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Sequencing-based assays (Page 61)
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GSE129037: Uncoupling histone H3K4 trimethylation from developmental gene expression via an epigenetic equilibrium of Polycomb, COMPASS and DNA methylation
The COMPASS family catalyzes histone H3 lysine 4 (H3K4) methylation and its members are essential fo...
GSE111603: Defects in the alternative splicing-dependent regulation of REST cause deafness - [mouse cultured organ of Corti].
The DNA-binding protein REST forms complexes with histone deacetylases (HDACs) to repress neuronal g...
GSE110879: RNA-seq gene expression profiling of livers from wild-type male and female mice, and from mice with a Double Knockout (DKO) of Ezh1 and Ezh2.
PolyA-selected RNA isolated from livers of adult male and female mice with a combined loss of EZH1 a...
GSE116982: Cancer associated mutants of eIF1A impair Rps3/Rps10 binding and enhance scanning of cell cycle genes [Mars-seq]
The Ribo-seq analysis demonstrated that eIF1A is predominantly essential for translation of genes wi...
GSE104873: RNA Seq of Alagille liver biopsies
Needle biopsies were performed to obtain liver samples from patients for clinical purposes from pati...
GSE104530: Endothelial Transcriptome Remodeling in a Mouse Model of Chronic Hypertension
Aims: Hypertension poses a significant challenge to vasculature homeostasis and stands as the most c...
GSE107131: U1 snRNP regulates chromatin retention of noncoding RNAs
RNA subcellular localization often correlates with its function and regulation. For many long noncod...
GSE117012: CD73 knockdown effect in pancreatic cancer cell lines
Recent studies have shown that non-enzymatic function of CD73 play a key role in tumor progression, ...
GSE107653: Single Cell RNA Sequencing Analysis of Mouse E14.5 Fetal Liver Runx1 P2-hCD4 plus and minus MEPs and CMPs
In recent years, highly detailed characterization of adult bone marrow (BM) myeloid progenitors has ...
GSE98562: A comparison of Illumina and Ion Torrent sequencing platforms in the context of differential gene expression
Background: Though Illumina has largely dominated the RNA-Seq field, the simultaneous availability o...
GSE121106: Selective Disruption of Core Regulatory Transcription [RNA-seq]
Activation of identity determining transcription factors (TFs), or core regulatory TFs, is governed ...
GSE110525: The long non-coding RNA MALAT1 contributes to the pathogenesis of multiple sclerosis through alternative splicing and backsplicing regulation
Since we found an upregulation of the long non coding RNA MALAT1 in Multiple Sclerosis (MS) patients...
GSE107401: Transcriptome analysis of sciatic nerve in mutant krox20 mice at 14 day post natal compared to wild-type mice
RNAseq was performed on sciatic nerves from controls and Krox20 mutants to elucidate the role of Kro...
GSE100067: The islet resident macrophage is in an inflammatory state and senses microbial products in blood
We examined the transcriptional profiles of macrophages that reside in the islets of Langerhans of N...
GSE106662: Inactivation of ARID1A-SWI/SNF Complex Alters Chromatin Compactness at Enhancer Regions and Affects Transcription of Key Tumor Signaling Circuitry [RNA-Seq, mouse]
Somatic mutations in ARID1A, a SWI/SNF chromatin remodeling gene, are prevalent in human malignancie...
GSE106775: Glioblastoma Hijacks Microglial Gene Expression to Support Tumor Growth
Background; Glioblastomas are the most common and lethal primary brain tumors. Microglia, the reside...
GSE99951: Maturation of Human iPSC-derived Astrocytes in 3D Cortical Spheroids
Single-cell RNA-seq: We used single-cell RNAseq to investigate the maturation of astrocytes within h...
GSE121223: RNA-seq profiles of WT and QK-KO microglia
This study is to analyze the transcriptomic profiles of 6 weeks 0.2% cuprizone treated Cx3cr1-CreER;...
GSE98297: Long Noncoding RNA Moderates microRNA Activity to Maintain Self-Renewal in Embryonic Stem Cells
Of the thousands of long non-coding RNAs expressed in embryonic stem (ES) cells, few have known role...
GSE107687: Next Generation Sequencing of skin from wild-type and ADAM17 cKO (Sox9-Cre x ADAM17fl/fl) mice
Purpose: Transcriptomic analysis of ADAM17 cKO mice, a mouse model of atopic dermatitis.; Methods: S...
GSE106487: Single-Cell RNA Sequencing Analysis Reveals Sequential Cell Fate Transition during Human Spermatogenesis
Spermatogenesis generates mature male gametes and is critical for the proper transmission of genetic...
GSE111307: Neuronal Development And The Onset Of Electrical Activity In The Human Enteric Nervous System
Objective: To assess the development of neuronal subtypes and the emergence of evoked electrical act...
GSE104969: Time series total RNA sequencing of a differentiation of human embryonic stem cells towards trophoblast lineage
Human embryonic stem cells (hESC) can be differentiated towards progeny resembling trophoblast upon ...
GSE108332: Next Generation Sequencing Facilitates Quantitative Analysis of mRNA expression of Wild Type and Mettl3-/- mice
Considering m6A modification in mRNA was reported to be important in many biology processes, like ce...
GSE106821: MARS Seq data from human cortical organoids
We analyze gene expression data of human organoid developmet SOURCE: Orly Reiner (orly.reiner@weizma...
GSE107826: Translational control of ERK signalling pathway by the mRNA cap-binding protein 4EHP
microRNA (miRNA)-mediated gene silencing is commonly deregulated in a wide variety of diseases. Ther...
GSE98569: High throughput single-cell whole transcriptome analysis of induced cardiomyocytes during direct cardiac reprogramming [Bulk-seq]
Direct lineage conversion offers a new strategy for tissue regeneration and disease modeling. Despit...
GSE108548: Transcriptome Profiling of Wild-type vs. A1CF -/- Mouse Whole Kidneys
Purpose: A1CF is an RNA binding protein that has not been extensively studied on a transcriptome-wid...
GSE98961: Gene expression profiling of CD25High and CD25Low regulatory T cell populations from mice lacking autophagy in their dendritic cells and their littermate controls.
The goal of this study is to compare the transcriptome profiling (RNA-seq) of two CD25 regulatory T ...
GSE116963: PRMT5 Interacts with the BCL6 Oncoprotein and is Required for Germinal Center Formation and Lymphoma Cell Survival
We have found that PRMT5 methylates BCL6 and is needed for its full transcriptional repressor activi...
GSE108083: RNA-seq analysis of aortic heart valves in mice
In order to asses differences between expression profiles of postnatal and adult mice, RNA-sequencin...
GSE110209: Spatiotemporal pattern of the transcriptional regulatory landscape of the mouse ventricle after myocardial infarction
Stress-response gene activity replaces cardiomyocyte lineage-specific program in a transcriptionally...
GSE110297: Cardiolipin Synthesis Governs Systemic Energy Homeostasis through Thermogenic Fat Mitochondria
Here we show that synthesis of the mitochondrial phospholipid cardiolipin is an indispensable driver...
GSE110571: Re-programing chromatin with a bifunctional LSD1/HDAC inhibitor induces therapeutic differentiation in DIPG [RNA-seq]
Histone H3 lysine 27 to methionine mutations (H3K27M) resulting in aberrant chromatin regulation are...
GSE99230: Remote memory and cortical synaptic plasticity require neuronal CCCTC-binding factor (CTCF), a central organizer of 3D chromatin architecture
Molecular mechanism of long-term memory has been extensively studied in the context of hippocampus-d...
GSE108293: Development of Specific Covalent MALT1 Inhibitors and Biomarkers for B-cell Lymphomas
The MALT1 paracaspase plays an essential role in Activated B-cell like Diffuse Large B-cell Lymphoma...
GSE113798: m6A/m-Seq of human B-lymphocyte cell lines from healthy controls and major depressive disorder patients
N6-Methyladenosine (m6A) and N6,2-O-dimethyladenosine (m6Am) are abundant mRNA modifications that re...
GSE99803: RNAseq skeletal muscle FUNDC1-mKO mice
This experiment was conducted to identify mRNA transcripts alteration in muscle from skeletal muscle...
GSE107461: Direct reprogramming of spiral ganglion non-neuronal cells into neurons: Towards ameliorating sensorineural hearing loss by gene therapy
The loss of primary auditory neurons (PANs) leads to permanent hearing impairment since they are inc...
GSE99991: Investigating the role of SMCHD1 in de novo X chromosome inactivation
To investigate the effect of Smchd1 ablation on de novo X chromosome inactivation (XCI), we derived ...
GSE113836: Sequencing of primary mouse machrophage and Raw 264.7 macrophage cell skewed in M1 or M2 conditions
We report the application of RNA sequencing to determine the transcriptional response of primary bon...
GSE108547: Transcriptome Profiling of Wild-type vs. A1CF -/- Mouse Livers
Purpose: A1CF is an RNA binding protein that has not been extensively studied on a transcriptome-wid...
GSE108084: Early response of human ovarian and fallopian tube surface epithelial cells to norepinephrine
The purpose of this study is to understand the effects of adrenergic signaling on the transcriptome ...
GSE99743: CNS lymphatic drainage and neuroinflammation are regulated by meningeal lymphatic vasculature
Neuroinflammatory diseases, such as multiple sclerosis, are characterized by invasion of the brain b...
GSE111669: Overlap in signaling between constitutively active forms of Smoothened and thesubunit of the heterotrimeric G protein G13
RNA sequencing was used to evaluate genes regulated in C3H10T1/2 cells by the Smo agonist purmorpham...
GSE129262: MYC-MIZ1 protein interaction in germinal center.
Characterisation of the splenic light zone germinal center B cells in mice carrying WT endogenous mo...
GSE110669: Transcriptional profiles of normal human mature B cells
Mature B cells leave the bone marrow as nave B cells and migrate to the secondary lymphoid organs w...
GSE111416: RNAseq of germinal center B cells from Blimp-1-GFP reporter mice
RNAseq of germinal center B cells with different Blimp-1-GFP reporter level. Sorted germinal center ...
GSE109350: Collagen 221 is a TGF early response gene in human skin that mediates the fibroblast to myofibroblast transition
Systemic sclerosis (SSc) is a complex multi-system autoimmune disease characterized by immune dysreg...
GSE112320: Comprehensive analysis of H3K9me2 oocytes, together with DNA methylation and expression analysis of G9a conditional KO oocytes and maternal KO preimplantation embryos
We report the first genome-wide landscape of H3K9me2 ChIP-seq profile in mouse oocytes. We also perf...
GSE132025: Rinf regulates pluripotency network and Tet enzymes in embryonic stem cells (ESCs)
In this study: (1) We have mapped the genome wide binding distribution and enrichment of Rinf/CXXC5 ...
GSE100397: Sensory neurons co-opt classical immune signaling pathways to mediate chronic itch [6 NaV1.8+ Jak1F/F mice treated with MC903 compared to skin from 4 littermates]
Mammals have evolved neurophysiologic reflexes such as coughing and scratching to expel invading pat...
GSE108581: Transcriptional control of macrophage inducible gene expression by cohesin [RNA-Seq I]
Although cohesin and CTCF are major determinants of interphase 3D genome organisation, their impact ...
GSE106611: mTORC2/Akt Activation in Adipocytes is Required forMycobacterium tuberculosisDerived Inflammation in Adipose Tissue
The association between type 2 DM (T2DM) and susceptibility to tuberculosis (TB) is well recognized....
GSE107472: Circular RNAs are super abundant in cervical tumor and plasma detected by high throughput microarray [RNA-Seq]
Circular RNAs (circRNAs) are a new class of endogenous and regulatory non-coding RNAs, but their exp...
GSE111690: RNAseq analysis of cells (siglecF+, CD11C+, MHCII high or low) from bleomycin treated and control mouse lungs
Cell suspensions were prepared from lungs dissociated from bleomycin treated mice and control mice. ...
GSE99837: NR4A3 plays a pivotal role in the differentiation of monocyte-derived dendritic cells
The molecular requirements that guide the differentiation of monocytes into macrophages or monocyte-...
GSE102959: Transient expression of T-bet epigenetically imprints the Ifng locus for its expression in a distinct Tfh cell subset
T follicular helper (Tfh) cells, which reside in the B cell follicles and help Ig class switching, e...
GSE128563: Genetic determinants of venetoclax resistance
Resistance to the first approved BCL-2 inhibitor venetoclax is emerging in lymphoid malignancies. Th...
GSE107854: PRMT5 regulates the homologous recombination DNA repair pathway by controlling the alternative splicing of key epigenetic factors
We found that PRMT5 deletion or inhibition impairs homologous recombination (HR) DNA repair, leading...
GSE108060: Mouse Obox and CrxOS modulate pre-implantation transcriptional profiles revealing similarity between paralogous mouse and human homeobox genes
We have ectopically expressed four V5-tagged mouse homeobox genes in mouse embryonic fibroblasts wit...
GSE110579: Permissiveness to Form Pluripotent Stem Cells May Be an Evolutionaily Derived Chracteristic in Mus musculus
We developed and report on a novel new technique to reprogramm fobroblasts from two non-permissive m...
GSE129240: Complete deconvolution of cellular mixtures based on linearity of transcriptional signatures
Difference in RNA content of different cell types introduces bias to gene expression deconvolution m...
GSE106575: IL-7-dependent STAT1 activation limits homeostatic CD4+ T cell expansion
IL-7 regulates homeostatic mechanisms that maintain the overall size of the T cell pool throughout l...
GSE140423: Collapse of the hepatic gene regulatory network in the absence of FoxA factors
FoxA transcription factors are critical for liver development through their pioneering activity, whi...
GSE111527: Single-cell transcriptomics characterizes cell types in the subventricular zone and uncovers molecular defects impairing adult neurogenesis.
Neural stem cells (NSCs) contribute to plasticity and repair of the adult brain. Niches harboring NS...
GSE104131: RNA sequencing of prostate cancer and normal tissue from African Americans and European Americans
Background:African American men (AAM) are at higher risk of being diagnosed with prostate cancer (PC...
GSE107839: All-RNA-seq data used in "Genetic resistance to DEHP-induced transgenerational endocrine disruption"
We Investigate the persistence of negative impacts on sperm parameters for more than one generation ...
GSE108096: Hepatic loss of Lis1 leads to fatty liver and predisposes to tumorigenesis in mice
We found that genetic deletion of Lis1 (also known as Pafah1b1) in mouse liver led to increased lipi...
GSE108337: Evidence against tetrapod-wide digit identities and for a limited frame shift in bird wings
In crown group tetrapods, individual digits are homologized in relation to a pentadactyl ground plan...
GSE106789: Western diet triggers NLRP3-dependent persistent functional reprogramming of myeloid cells II [RNA-Seq]
Here we investigated whether sterile triggers of inflammation induce trained immunity and thereby in...
GSE108596: Genes altered in expression by knockdown of PTK2 in breast cancer cell lines
PTK2 was knocked down by doxycycline-dependent expression of small hairpin RNA against PTK2 in Breas...
GSE112502: Regulatory Discrimination of mRNAs by FMRP Controls Adult Neural Stem Cell Differentiation
Fragile X syndrome (FXS) is caused by the loss of fragile X mental retardation protein (FMRP), a tra...
GSE108069: RNA sequencing of a Spinocerebellar ataxia type 3 (SCA3) mouse model containing the full human ATXN3 gene with a repeat expansion of 75-80 CAGs II
We have performed RNA sequencing analysis of brain tissue and blood from the MJD84.2 mouse model for...
GSE108582: Transcriptional control of macrophage inducible gene expression by cohesin [RNA-Seq II]
Although cohesin and CTCF are major determinants of interphase 3D genome organisation, their impact ...
GSE131400: Downregulation of the Ubiquitin-E3 Ligase KPC1 promotes glioblastoma progression through upregulation of SerpinE1 [RNA-seq]
We identified RNF123 (KPC1) ubiquitin E3 ligase is involved in glioblastoma progression through NF-k...
GSE123847: RNA sequencing after forced turnover of adult and aged microglia
The goal of this study was to determine whether depletion and repopulation of microglia in adult and...
GSE100088: MED12cKO heart ventricles from male mice [RNA-seq]
The Mediator complex regulates gene transcription by linking basal transcriptional machinery with DN...
GSE110951 (human): Solid phase chemistry to covalently and reversibly capture thiolated RNA
Here, we describe an approach to enrich newly transcribed RNAs from primary mouse neurons using 4-th...
GSE110586: Identification of the tumour transition states occurring during EMT [p63 overexpression RNA-seq]
EMT in cancer has been associated with tumour stemness, metastasis and resistance to therapy. It has...
GSE119461: Gut Adaptation of Ahr Expression Cell-intrinsically Restricts Group 2 Innate Lymphoid Cell Function
Innate lymphoid cells (ILCs) are important for mucosal immunity. The intestine harbors all ILC subse...
GSE111668: PNPase knockout results in mtDNA loss and an altered metabolic gene expression program
Polynucleotide phosphorylase (PNPase) is an essential mitochondria-localized exoribonuclease implica...
GSE117609: circ-ZNF609 regulates G1-S progression in Rhabdomyosarcoma
Circular RNAs (circRNAs) represent a class of covalently closed RNAs, derived from a non-canonical s...
GSE104708: S1P-dependent inter-organ trafficking of group 2 innate lymphoid cells supports host defense
Innate lymphoid cells (ILCs) are considered to be the innate counterparts of adaptive T lymphocytes ...
GSE100061: The C-terminal multimerization domain is essential for leukemia development by CBF-SMMHC
The recurrent chromosome 16 inversion in acute myeloid leukemia generates a fusion gene between CBFB...
GSE107222: Global transcriptional responses to KI-MS2-008 treatment and Myc inactivation via doxycycline addition
The Myc/Max heterodimer has crucial roles in normal cellular processes such as cell proliferation, m...
GSE99656: SHP2 Is Required for BCR-ABL1-Induced Hematologic Neoplasms
BCR-ABL1-targeting tyrosine kinase inhibitors (TKIs) have revolutionized treatment of Philadelphia c...
GSE115850: RNA deep sequencing analysis of human brain microvascular endothelial cells (ECs) treated with glioma-conditioned medium (glioma-CM)
To determine the effects of glioma-conditioned medium on global gene expression in ECs. SOURCE: Yi F...
GSE111702: The role of PKC-beta in B cell activation
PKCb-null (Prkcb-/-) mice are severely immunodeficient. Here we show that mice whose B cells lack PK...
GSE130813: Transcription as a function of tissue environment
We are interested in whether fibroblasts (CD45-CD31-Epcam-PDPN+PDGFRA+) cells exhibit unique transcr...
GSE111205: The bipartite TAD organization of the X-inactivation centre ensures opposing developmental regulation of Tsix and Xist
The mouse X-inactivation center (Xic) locus represents a powerful model for understanding the links ...
GSE108354: A Forward Genetic Screen Targeting the Endothelium Reveals a Regulatory Role for the Lipid Kinase Pi4ka in Myelo- and Erythropoiesis [clonality]
Definitive hematopoietic cells arise from hemogenic endothelium during mid-gestation, indicating a d...
GSE112575: Frontal cortex transcriptomic analysis of a TDP-43 Q331K knock-in mouse [20month]
Here we analyse transcriptome profiles within the frontal cortex between wild type, heterozygous and...
GSE156819: Brd4-bound enhancers drive cell intrinsic sex differences in glioblastoma [RNA-Seq]
We report the application of RNA-seq for high-throughput profiling of transcriptom in male and femal...
GSE109003: Xrn2 accelerates termination by RNA polymerase II, which is underpinned by CPSF73 activity
Termination is a ubiquitous phase in every transcription cycle but is incompletely understood and a ...
GSE98802: Loss of CNFy toxin-induced inflammation drives Yersinia pseudotuberculosis into persistency
Gastrointestinal infections caused by enteric yersiniae can become persistent and complicated by rel...
GSE108993: Dazl maintains proliferating germ cells through a network of polyA-proximal mRNA interactions [GFP cells RNA-Seq]
Dazl (deleted in azoospermia like) is a member of the DAZ family of germ cell-restricted RNA binding...
GSE109064: RNA-seq of shEZH2 cells
Downregulation of EZH2 Leads to Cellular Senescence with Features of SASP SOURCE: John Sedivy Brown ...
GSE139884: Huntingtons disease as a lamin B1 nuclear envelopathy
Lamins, the major structural proteins within the nuclear lamina, are crucial for the functionality o...
GSE109040: Transcriptional analysis of resting or inflamed murine Macrophages with Immune complex stimulation
We wished to investigate differential effects of stimulation with immune complex on colonic macropha...