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Sequencing-based assays page 36
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GSE67052: RNA-sequencing of DYRK1A-deficient (CKO) pre-B and pre-T cells
Pre-B and pre-T lymphocytes must orchestrate a transition from a highly proliferative state to a qui...
GSE108946: Transcriptome time course of mouse acute myeloid leukemia cells upon PU.1 restoration and knockdown
We have utilized advanced RNAi technology to dynamically restore and subsequently knock down endogen...
GSE71713: Acquired tissue-specific promoter bivalency is a basis for PRC2 necessity in adult somatic cells
To define H3K27me3 modified genes in intestinal stem, progenitor and epithelial cells, we performed ...
GSE69240: A Molecular Portrait Of High-Grade Ductal Carcinoma In Situ (DCIS) [RNA-seq]
DCIS is a non-invasive precursor lesion to invasive breast carcinoma. We still have no understanding...
GSE65970: Troy+ brain stem cells cycle through quiescence and regulate their number by sensing niche occupancy
The adult mouse subependymal zone (SEZ) provides a niche for mammalian neural stem cells (NSCs). How...
GSE122592: Transcriptome of lesional skin of patients suffering from Acne inversa
Transcriptome of skin from Acne inversa lesions show specific alterations compared to healthy donor ...
GSE52463: Transcriptome analysis reveals differential splicing events in IPF lung tissue
Objectives: Idiopathic pulmonary fibrosis (IPF) is a complex disease in which a multitude of protein...
GSE65994: Ten-Eleven Translocation 2 regulates adult neurogenesis through modulating 5mC oxidation dynamics at distinct regulatory elements
Emerging evidence suggests that various epigenetic mechanisms play important roles in regulating adu...
GSE71491: RNA-seq analysis of immunogenic actions of metronomic cyclophosphamide treatment: dependence of gene responses on tumor model, mouse host, and drug schedule
RNA-seq analysis was performed using RNA isolated from three tumor models (GL261 glioma, LLC Lewis l...
GSE70803: Total RNA profiles associated with DDX3 wild-type (WT) or R534H variant expression with or without sodium arsenite treatment [RNA-seq]
RNA expression profiles are not significantly altered by DDX3 WT or R534H expression as well as by 4...
GSE71382: Functional coordination and HuR-mediated regulation of mRNA stability during T cell activation
We evaluated changes in mRNA stability and transcription using 4sU metabolic pulse labeling across a...
GSE74547: ETO Family Protein Mtgr1 Mediates Prdm14 Functions in Stem Cell Maintenance
Prdm14 is a sequence-specific transcriptional regulator of embryonic stem cell (ESC) pluripotency an...
GSE139576: Fxr1 regulates sleep and synaptic homeostasis
Comparison of ribosome associated RNA between Ctrl vs EW (or SD) and EW (or SD) vs EWFxr1 (or SDFxr1...
GSE120642: RNA sequencing in healthy controls, intermittent claudicant, and CLI patient skeletal muscle
Gastrocnemius muscle biopsies were obtained from 15 health older adults without peripheral artery di...
GSE71126: Sequence Features Accurately Predict Genome-wide MeCP2 Binding in vivo
MECP2 is critical for proper brain development and expressed at near-histone levels in neurons, but ...
GSE94937: Generation of KRAS signatures using immortalized isogenic lung cells.
We generated RNAseq profiles from Small Airway Epithelial Cells (SALE) expressing either KRAS G12V o...
GSE71499: Study of the impact of G9a on DNA methylation in mouse embryonic cells [seq]
We explored the role of the lysine-methyltrasferase G9a in the control of DNA methylation during mou...
GSE72482: Sequence dependency and regulatory function of dimeric NOTCH1/RBPJ complexes on coding and non-coding transcription in T-lymphoblastic leukemia
NOTCH/RBPJ/MAML ternary transcriptional complex binds to regulatory element and drives gene expressi...
GSE130522: A novel P300 inhibitor reverses DUX4-mediated global histone H3 hyperacetylation, target gene expression and cell death
DUX4-induced gene expression was compared in the presence vs. absence of the p300 inhibitor, iP300w ...
GSE135155: Adipocyte serine uptake curbs ROS generation and visceral adiposity [Human]
Obesity, and visceral adiposity in particular, increases the risk of common metabolic diseases, incl...
GSE71702: DNA Methylation Dynamics of Germinal Center B Cells Are Mediated by AID
Changes in DNA methylation are required for the formation of germinal centers (GC), but the mechanis...
GSE72136: The Estrogen Receptor Co-Regulator Protein, Proline Glutamic Acid and Leucine Rich Protein 1 (PELP1) Mediates Estrogen Rapid Signaling and Neuroprotection in the Brain
We examined the role of PELP1 in E2-ER-mediated transcription in the hippocampus under conditions of...
GSE74552: Transcriptional profiling of post-positive selection thymocytes from HOIL- and SHARPIN-deficient mice
Mice lacking components of the linear ubiquitin chain assembly complex (LUBAC) exhibit defects in th...
GSE118919: Transcriptome-wide analysis upon DCP1A knockout
We analyzed the effect of DCP1A knockout on total RNA population in undifferentiated mouse embryonic...
GSE74189: Master epigenomic writers MLL4 and CBP shape dynamic enhancer landscapes in adipogenesis
MLL3/MLL4 are H3K4me1/2 methyltransferases enriched on enhancers. CBP/p300 are H3K27 acetyltransfera...
GSE77729: RNAseq Expression data for mouse liver, Phenobarbital exposed livers and resulting liver tumours.
Through the analysis of mouse liver tumours promoted by distinct routes (DEN exposure alone, DEN exp...
GSE78902: RNAseq analysis of the colon of intestine-specific adult Nkx2.2 mutant mice
Aim: Transcriptional analysis of the colon of adult Nkx2.2flox/flox;Villin-Cre (Nkx2.2int) mice vers...
GSE118152: Selective Inhibition of the Second Bromodomain of BET Family Maintains Anti-Tumor Efficacy and Improves Tolerability
Here we report the discovery of ABBV-744, a first in class, highly potent and selective inhibitor of...
GSE68177: Cell type transcriptomics of hypothalamic energy-sensing neuron responses to fasting
AGRP neurons are a hypothalamic population that senses physiological energy deficit and consequently...
GSE116907: Response of triple negative breast cancer to BAZ2A/B inhibition and BET bromodomain inhibition alone and in combination (RNAseq)
Three triple negative breast cancer cell lines (MDAMB231, SUM159, and HCC1806) were treated with sma...
GSE79039: Store-operated Ca2+ entry in follicular T cells controls humoral immune responses and autoimmunity
T follicular helper (TFH) cells promote affinity maturation of B cells in germinal centers (GCs), wh...
GSE123296: Induction of YAP5SA-GFP vs nGFP expression in FlipinTrex293 cells
Dox-inducible YAP5SA-GFP/nGFP were treated with Doxycycline for 24 hours each and compared to non-tr...
GSE71709: Poly(A)-specific ribonuclease (PARN) mediates 3' end maturation of the telomerase RNA component
Mutations in the poly(A) ribonuclease (PARN) gene cause telomere diseases including familial idiopat...
GSE73226: Transcriptome analysis of AGS cells infected with Helicobacter pylori P12
Transcriptome analysis of AGS cells infected with Helicobacter pylori P12 SOURCE: Frithjof Glowinski...
GSE67186: Apc restoration promotes cellular differentiation and reestablishes crypt homeostasis in colorectal cancer
The Adenomatous Polyposis Coli (APC) tumor suppressor is mutated in the vast majority of human color...
GSE154730: Transcriptome datasets of the Quaking (QKI) gene knock-down human oral squamous cell carcinoma (OSCC) cells
Here, we elucidated whether miR-200 family members control RNA-binding protein quaking (QKI), a newl...
GSE73560: Gene expression analysis to identify Klf2 target genes in B-cell progenitors [Klf2_KO]
The sequential activation of distinct developmental gene networks governs the ultimate identity of a...
GSE70517: Alterations to chromatin in intestinal macrophages link IL-10 deficiency to inappropriate inflammatory responses
Intestinal macrophages (IMs) are uniquely programmed to tolerate exposure to bacteria without mounti...
GSE79680: HEK293 Heat-shock experiment
HEK293 cells were heatshocked and differentially expressed transcripts were identified SOURCE: Jon B...
GSE79027: Expression profiling of IL-13 stimulated PBMCs with and without an IL-13R antagonist
This experiment aims to identify the biological pathways and diseases associated with the cytokine I...
GSE74016: Dynamics of the human and viral m6A RNA methylomes during HIV-1 infection of T cells
Significance of RNA methylation in the context of HIV-1 infection in human T cells SOURCE: Christoph...
GSE137308: RNA sequencing for lncRNA, miRNA and mRNA expression analysis in human laryngeal cancer
Accumulating evidence indicates that long noncoding RNAs can interact with microRNAs to regulate tar...
GSE70546: Foxd3 promotes the exit from nave pluripotency and prevents germline specification through enhancer decommissioning [RNA-Seq]
Following implantation, mouse epiblast cells transit from a nave to a primed state in which they are...
GSE135116: JAK inhibition differentially affects NK cell and ILC1 homeostasis
We report the application of single-molecule-based RNA sequencing technology for comparing the trans...
GSE71529: PATZ1 is a DNA damage responsive transcription factor that inhibits p53 function [doxorubicin treatment]
Insults to cellular health cause p53 protein accumulation and loss of p53 function leads to tumorige...
GSE110580: High-throughput RNA sequencing on circular RNA profiles of human pancreatic cancer cell lines and gemcitabine resistant pancreatic cancer cell lines.
Gemcitabine resistance is currently the main problem of chemotherapy for advanced pancreatic cancer ...
GSE71756: microRNA suppresses prostate cancer stem cells and metastasis by inhibiting a cohort of pro-metastasis targets including CD44, Rho GTPases and EZH2
microRNA plays important roles in tumor initiation and progression. Here we showed that, one of the ...
GSE129939: Loss of Imprinting of Clustered MicroRNAs within the Sfmbt2 Gene Is Responsible for Clone-Associated Placental Enlargement in Mice [RNA-Seq]
Abnormal placentation in cloned animals remains an unsolved problem. We demonstrated the involvement...
GSE73993: Transcriptome of ESCs, EpiSCs and reverted ES by MM401 (Mll1 inhibitor) #2
This study describes the transcriptome profiling of: 1) mouse ES cells in LIF/KSR medium; 2)EpiSCs i...
GSE71463: Regulation of genes expression in photoreceptor and other retinal cells by histone H3 tri-methylation at K27 during retinal development
To analyze roles of histone H3 tri-methylation for transcription in retina, global transcription pat...
GSE122658: Breast tumor from Pik3caH1047R/+ mammary gland transduced with single or pooled lentivirus.
RNA-seq of breast tumor from Pik3caH1047R/+ mammary gland transduced with single or pooled lentiviru...
GSE66814: The interaction of PRC2 with RNA or chromatin is mutually antagonistic [RNA-Seq]
Polycomb repressive complex 2 (PRC2) maintains developmental regulator genes in a repressed state th...
GSE136152: Extracellular vesiclesfrom hepatocytesaretherapeuticfortoxin-mediated fibrosis and gene expression in the liver
Norm mouse hepatocyte-derived extracellular vesicles were used to treat CCl4-injured mice and the he...
GSE72628: Acute loss of TET function results in aggressive myeloid cancer in mice [RNA-Seq]
TET-family dioxygenases oxidize 5-methylcytosine (5mC) in DNA, and exert tumor suppressor activity i...
GSE122180: RNA sequence analysis to compare Elf5+ and Elf5- tumor cells in C3-T; Elf5-GFP reporter mice tumors
The data generated here shows increased interferon gamma gene signatures in Elf5- tumor cells in C3...
GSE72790: Cancer associated SF3B1 hotspot mutations induce cryptic 3' splice site selection through use of a different branch point
Recurrent mutations in the spliceosome are observed in several human cancers but their functional an...
GSE122702: Early termination of a Phase 1 trial of tenofovir disoproxil fumarate intravaginal ring linked to inflammation
Objective: To assess safety in women of tenofovir disoproxil fumarate (TDF) polyurethane intravagina...
GSE116236: Gene expression analysis of Trem1-deficient Kupffer cells subjected to carbon tetracloride (CCl4) in liver fibrogenesis.
Analysis of Kupffer cells at gene expression level. The hypothesis tested in the present study was t...
GSE118165: RNA-seq data
The immune system depends on a balanced interplay among a variety of specialized cell types transiti...
GSE132368: Next Generation Sequencing timecourse of murine hepatocytes with or without paracetamol treatment
Untreated mice or mice treated with paracetamol, in the presence or absence of TSA, were culled afte...
GSE71924: RNA-seq analysis of acute Rb1 deletion in adult mouse tissues
Abstract:The pRb tumor suppressor protein associates with chromatin and regulates gene expression. N...
GSE129996: RNA-sequencing of microglia, T cells and ILC2 from the brains of IL-33 treated aged (20-22mos) mice
ILC2 are potent producers of IL-5 and IL-13 and Th2 cytokines have been found to promote neurogenesi...
GSE68391: Efficacy of retinoids in IKZF1-mutated BCR-ABL1 acute lymphoblastic leukemia
Alterations of IKZF1, encoding the lymphoid transcription factor IKAROS, are a hallmark of high risk...
GSE70831: MiR-26 dampens IL-6 production by down-regulating TNF-a/NF-kB signaling through silencing HMGA1 and MALT1 and not by directly targeting IL-6 mRNA
We found NF-kB signaling as a major target of miR-26 based on an analysis of the changes in gene act...
GSE83786: JUNB is a critical AP1 component for SMAD2/3 binding after TGF stimulation [RNA-seq]
We performed SMAD2/3 ChIP-seq analysis in MCF10A MII cells. To validate whether the changes in SMAD2...
GSE118719: Transcriptomic profiling of nasopharyngeal carcinoma (NPC) and normal control samples
To understand the genes and pathways that may potentially drive nasopharyngeal carcinoma (NPC) patho...
GSE69771: Histone H3.3 maintains genome integrity during mammalian development
Histone H3.3 is a highly conserved histone H3 replacement variant in metazoans, and has been implica...
GSE134808: Transcriptional characterization of mPFCs
Medial prefrontal cortices (mPFCs) were dissected from the brian of control of antibiotic-treated 10...
GSE72612: Dissection of heterogeneity during cardiac maturation process by single-cell RNA sequencing
To improve the maturity and reduce the heterogeneity of iPSC-cardiomyocytes, we addressed the divers...
GSE75184: A transcriptional regulatory network connects mitochondrial biogenesis and metabolic shift with stem cell commitment to hepatic differentiation
Mitochondrial biogenesis and metabolism recently emerged as critical modulators of stemness properti...
GSE71261: Next Generation Sequencing Facilitates Quantitative Analysis of PBX3 Regulated Transcriptomes
The goals of this study are to analyze the transcriptome profiling (RNA-seq) after PBX3 overexpressi...
GSE72196: Histone deacetylase 3 in concert with MeCP2 and FoxO regulate autism-associated behaviors.
ChIP-Seq data of HDAC3 in mouse C57BL/6J hippocampus and RNA-Seq data of hippocampal CA1 in control ...
GSE66882: The microRNA-212/132 cluster regulates B cell development and apoptosis by targeting SOX4
MicroRNAs have emerged as key regulators of B cell fate decisions and immune function. Deregulation ...
GSE72275: Mapping Replication Stress-Dependent Transcriptional Events Dependent on ATM or ATMIN by RNA-seq
The cellular response to replication stress requires the DNA-damage responsive kinase ATM and its co...
GSE118787: BCL6 de-repression induces the fasting transcriptome and protects from steatosis (RNA-Seq)
Here, we find that the B cell lymphoma 6 (BCL6) repressor is enriched upon feeding and converges gen...
GSE137782: Endogenous retroviruses are associated with hippocampus-based memory impairment
Retrotransposons comprise a staggering 40% of the mammalian genome. Among them, endogenous retroviru...
GSE66364: Role of PML on histone variant H3.3 loading on chromatin
Histone variant H3.3 is incorporated into various chromatin domains by distinct chaperones including...
GSE71876 (human): Survival of pancreatic cancer cells lacking KRAS function
Activating mutations in the proto-oncogene KRAS are a hallmark of pancreatic ductal adenocarcinoma (...
GSE93755: Constrained pioneering and partner factor redirection by PU.1 shape early T-cell gene regulation
A major problem with linking transcription factor binding to function is that many factors bind to a...
GSE72833: Regulatory complexity revealed by integrated cytological and RNA-seq analyses of meiotic substages in mouse spermatocytes
The juvenile onset of spermatogenesis in mice is analyzed by combining cytological and transcriptomi...
GSE118774: Genome wide expression change in LCC2 and MCF-7 cells
We aim to the investigate the role of tamoxifen in breast cancer progression. LCC2 and MCF-7 cells w...
GSE70872: A protein interaction network of mental disorder factors in neural stem cells
Mental disorders (MDs) such as intellectual disability (ID), autism spectrum disabilities (ASD) and ...
GSE74142: GRO-seq in MCF-7 Human Breast Cancer Cells Upon Knockdown of PARP-1
In order to understand the molecular effects of PARP-1 on basal and signal-regulated transcription...
GSE101966: ARID1A and ARID1B loss in HCT116 cells
ARID1A, a subunit of the SWI/SNF chromatin remodeling complex, is frequently mutated in cancer. Defi...
GSE67294: Length-dependent gene misregulation in Rett syndrome (RNA-Seq)
Disruption of the MECP2 gene leads to Rett syndrome (RTT), a severe neurological disorder with featu...
GSE71362: Comparison of WapCre;Rank;Brca1;p53 and WapCre;Brca1;p53 mouse primary mammary tumors
The transcriptional profile of WapCre;Rank;Brca1;p53 and WapCre;Brca1;p53 mouse primary mammary tumo...
GSE134311: scRCAT-seq: simultaneously profile RNA TSS and TES at single-cell level
We developed a new single cell sequencing method to simultaneously identify RNA TSS and TES at singl...
GSE72862: Next Generation Sequencing Facilitates Quantitative Analysis of mesoderm posterior bHLH transcription factor 1(MESP1)+ and MESP1- cells' Transcriptomes
Purpose: To compare the transcriptome of MESP1-mTomato reporter cells at undifferentiated state, car...
GSE100363: Identification of differentially expressed circRNA in gallbladder cancer compared with matched normal tissue
We hypothesized that the circRNA will play an important role in the progresion of gallbladder cancer...
GSE91396: Neuropathic pain promotes gene expression adaptations in brain networks involved in stress and depression
Neuropathic pain is a complex chronic condition, characterized by a wide range of sensory, cognitive...
GSE124072: The RNA helicase DDX6 regulates self-renewal and differentiation of human and mouse stem cells [RNA-Seq]
Analysis of adult progenitor cells depleted for DDX6. Results provide insight into the regulation of...
GSE70721: De novo DNA methyltransferases DNMT3A and DNMT3B are essential of global DNA methylation maintenance [RNA-Seq]
DNA methylation is the net result of deposition by DNA methyltransferases (DNMT1, 3A and 3B) and rem...
GSE93717: miR941 overexpression experiment
miRNA sponge, a special class of miRNA target, has been emerging as a pivotal player in miRNA media...
GSE121095: Epigenetic reprogramming of melanoma cells by vitamin C treatment
In this study we show that ascorbate (vitamin C) shifts the transcriptome of melanoma cells, and de...
GSE73111: Gene expression analysis of Lgr5/Tspan8 expressing cells in the adult mammary gland
Purpose: The aim of this study is to identify genes that are differentially expressed in the differe...
GSE122711: Mitochondrial Pyruvate Carrier 1 (MPC1) enforces T cell homeostasis by enabling pyruvate oxidation in the mitochondria
The transporter which uptakes pyruvate into the mitochondria during pyruvate oxidation, called the M...
GSE75526: Transcriptomic profiling of bone marrow derived mast cells (BMMCs) [RNA-seq]
Allergy is one of the least understood immunological response partly due to the diversity of allerge...
GSE99232: Transcriptome profile of wildtype and Ret homozygote null male mouse guts at E10.5
Total mRNA seq was perfomed on widtype and Ret null male mouse embryonic gut at E10.5 SOURCE: Sumant...
GSE69800: Ribosome profiling analysis of GADD34 null cells
Accumulation of misfolded proteins in the endoplasmic reticulum (ER) triggers the unfolded protein r...
GSE127834: Human inflammatory mucosal T cells in the female reproductive tract are poised to participate in immunity to infection
The hypothesis is that HIV affects TRM, by decreasing their numbers and possibly affecting their fun...