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Sequencing-based assays page 64
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GSE111894: Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer [scRNA-seq]
High numbers of tissue-resident memory T (TRM) cells have been associated with better clinical outco...
GSE110577: Notch signaling facilitates in vitro generation of cross-presenting classical dendritic cells
The IRF8-dependent subset of classical dendritic cells (cDC), termed cDC1, is important for cross-pr...
GSE102685: Next Generation Sequencing Facilitates Quantitative Analysis of Control and FoxM1-knockdown C2C12 Transcriptomes
Purpose:To identify FoxM1-dependent genes and the molecular pathways involved in the regulation of m...
GSE112641: Comparative Transcriptomics of STR/ort, C57BL/6 and MRL/MpJ Knee Joints
Injuries to the anterior cruciate ligament (ACL) often result in post-traumatic osteoarthritis (PTOA...
GSE109285: Pancreatic Islet-Autonomous Signals Modulate Identity Changes of Glucagon+ -Cells
The mechanisms restricting regeneration and maintaining cell identity upon injury are poorly charact...
GSE116250: RNA-seq of heart failure in human left ventricles
The goal of this dataset was to use RNA-seq in human heart tissue to delineate etiology-specific gen...
GSE104238: Comparison of RNA expression of conditional Nmi knockout mammary epithelial cells to the wildtype control
The goal of this study was to compare mRNA from mammary epithelial cells of 3 mammary-specific Nmi k...
GSE109788: Expression profiling analysis to identify POH1-regulated genes
This work determined the POH1 regulated genes in the absence or presence of TGF- in SMMC-7721 cells ...
GSE111029: Gene expression analysis in mouse mature T-cells either upon overexpression of the NICD or knockout of H2A.Z
Genes induced by the Notch-Intracellular domain (NICD) in mouse mature T-cells (MT) are identifed. A...
GSE102688: Structural and mechanistic insights into ATRX-dependent and independent functions of the histone chaperone DAXX [RNA-seq]
The histone variant H3.3 is incorporated in a replication-independent manner at heterochromatic regi...
GSE110380: Proximity-CLIP provides a snapshot of occupied cis-acting elements on RNA in different subcellular compartments on a transcriptome-wide scale
Many cellular RNAs localize to specific subcellular compartments. Currently, methods to systematical...
GSE100934: Whole transcriptome sequencing of mouse notochord-derived cells at developmental stages E12.5 and P0
Recapitulation of developmental signals represents a promising strategy for treating intervertebral ...
GSE110708: Cytokine Stimulation of ADAR-deleted B16 murine melanoma cells
ADAR was deleted from the B16 murine melanoma line using CRISPR/Cas9. The loss-of-function phenotype...
GSE111904: Osmostress induced changes of chromatin architecture and transcription in mammalian cells [RNA-Seq, HiC]
Osmostress causes chromatin compaction and simultaneously triggers a massive transcriptional respons...
GSE113162: The miR-200b/200a/429 cluster prevents metastasis and induces dormancy in murine claudin-low mammary tumor cells
The miR-200 family of microRNAs consisting of miR-141, miR-200a, miR-200b, miR-200c and miR-429 are ...
GSE118271: RNA-seq analysis of paired kidney-infiltrating and splenic T cells in the MRL/lpr murine model of systemic lupus erythematosus.
Purpose: The goal of this study is to compare the transcriptional phenotype of lymphoid and kidney-i...
GSE110703: Uncoupling of transcription and cytodifferentiation in mouse spermatocytes with impaired meiosis
We use the cytologically well-defined Prdm9 mutant mouse as a model of developmental arrest to demon...
GSE109844 (mouse): The expression profiles of CD4low(HLA-G+) T cells
The aim of the dataset was to demonstrate that CD4low T cells were murine homolog of CD4lowHLA-G+ T ...
GSE112677: EZH2-mediated primary cilium deconstruction drives metastatic melanoma formation
Human melanomas frequently harbor amplifications of EZH2. However, the oncogenic contribution of thi...
GSE138806: Oncogenic changes and EMT in normal human bile duct epithelial cells are caused by parasite-derived materials and N-nitrosodimethylamine
A total of 1,301 differentially expressed genes were identified: 521 upregulated and 780 downregulat...
GSE111039: Maternal Plag1 deficiency delays two-cell stage embryo development and embryonic genome activation [Embryos]
Pleomorphic adenoma gene 1 (PLAG1) encodes a transcription factor involved in cancer and growth. We ...
GSE115618: Comparison of global gene expression in homeostatic and regenerating endothelium of the adult mouse aorta
We report the global transcript levels in an endothelial-enriched cell fraction from homeostatic and...
GSE100958: rahu is a mutant allele of Dnmt3c, encoding a DNA methyltransferase homolog required for meiosis and transposon repression in the mouse male germline [RNA-seq]
Transcriptional silencing by heritable cytosine-5 methylation is an ancient strategy to repress tran...
GSE101909: Fgf8 signaling alters the osteogenic cell fate in anterior hard palate
FGF signaling has been implicated in the regulation of osteogenesis in both intramembranous and endo...
GSE111071: Comparative Transcriptome analysis of hESCs- and iPSCs-derived lentoid body
Purpose: To investigate the transcriptomes of H9 human embryonic stem cells (hESCs)- and peripheral ...
GSE113179: Dysregulation of p53-RBM25-mediated circAMOTL1L biogenesis contributes to prostate cancer progression (RNA-seq data set)
To clarify the effect of p53 on RBP gene expression, we knocked out p53 gene in PC3 cells to generat...
GSE103400: RNA sequncing of HCN3+ urinary tract pacemaker cells
Purpose: to analyze the mRNA content of highly purified HCN3+ urinary tract pacemaker cells compared...
GSE153368: YB-1 inhibits proliferation of mesothelioma cells through multiple mechanisms
Here we utilized an unbiased whole RNA-seq approach to characterize the transcriptional effects of Y...
GSE101097: A regulatory circuitry between the Gria2 mRNA and miR-409/miR-495 is altered in mESC-derived motor neurons carrying an ALS-associated FUS mutation
Mutations in FUS/TLS have been genetically associated to Amyotrophic Lateral Sclerosis (ALS). Since...
GSE83518: Gene profiling of human adult and pediatric liver cancer cells
In an effort to comprehend some of the molecular differences between two cancers that originate in t...
GSE110749: Dimethyl itaconate inhibits secondary wave of NF-B signaling in macrophage activation
Natural metabolite itaconate and its membrane permeable derivative dimethyl itaconate (DI) selective...
GSE111102: Transcriptional analysis of PPARgamma activation in control and PPARgamma null macrophages [RNA-seq]
The nuclear receptor Peroxisome Proliferator Activated Receptor gamma (PPARgamma) is known to regula...
GSE110680: Inhibiting WNT and NOTCH in renal cancer stem cells: implications for human patients
We detected and characterized CXCR4+MET+CD44+ cancer stem cells (CSCs) that were quantitatively corr...
GSE111097: Transcriptome analysis of infected and uninfected mice with Citrobacter rodentium
Transcriptome analysis of infected and uninfected mice with Citrobacter rodentium SOURCE: Maxim,Niko...
GSE130975: RNA seq on SP specific CD8+ T cells, Ly49+ and Ly49-CD8+ T cells from MOG and MOG + SP immunized mice [RNA-Seq]
In experimental autoimmune encephalomyelitis (EAE), a model for multiple sclerosis (MS), induction g...
GSE100679: A New Family of Vertebrate Specific Polycomb Proteins Encoded by the LCOR and LCORL Gene Loci Reveal Antagonism Between PRC2 Subtypes
The Polycomb Repressive Complex 2 (PRC2) is composed of core subunits SUZ12, EED, RBBP4/7 and EZH1/2...
GSE65185: RNAseq changes in pre MAPKi treatment and post MAPKi resistance Melanomas
Melanoma resistance to MAPK- or T cell checkpoint-targeted therapies represents a major clinical cha...
GSE111163: Large-scale expansion of human iPSC-derived skeletal muscle cells for disease modeling and cell-based therapeutic strategies
Although skeletal muscle cells can be generated from human iPSCs, transgene-free protocols include o...
GSE102748: Gene expression profiling during active Lyme arthritis development (22 days post infection with B. burgdorferi) in CD45 negative cells isolated from joint tissue of highly genetically similar mouse strains: B6, ISRCL4, and ISRCL3
Previously, using a forward genetic approach we identified B. burgdorferi arthritis-associated locus...
GSE118928: Transcriptional profiling of healthy, eutopic and ectopic endometrial organoids
We performed RNA-seq on RNA samples of organoids derived from healthy, eutopic (endometrium of patie...
GSE110374: Ribotag analysis of proprioceptive dorsal root ganglion neurons in cell culture
We analyzed ribosome-associated RNA (raRNA) in dorsal root ganglion neurons in TrkC+ proprioceptive ...
GSE114702: Social Interaction-induced Activation of RNA Splicing in the Amygdala of Microbiome-Deficient Mice
Social behaviour is regulated by activity of host-associated microbiota across multiple species. How...
GSE111892: Single-cell transcriptomic analysis of tissue resident memory T cells in human lung cancer [ bulk RNA-seq]
High numbers of tissue-resident memory T (TRM) cells have been associated with better clinical outco...
GSE110791: Comparison of single hWJSCs and hBMMSCs
The Whartons jelly of the human umbilical cord contains a population of mesenchymal stem cells that ...
GSE102271: Expression analysis of melanocyte stem cells from Mitfmi-vga9/+ mice reveals a role for MITF in the transcriptional regulation of innate immune gene expression
Melanocyte stem cells (McSCs) and mouse models of hair graying serve as useful systems to uncover me...
GSE121029: Stabilizing Heterochromatin by DGCR8 Alleviates Senescence and Osteoarthritis (RNA-seq)
DiGeorge syndrome critical region 8 (DGCR8) is a critical component of the canonical microprocessor ...
GSE111697: Loss of TET2 results in gene expression represssion in mouse GC B-cells and lymphoma cells (RNA-Seq data set)
Absence of Tet2 at mouse cells results in reduced gene expression SOURCE: Sheng LiLi Lab The Jackson...
GSE114668: Intestinal and thymic tuft cell RNA-seq
The goal of the study was to sequence mRNA from tuft cells (identified as CD45-;EpCAM+;IL-25+ using ...
GSE111779: Quantitative Analysis of Follicular Helper T cell Transcriptomes from Wild Type and Apoe-/-
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular path...
GSE110748: In utero exposure to diesel exhaust particulates is associated with alterations of the neonatal cardiomyocyte transcriptome, metabolic parturbation and a global decrease in DNA methylation. [RNA-Seq]
Developmental exposure to particulate matter air pollution is harmful to cardiovascular health, but ...
GSE118842: Description of transcriptome in non-small cell lung cancer cell lines without KEAP1/NRF2 mutations in response to an electrophilic reagent dimethylmaleate (DEM)
We report DEM-induced changes in the transcriptome of ABC1 and HCC4006 cell lines. SOURCE: Hozumi Mo...
GSE114164: Transcriptome analysis of nascent hematopoietic cells
During ontogeny, hematopoietic stem cells (HSCs) and erythroid-myeloid progenitors (EMPs) are genera...
GSE101239: Next Generation Sequencing Facilitates Quantitative Analysis of Transcriptomes of neural stem/progenitor cells (NS/PCs) in control and prenatal valproic acid (VPA) exposed mice with or without voluntary exercise
Purpose: The goals of this study are to investigate the effect of prenatal VPA exposure on transcrip...
GSE101398: Retinal vein occlusion induced by laser treatment in mice
Purpose: Several animal models are available for investigating retinal vein occlusion (RVO). Laser-i...
GSE110731: Epigenetic dysregulation of enhancers in neurons is associated with Alzheimers disease pathology and cognitive symptoms (RNA-Seq)
Epigenetic control of enhancers alters neuron functions and may be involved in Alzheimers disease (A...
GSE111831: The transcriptomic profile of stem-cell derived neurons in 3D culture conditions and stem-cell derived astrocytic cells
Understanding neurological diseases requires tractable genetic systems. Three-dimensional (3D) neura...
GSE101906: High-fat diet exposure, regardless of the induction of obesity, is associated with altered expression of genes critical for normal ovarian function
High-fat diet (HFD) induces diminished ovarian reserve and subfertility in female mice, irrespective...
GSE109085: Epigenetic evolution and lineage histories of chronic lymphocytic leukemia
Genetic and epigenetic intra-tumoral heterogeneity cooperate to shape the evolutionary course of can...
GSE111201: IKZF1 as a Master Regulator of Immune Infiltrate Recruitment in Solid Tumors
Regulatory network analysis of TCGA tumor cohorts to identify MR-based susceptibility to immune infi...
GSE109163: Derivation and Characterization of a UCP1 Reporter Human ES Cell Line
Interest in human brown fat as a novel therapeutic target to tackle the growing obesity and diabetes...
GSE101340: Transcriptomic profiles of CD4+ T lymphocytes from RhoA wild type (WT) and RhoA G17V mice were generated by deep sequencing in duplicate, using Illumina poly-A RNA seq.
The goal of this study is to identify transcriptomic effects of RhoA G17V expression in mouse CD4+ T...
GSE110451: Profiling in vivo Bone Lesion (IVBL) and Orthotopic tumors by Next Generation Sequencing
Based on RNA-seq, we performed transcriptomic profiling to examine the differences between Orthotopi...
GSE114637: Transcription differences in DLBCL cell lines U2932, DOHH2 on treatment with TK compound compared to DMSO
These experiments were designed to investigate the effectiveness of TK compound in treating DLBCL. E...
GSE111078: Cell non-autonomous regulation of chromosome segregation
Chromosome segregation has been assumed to be a cell-autonomous process. We tested this assumption b...
GSE112358: The mediator subunit Med23 serves as a gatekeeper of the myeloid-primed state of hematopoietic stem cells (RNA-Seq)
To ensure the rapid response to stimuli, some HSCs are specifically prepared (primed) for tasks invo...
GSE112634: A network of noncoding regulatory RNAs acts in the mammalian brain II
Noncoding RNAs (ncRNAs) play increasingly appreciated gene-regulatory roles. Here, we describe a reg...
GSE112595: Pyruvate dehydrogenase kinase is a metabolic checkpoint for polarization of macrophages to the M1 phenotype
Metabolic reprogramming during macrophage polarization supports the effector functions of these cell...
GSE112043: Allele-specific RNA-seq in Smchd1 control and Smchd1 deleted female neural stem cells.
We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conform...
GSE109190: An RNA-centric dissection of host complexes controlling flavivirus infection [RNA-Seq]
Flaviviruses including dengue virus (DENV) and Zika virus (ZIKV) cause significant human disease. Co...
GSE101336: RNA-seq in KPC mice treated with a hypomethylating drug (decitabine) and in untreated KPC mice
Background: Treatment with single-agent decitabine (5aza-dC; DAC), a well-tolerated DNA hypomethylat...
GSE108388: Systematic functional characterization of BAF mutations yields novel intra-complex synthetic lethalities [RNA-Seq]
Here we develop and characterize an isogenic cell line model consisting of knock-out clones for 22 t...
GSE130575: POSH2 Promotes Breast Cancer Stem-Like Properties through JNK Activation and PTX3 Upregulation [HMLER_sublines]
We conduct transcriptome comparison of HMLER-derived CD44H,CD44LS and CD44L subpopulation cells to g...
GSE111178: Cytoplasmic NPM1 maintains the leukemic state through HOX expression [RNA-seq]
NPM1 is the most frequently mutated gene in cytogenetically normal acute myeloid leukemia (AML). In ...
GSE112732: Genome-wide transcriptional analysis of human patterned induced neurons (hpiNs)
We report that combining NGN2 programming with SMAD and WNT inhibition generates patterned induced n...
GSE111348: RNA-sequencing of Adult Mouse Inner Hair Cells and Outer Hair Cells of the organ of Corti
To further understand the biological properties of hair cells of the mammalian cochlea, we examined ...
GSE112694: RNA-seq analysis of osteogenic differentiating mouse wild type (WT) and Zfp384 (Nmp4) knockout mesenchymal stem/progenitor cells (MSPCs)
A goal of osteoporosis therapy is to restore lost bone with structurally sound tissue. Mice lacking ...
GSE138234: Gtf2i and Gtf2ird1 E13.5 whole brain ChIP-seq and RNA-seq
HetxHet breeding pairs for the Gtf2i/Gtf2ird1 double mutants and Gtf2ird1 were set up for timed bree...
GSE112153: Ldb1 mediates trans enhancement in mammals
The monoallelic expression of olfactory receptor (OR) genes is governed by a large number of interge...
GSE101930: Tissue-resident PDGFR stromal cells modulate both fibrosis and tissue revascularization during wound repair
PDGFR+ cells are interstitial/perivascular mesenchymal progenitor cells that have been associated wi...
GSE101682: HDAC1 and HDAC2 regulates TGF-b during Endothelial-to-Hematopoietic Transition [RNA-Seq]
The first hematopoietic stem cells originate from hemogenic endothelium (HE), that trans-differentia...
GSE110810: RNA sequencing Facilitates Quantitative Analysis of luminal breast cancer cells and basal breast cancer cells Transcriptomes
We conduct transcriptome comparison of lumianl breast cancer cells and basal cells to gain genomic i...
GSE117711: Differential gene expression of TLR7 overexpressing inflammatory hemophagocytes, Ly6Chi Monocytes, and Red Pulp Macrophages
We have defined a novel population of monocyte-derived hemophagocytes (inflammatory hemophagocytes (...
GSE111203: Effect of Polybrominated diphenyl ethers (PBDEs) on gene expression of MCF7 cells
RNA sequence analysis showed that PBDE47 had estrogenic activity through cell cycle regulation, and ...
GSE109345: Uncovering a Predictive Molecular Signature for the Onset of NASH-Related Fibrosis in a Translational NASH Mouse Model
SUMMARY: This article presents a predictive molecular signature that marks the early onset of fibros...
GSE110935 (mouse): The role of CFTR in islet function
Cystic fibrosis (CF)-related diabetes (CFRD) is an increasingly common and devastating comorbidity o...
GSE102123: Expression of receptors for inflammatory mediators in murine vagal nodose versus jugular capsaicin-sensitive (Trpv1-positive) C-fiber neurons
Capsaicin-sensitive (Trpv1-positive) sensory C-fibers derived from vagal ganglia innervate the visce...
GSE110434: Genome wide gene expression profiling demonstrated that mouse ESC and iPSC differentiated osteoblast progenitors resemble osteoblasts
We differentiated mouse Col2.3 GFP ESCs and iPSCs to osteoblast progenitors and confirmed the osteob...
GSE110826: Human iPSC-derived cells and microengineered Organ-Chip enhance neural development.
We show neural enhancement and induction of vascular interaction genes in iPSC-derived spinal motor ...
GSE113143: LncRNA-directed Antigenicity Loss Suppresses Immunosurveillance
Expression profiles of mouse breast cancer tissues and mammary gland tissues. SOURCE: Youqiong Ye (y...
GSE103967: Large-scale single cell mapping of the thymic stroma identifies a new thymic epithelial cell lineage [single-cell RNA-seq]
T cell development and selection is orchestrated in the thymus by a specialized niche of diverse str...
GSE113098: Functional separation of IL7R/KLRG1-defined CD8+ T cell populations in humans
During acute viral infections in mice, IL-7R and KLRG1 together are used to distinguish the short-li...
GSE103053: Long-Range Enhancer Interactions Are Prevalent in Mouse Embryonic Stem Cells and Are Reorganized upon Pluripotent State Transition
Transcriptional enhancers, including super-enhancers (SE), form physical interactions with promoters...
GSE119669: Generation of induced neural stem cells from urine derived cells by synthetic mRNA
Analysis of induced neural stem cells from urine derived cells by synthetic mRNA vs. H9 embryonic st...
GSE113107: Differential responses by human respiratory epithelial cell lines to respiratory syncytial virus reflect distinct patterns of infection control
We compared constitutive gene expression between two respiratory epithelial cell lines SOURCE: Sijun...
GSE110802: High-throughput profiling of mRNA from parental and Enzalutamide resistant C4-2b prostate cancer cell lines
We established an enzalutamide-resistant C4-2b prostate cell line that has an active androgen recept...
GSE129575: Defining genetic variation in widely used congenic and backcrossed mouse models reveals varied regulation of genes important for immune responses [RNA-seq]
In our study, we developed an alternative next-generation sequencing dataset processing strategy to ...
GSE111949: Differential expression analysis from MV4-11 cells treated with or without APTO-253 for 6 hours.
RNA-seq and differential gene expression analysis were used to detect specific genes and pathways ei...
GSE111345: RNA-seq analysis of RALD iPSCs after in vitro differentiation
We investigated roles of KRAS on stemness maintenance and differentiation propensity in the context ...
GSE110459: Identification of transcriptional targets of FGF20.
Fgf20 is expressed from the hair follicle placode and is required for development of the dermal cond...
GSE116984: Genome-wide maps in MCF-7 cells with six2 or CYP4Z1 3'UTR or CYP4Z2P 3'UTR overexpression or not
Analysis of MCF-7 cells following six2 or CYP4Z1 3'UTR or CYP4Z2P 3'UTR overexpression. Overexpress...