transcription factors couple breast cancer subtype with metastatic relapse to lung or brain [RNAseq]
Breast cancer metastasis is the leading cause of breast cancer-related mortalities in women. Differe...
GSE139159: Induction of a timed metabolic collapse to overcome cancer chemoresistance
We identified a transient increase in metabolites involved in glutamine metabolism in chemoresistant...
GSE140345: Sleep-wake driven and circadian contributions to daily rhythms in gene expression and chromatin accessibility in the murine cortex
We monitored gene expression and chromatin accessibility in the cerebral cortex of 10-12 week-old ma...
GSE146133: Total RNA Sequencing in microglia isolated from N-AS treated APP/PS1 mice
To examine the regulation of microglia by N-AS-triggered SPMs, we analyzed the gene expression patte...
GSE140895: Inducible cell-specific mouse models for paired epigenetic and transcriptomic studies of microglia and astroglia: RNA-Seq Data
Studies of neuroepigenetic mechanisms in health and disease are hindered by a lack of approaches to ...
GSE138760: High resolution and allelic-specific annotation of preimplantation embryo transcriptome using long-read sequencing
We used an combination of long-read and short-read sequencing data to explore the transcriptome of p...
GSE107071: MEF2C phosphorylation is required for chemotherapy resistance in acute myeloid leukemia [inhibitor MRT199665]
In acute myeloid leukemia, chemotherapy resistance remains prevalent and poorly understood. Using fu...
GSE140282: Transcriptome analysis of dark zone (DZ) and light zone (LZ) compartments of Wild type (WT) and SykY317F mice
Analysis of DZ and LZ compartments in the germinal center of WT and SykY317F mice revealed that Syk ...
GSE132263: Whole lung transcriptomics of a house dust mite model of mild/moderate asthma
Purpose: Identify whole lung gene expression patterns in a house dust mite model of mild/moderate a...
GSE145005: Determining transcriptome changes in whole spinal cord of YarsE196K mice [19-burgess-002]
To determine transcriptome changes in adult spinal cord induced by the YarsE196K mutation.; How muta...
GSE140872: Integrative QTL analysis of gene expression and chromatin accessibility identifies multi-tissue patterns of genetic regulation (RNA-seq)
Gene transcription profiles across tissues are largely defined by the activity of regulatory element...
GSE143790: Gene expression in DCIS.COM with BCL9 knockdown
There is limited research on which specific Wnt targets are regulated by B-Cell Lymphoma-9 (BCL9) an...
GSE132072: RNA-Seq analysis of MIN6 cells following control KD or Paupar KD
Aim:Transcriptional analysis of the MIN6 beta cell line following control or Paupar lncRNA KD to ide...
GSE132033: Tox reinforces the phenotype and longevity of dysfunctional T cell populations during chronic viral infection [WT vs KO +/- Tim3]
Chronic CD8 T-cell stimulation in persisting infections or tumors can induce a stable gene expressio...
GSE139169: RUNX2/CBFB modulates the response to MEK inhibitors through activation of receptor tyrosine kinases in KRAS mutant colorectal cancer
Investigation of the transcriptional consequences of RUNX2 and CBFB loss in the presence and absence...
GSE140289: RNA seq of mammary epithelial cells with loss-of-function Pten mutations
The PTEN tumor suppressor controls cell death and survival by regulating functions of various molecu...
GSE145022: Combined deletion of Bap1, Nf2, and Cdkn2ab causes rapid onset of malignant mesothelioma in mice
Here we describe a mouse model of mesothelioma with combined deletion of Bap1, Nf2, and Cdkn2ab that...
GSE132942: Gene expression profiling of Eomes/ and Wild Type Murine NK cells
Gene expression profiling of Eomes/ and Wild Type Murine NK cells sorted into specific maturaion sta...
GSE139079: Single-cell RNA sequencing of human fallopian tubes from benign donors
The inter-differentiation between cell states promotes cancer cell survival under stress and fosters...
GSE143812: RNA seq analysis of primary tumors and metastases from the NPK (Nkx3.1CreERT2/+; Ptenflox/flox; KrasLSL-G12D/+; R26R-CAG-LSL-EYFP/+) prostate cancer mouse model
Transcriptome analysis of lineage-marked prostate primary tumors and metastases from the NPK mouse m...
GSE139134: Transcriptomic profiling of LPS-induced adrenal inflammation in sorted adrenal endothelial cells from C576L6 mice
Altogether, this is the first study presenting the global changes of the transcriptome in the adrena...
GSE141205: GM-CSF controls Mycobacterium tuberculosis infection by limiting type I IFN-driven neutrophil extracellular trap formation [Lung]
Tuberculosis (TB) remains the worlds top infectious killer. Understanding how immune mediators deter...
GSE139451: The effect of beta-glucan - induced trained immunity on the transcriptomic profile of tumor-associated monocytes
Induction of trained immunity by beta-glucan has been shown to promote transcriptomic alterations in...
GSE140304: DNMT3A Reads and Connects Histone H3K36me2 to DNA methylation [RNA-seq]
DNA methylation at the 5-position of cytosine (5mC) is a crucial epigenetic mark in regulating biolo...
GSE139171: CD4 T cell response in AKI
CD4+ T cells mediate the pathogenesis of ischemic and nephrotoxic acute kidney injury (AKI), as well...
GSE134795: Nucleosomes protect DNA from irradiation-induced double strand breaks in living cells (RNA-seq)
The depletion of HMGB1 reduces the deposition of histones on naked DNA (Celona et al, 2011). in prim...
GSE152181: Reduced left atrial cardiomyocyte PITX2 and elevated circulating BMP10 predict atrial fibrillation after ablation
Background: Genomic and experimental studies suggest a role for PITX2 in atrial fibrillation (AF). T...
GSE140892: Innate immune function of galectin-1 as a DAMP
Galectin-1 is a prototype member of the galectin family of b-galactoside-binding proteins with sever...
GSE140363: Defining the relative and combined contribution of CTCF and CTCFL to genomic regulation
We analyzed the impact of CTCFL and CTCF-CTCFL fusion proteins in the presence and absence of CTCF t...
GSE134846: An insulin-stimulated proteolytic mechanism links energy expenditure with glucose uptake
Mechanisms to coordinately regulate oxidative metabolism and glucose transport into cells are not we...
GSE138863: Effect of disulfiram treatment on pediatric high grade glioma
RNA-seq analysis was performed to compare gene expression between glioma cells treated with disulfir...
GSE139469: Comparative genome-wide analysis of whole skin from mice vaccinated with E7SH/ISG15-GG versus E7SH/EV
Purpose: To understand the mechanistic basis of the adjuvant role of extracellular ISG15 to support ...
GSE132056: Removing a Double Bond from Ceramides Ameliorates Insulin Resistance and Hepatic Steatosis
Ceramides contribute to the lipotoxicity that underlies diabetes, hepatic steatosis, and heart disea...
GSE132731: Temporo-spatial distribution and transcriptional profile of retinal microglia in the oxygen-induced retinopathy mouse model
Myeloid cells such as resident retinal microglia or infiltrating blood-derived macrophages accumulat...
GSE130904: Loss of the epigenetic modifierSetd2and H3K36me3 impairs non-homologous end-joining in lymphogenesis and neurogenesis
The resolution and repair of DNA double stranded breaks (DSB) in normal, early lymphocyte and post- ...
GSE138884: Discrimination of dormant and active hematopoietic stem cells by G0 markers reveals dormancy regulation by cytoplasmic calcium
High-throughput small molecule screening revealed that high concentrations of cytoplasmic calcium (...
GSE139450: The effect of beta-glucan - induced trained immunity on the transcriptomic profile of tumor-associated neutrophils (TAN)
Induction of trained immunity by beta-glucan has been shown to promote transcriptomic alterations in...
GSE140101: RNA-seq analysis of HD and MDS MSCs and MSC-conditioned monocytes
Altered bone marrow hematopoiesis and immune suppression is a hallmark of myelodysplastic syndrome (...
GSE140378: RNAseq analysis of 8week old islets from murine Abca12 KO pancreas
The goal of this study was to identify changes in the transcriptome that occur following Abca12 gene...
GSE138911: YAP and TAZ protect against white adipocyte cell death during obesity
Investigation of the effect of YAP/TAZ on white adipocyte survival during obesity SOURCE: Stefan Gün...
GSE139668: Gene Expression Analysis of WT and dnTCF4-expressing Short-Term Hematopoietic Stem Cells (ST-HSC)
The canonical Wnt signaling pathway is mediated by interaction of b-catenin with the TCF/LEF transcr...
GSE140357: Transcriptome anaylisis of WT and GFAT-1 G451E engineered N2a cells by RNA-Seq
Transcriptome of N2a cells carrying a GFAT-1 gain-of-function point mutation that results in a G451E...
GSE143211: Geminin is required for Hox gene regulation to pattern the developing limb
Development of the complex structure of the vertebrate limb requires carefully orchestrated interact...
GSE139461: Selective Mediator-dependence of cell type-specifying transcription [Quant-Seq]
The Mediator complex directs signals from DNA-binding transcription factors to RNA polymerase (Pol) ...
GSE141433: Type II but not type I interferon signaling is indispensable for TLR7-promoted development of autoreactive B cells and systemic autoimmunity
The gene transcripts in splenic tissues derived from imiquimod treated B6.Sle1b and B6.Sle1b.IFNgR-/...
GSE139508: MeCP2 represses the rate of transcriptional initiation of highly methylated long genes (RNA-Seq II)
Mutations in the methyl-DNA-binding repressor protein MeCP2 cause the devastating neurodevelopmental...
GSE130957: Primitive endoderm stem cell lines in mice
A blastocyst consists of three distinctive cell types: epiblast (EPI), trophoblast (TB), and primiti...
GSE138924: Differential contribution of p300 and CBP to regulatory elements in mESCs [RNA-seq]
In this study we analyze the individual contribution of p300 and CBP to the H3K27ac landscape, chrom...
GSE140956 (mouse): The Msi1-mTOR pathway drives the pathogenesis of Paget's disease
We report the single cell transcriptomes of normal and Extramammary Paget Disease (EMPD) human scrot...
GSE139193: Human iPSC-derived microglia assume a primary microglia-like state after transplantation into the neonatal mouse brain [Single Cell RNAseq]
iPSC derived microglial precursors were tranplanted into the brains of neonatal mice, FACS sorted ou...
GSE141239: Biological significance of CDYL in endometrial receptivity
Impaired endometrial receptivity is one of the major causes of recurrent implantation failure (RIF),...
GSE140377: RNAseq analysis of 5week old islets from murine Abca12 KO pancreas
The goal of this study was to identify changes in the transcriptome that occur following Abca12 gene...
GSE138903: Bulk RNA-seq of mouse embryonic progenitor cells
Population RNA-Seq analysis shows distinct gene expression profiles in specification of Nkx2-1+ endo...
GSE140937: Chromatin Remodeling and Immediate Early Gene Activation by SLFN11 in Response to Replication Stress [RNA-seq_CPT]
Schlafen 11 (SLFN11) has recently arisen as a novel cellular restriction factor against replication ...
GSE110268 (human): Upregulation of FOXD1 by YAP alleviates senescence and osteoarthritis
Cell senescence is a driver of various aging-associated disorders including osteoarthritis. Here, we...
GSE145286: Synovial fibroblast positional identity controlled by inductive Notch signaling underlies pathologic damage in inflammatory arthritis
Effect of Notch3 perturbation on healthy and arthritic mouse synovium. SOURCE: Ilya Korsunsky (ikors...
GSE130979: CCL21 Expression in Beta Cells Induces Antigen-Expressing Stromal Cell Networks in the Pancreas and Prevents Autoimmune Diabetes in Mice
Tumors induce tolerance towards their antigens by producing the chemokine CCL21, leading to the form...
GSE138774: RNA-seq analysis using glomeruli isolated from control and podocyte-specific bPIX deficient mice
We found that podocyte-specific bPIX deficient (KO) mice developed progressive proteinuria starting ...
GSE131082: Cell-type specific action of Bcl11b in early T-lineage and group 2 innate lymphoid cell
The zinc finger transcription factor, Bcl11b, is expressed in T cells and group 2 innate lymphoid ce...
GSE140956 (human): The Msi1-mTOR pathway drives the pathogenesis of Paget's disease
We report the single cell transcriptomes of normal and Extramammary Paget Disease (EMPD) human scrot...
GSE139135: Molecular characterization of BRSK2 and BRSK1 kinases as negative regulators of the NRF2 transcription factor
We found that the understudied Brain Specific Kinase 2 and 1 (BRSK2/1) proteins suppress NRF2-depend...
GSE131060: The histone deacetylase complex MiDAC regulates a neurodevelopmental gene expression to control neurite outgrowth [RNA-Seq]
Cell type diversity during neuro-ectodermal (NE) differentiation is achieved through selective activ...
GSE132898: Diploid genome architecture revealed by multi-omic data of hybrid mice
While mammalian genomes are diploid, previous studies extensively investigated the average chromatin...
GSE139150: A transcriptional toolbox for exploring peripheral neuro-immune interactions
Correct communication between immune cells and peripheral neurons is crucial for the protection of o...
GSE145263: RNA sequencing of cardiac endothelial cells from the cardiovascular disease risk factor mouse models
Purpose: Our objective is to profile and compare the cardiac endothelial cell transcriptome, identif...
GSE140929: Colibactin causes genomic instability and promotes Wnt independence in primary colon epithelial cells
Colorectal cancer is driven by a sequential cascade of mutations known as the adenoma-carcinoma sequ...
GSE141171: Genome-wide CRISPR screen Identifies Host Dependency Factors for Influenza A Virus Infection
In this study, we performed a genome-wide CRISPR screen in A549 cells to identify host genes that ar...
GSE138937: Effect of CTCF and Rad21 knockdown on SLK cells and KSHV gene expression
CTCF and the cohesin complex modify chromatin by binding to DNA and interacting with each other and ...
GSE140965: Transcriptome study of MYBPC3 loss of function mutations
Induced pluripotent stem cells were gene edited to introduce heterozygous (promoter deletion, start ...