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Sequencing-based assays (Page 58)
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GSE133050: The Circadian Protein Nocturnin Regulates Metabolic Adaptation in Brown Adipose Tissue
Fine-tuning of transcriptional responses can be critical for long-term outcomes in response to an en...
GSE99401: MiR-34a controls proliferation and plasticity of early-progenitors in the normal mammary gland and in breast cancer
The miR-34 is a tumor-suppressor miRNA family involved in various human cancers, including breast. H...
GSE125509: Transcriptome profiling of H1-iCas9 cells grown on laminin and on MEFs
This experiment is part of a study of differentially essential genes in H1 hPSCs grown on different ...
GSE103559: The histone variant H3.3 G34W substitution in giant cell tumor of the bone link chromatin and RNA processing
While transcription as regulated by histones and their post-translational modifications have been we...
GSE103257: Gene expression analysis of wild type and YAP-activated embryonic mouse stomach
Hippo-YAP signaling plays important roles in gut development and homeostasis. In this study, we use ...
GSE134414: Similarity of therapeutic networks induced by a multi-component herbal remedy in neurovascular unit cells
The neurovascular unit, which includes neurons, glial cells, and vascular cells, plays crucial roles...
GSE104657: Polycomb Repressive Complex 2 methylates Elongin A to regulate transcripiton [RNA-seq]
Polycomb repressive complex 2 (PRC2-EZH2) methylates histone H3 at lysine 27 (H3K27) and is required...
GSE110114: A practical evaluation of alignment algorithms for RNA variant calling analysis
We performed RNA-seq with ten pieces of breast cancer (invasive ductal carcinoma; luminal B type) ti...
GSE97013: Mechanisms of colitis-accelerated colon carcinogenesis and its prevention with the combination of aspirin and curcumin: Transcriptomic analysis using RNA-seq
Colorectal cancer (CRC) remains the leading cause of cancer-related death in the world. Aspirin (ASA...
GSE102873: Genome-wide transcriptome analysis of NIPBL iPSC and commited cardiomyoctes
The purpose of this study was to compare the transcriptome of NIPBL patient derived iPSCs and patien...
GSE95739: Cellular Interplay and Cytokine Hierarchy Cause Pathological Cardiac Hypertrophy in RAF1-Mutant Noonan Syndrome
Noonan syndrome (NS) is caused by mutations in RAS/ERK pathway genes, and is characterized by cranio...
GSE95595: Successful transplantation of islets into inguinal subcutaneous white adipose tissue
Islet transplantation is an attractive treatment for patients with insulin-dependent diabetes mellit...
GSE103261: RNAseq and ChIPseq on Mouse Embryonic Stem Cells and Sorted Mesendoderm Progenitor Cells [RNA-seq]
We mapped the enhancer and long non-coding transcriptional landscape during mesendoderm specificatio...
GSE98715: Protein kinase 7 regulating extracellular matrix assemblies and intracellular RAC1 and myosin II activities in the mesenchyme is important to Wolffian duct morphogenesis.
Wolffian/epididymal duct morphogenesis highly coordinates with its specialized function of providing...
GSE113114: Transcriptomic analysis of myosin IIa-deficient B cells
Myosin IIa-deficient follicular B cells have a hyperactivated phenotype. To identify what pathways a...
GSE105159: Selective endosteal remodeling of blood vessels in acute myeloid leukemia promotes malignancy at the expense of hematopoietic stem cells
Hematopoietic stem cell (HSC) function requires bone marrow vascular niches, which have been propose...
GSE106138: CBF- and Runx transcription factors promote adaptive NK cell responses [RNA-Seq]
Natural killer (NK) cells are innate lymphocytes that possess features of adaptive immunity such as ...
GSE103568 (mouse): Sensitive and powerful single-cell RNA sequencing using mcSCRB-seq
Single-cell RNA sequencing (scRNA-seq) has emerged as a central genome-wide method to characterize c...
GSE108634: Glucocorticoid Receptor Quaternary Structure Drives Chromatin Occupancy and Transcriptional Outcome
Most transcription factors, including nuclear receptors, are widely modeled as binding regulatory el...
GSE98140: SET1A/COMPASS and shadow enhancers in the regulation of homeotic gene expression
The homeotic (Hox) genes are highly conserved in metazoans, where they are required for various proc...
GSE104559: HNRNPH1 is required for rhabdomyosarcoma cell growth and survival
Rhabdomyosarcoma (RMS) is an aggressive and difficult to treat cancer characterized by a muscle-like...
GSE96690: Loss of CTCF reveals basic properties of post-mitotic epigenomes and induces heart failure [RNA-seq]
Understanding the principles of endogenous chromatin structure has key implications for epigenetic t...
GSE98249: Mouse CD11b+ macrophages - Aging of hematopoietic stem cells is driven by regional specialization of marrow macrophages
The human aged hematopoietic system is prone to dysfunction and clonal selection. Aged hematopoietic...
GSE104308 (mouse): A TFIID-SAGA perturbation that targets MYB and suppresses acute myeloid leukemia (RNA-seq)
Targeting of general coactivators, such as BRD4, is an emerging strategy to interfere with oncogenic...
GSE107536: RNA-sequencing of cTECs, mTECs, and thymocyte maturation subsets SM, M1 and M2 from the CD4 and CD8 lineages from WT and Psmb11-deficient mice [DSP405]
Purpose: Cortical thymic epithelial cells (cTECs) contain a unique type of proteasomes, thymoproteas...
GSE107583: Myc and YAP roles in the control of the cell cycle [MEF RNA-seq pharmacological treatment]
Expression profiling by RNA-seq SOURCE: stefano campaner (stefano.campaner@iit.it) - Cancer Biology ...
GSE126957: The regeneration transcriptome of corticospinal neurons
In the present study, we identify transcriptional mechanisms associated with corticospinal regenerat...
GSE104508: Characterizing the transcriptional profile of murine 3T3-L1 adipocytes with altered expression of Dnmt3a
We report RNA-Seq data file from 3T3-L1 adipocytes following overexpression and knock-down of Dnmt3a...
GSE105790: Gene expression profiling of myofibroblasts in young and aged day 5 wound beds
Mesenchymal cells were isolated from day 5 dorsal skin wound beds of 7-weeks old and >24-months old ...
GSE99260: Menin controls the memory Th2 cell function by maintaining the epigenetic integrity of Th2 cells. [RNA-Seq]
Post-translational modifications of histones are well-established epigenetic modifications that play...
GSE103971: RNASeq analysis to detect any molecular changes in skin of Dlx4 ablated mice compared to Wild type littermates.
DLX4 is a member of DLX family of mammalian homeobox genes and cis linked sister gene of Dlx3. Misex...
GSE107643: RNA sequencing of dendritic cells undergoing interaction with T cells in vivo
We used RNA sequencing to characterize gene expression of dendritic cells from mouse lymph node that...
GSE94857: Fra-2 negatively regulates postnatal alveolar septation by modulating myofibroblast function
Purpose: Compare the transciptome between lung myofibroblasts that contituatively express Fra-2 to c...
GSE108212: RNA sequencing on LNCaP cells
RNA sequencing on LNCaP cells was carried out to study how tunicamycin-induced gene expression is af...
GSE105173: DHX36 is the missing link to understand RNA G-quadruplex structures, mRNA stability, and translation [RNA-seq]
DHX36 is a ATP-dependent, 3-5 RNA helicase of the DEAH family. Previous publications reported this h...
GSE113125: Transcriptional alteration after ionizing radiation exposure in human fibroblasts, iPSCs and NPCs
RNA sequencing was performed to investigate ionizing radiation-dependent transcriptional change in h...
GSE108521: Disruption of the TFAP2A regulatory domain causes Branchio-Oculo-Facial Syndrome (BOFS) and illuminates pathomechanisms for other human neurocristopathies [RNA-seq data set 1]
BOFS is a rare congenital syndrome that arises due to defects during neural crest (NC) development a...
GSE106078: MYC functions as a switch for natural killer cell-mediated immune surveillance of lymphoid malignancies
We delineate the immunobiology during MYC oncogene-driven lymphomagenesis by RNA sequencing analysis...
GSE114491: Role of miR-146a in mouse brain development: relevance for developmental brain disorders
MicroRNAs (miRNAs) are short non-coding RNAs that regulate gene expression post-transcriptionally. m...
GSE106999: Phf21b is a novel histone reader essential for epigenetic silencing of cell cycle genes during neurogenesis
The role of chromatin-mediated regulation in cell-fate specification during mammalian development is...
GSE104651: Non-monotonic changes in Progenitor Cell Behavior and Gene expression during aging of the Adult Neural Stem Cell Niche
Neural stem cell activity in the ventricular-subventricular zone (V-SVZ) decreases with aging, thoug...
GSE105158: RNA-Seq data on KMO inhibitor (CHDI-00340246) subchronic treated R6/2 mice.
Dysregulation of the kynurenine (Kyn) pathway has been associated with the progression of Huntington...
GSE107552: Mapping human pluripotent stem cell differentiation pathways via high throughput single-cell RNA-sequencing
Human pluripotent stem cells (hPSCs) provide both powerful models for studying cellular differentiat...
GSE142866: Ethyl acetate fraction of Lentinula edodes (LEA) inhibits osteoclastogenesis by suppressing NFATc1 expression
To screen for altered gene expression during osteoclastogenesis, BMM cells treated with RANKL or RA...
GSE106873: Nicotinamide Nucleotide Transhydrogenase as a novel treatment target in adrenocortical carcinoma
RNA-seq samples used to support a study in to the understanding of antioxidant targeting in adrenoco...
GSE103584: Identification of relationships between Molecular and Imaging Phenotypes in Non-small cell lung cancer using radiogenomics Map
Purpose: To create a radiogenomic map linking computed tomographic (CT) image features and gene exp...
GSE107592: Gene expression profiling of mouse BMPR1B+ chondrocytes
We profiled gene expression of mouse chondrocytes from embryonic and adult samples. SOURCE: Denis,A,...
GSE98567: High throughput single-cell whole transcriptome analysis of induced cardiomyocytes during direct cardiac reprogramming [RNA-seq]
Direct lineage conversion offers a new strategy for tissue regeneration and disease modeling. Despit...
GSE104714: Clustering gene expression time series data using an infinite Gaussian process mixture model
In order to identify and characterize novel human gene expression responses to glucocorticoids, we e...
GSE112300: Identification of HOXB13 target genes responsive to BET inhibitors
We identified BRD4 as an epigenetic regulator of the prostate lineage specific gene HOXB13 during ...
GSE117520: RNA-sequencing of primary intestinal epithelial cells from wild-type mice
This dataset consists of RNA-sequencing of isolated mouse intestinal epithelial cells. Intestinal ep...
GSE108044: ketu mutant mice uncover an essential meiotic function for the ancient RNA helicase YTHDC2
Mechanisms regulating mammalian meiotic progression are poorly understood. Here we identify mouse YT...
GSE104537: Integrated analysis of motif activity and gene expression changes of transcription factors
The ability to predict transcription factors based on sequence information in regulatory elements is...
GSE104325: Early-life gene expression in neurons modulates lasting epigenetic states. [RNA-seq 2]
In mammals during the early postnatal period the environment plays a critical role in promoting the ...
GSE99619: Liver DGE analysis of hemophilia mice (hFIX9-R29X) treated with ASOs inhibiting NMD
To evaluate the impact of ASO-mediated depletion of NMD factor Upf1 and Upf3b on the normal transcri...
GSE107144: Inflammatory mediators regulate long non-coding RNA-PPTG1-1:1 in myeloid leukemia.
The experiment aims to distinguish the transcriptome influenced by the extinction of the lncRNA, aft...
GSE154996: Conservedinterferon-gamma signaling and decreased immune exclusion programs in responses to immune checkpoint blockade therapy
Purpose: We treated melanoma cell lines with IFNG to assess which ones would be resistant or respon...
GSE110371: Single cell RNA-seq reveals heterogeneity and hierarchy of mouse mammary epithelia
The mammary epithelia are mainly composed of two distinct lineages, the basal and luminal cells. Due...
GSE112398: Polycomb repressive complex 1 (PRC1) role in skin epithelium development [Epidermis I53A]
Polycomb repressive complexes (PRC) 1 and 2 are essential chromatin regulators of cell identity. PRC...
GSE110215: Gender-Specific Regulatory Landscapes in Pluripotency and Reprogramming
How gender influences the molecular properties of pluripotent stem cells (PSCs) remains incompletely...
GSE107717: RNASEQ Analysis of sh-TRC and sh-MIR100HG in the triplex negative breast cancer
Purpose:The goals of this study are using next generation sequencing to identify differentially expr...
GSE99333: Bacterial translocation is required for pre-leukemic myeloproliferation in Tet2 deficient mice
Ten-Eleven-translocation (Tet2) encodes an epigenetic modifier enzyme and is mutated somatically dur...
GSE103847: Sympathetic neuron-associated macrophages contribute to obesity by importing and metabolizing norepinephrine
The cellular mechanism(s) linking macrophages to norepinephrine (NE)-mediated regulation of thermoge...
GSE96747: Next Generation Sequencing Facilitates Quantitative Analysis of Murine Salivary Gland Transcriptomes
Purpose: Next-generation sequencing (NGS) has revolutionized systems-based analysis of cellular func...
GSE104591: Integrated in vivo quantitative proteomics and nutrient tracing reveals age-related metabolic rewiring of pancreatic beta-cell function
Aging is associated with fundamental changes in pancreatic -cell physiology; yet, the mechanisms tha...
GSE110512: Gene expression analysis of dengue-infected cells
We use RNA-seq on mRNA to identify genes that are differential expressed in human cells following de...
GSE103831: Exploring the RNA landscape of endothelial exosomes
Exosomes are small extracellular vesicles of around 100nm of diameter produced by most cell types. T...
GSE103903: Sensors, Pathways and Transcription factors regulating IR-induced inflammatory transcriptional output [RNA-seq data set 2]
RNA-seq of mRNA from five stimulation time point (LipidA, 100ng/ml) of bone marrow-derived macrophag...
GSE109084: The dynamic landscape of coding and non-coding RNAs in the innate immune response to microbial pathogens
We performed a systematic analysis of the coding and non-coding transcriptomes of human macrophages ...
GSE106554: Systemic inflammation drives rapid conversion of conventional CD4+ T cells to Treg in vivo
The immune system faces a task that approximates cognition in its complexity as it processes a multi...
GSE111434: Genome wide gene expression analysis of acutely injured primary mouse neurons
We aimed at identifying a common transcriptional response of neurons to acute injury by conducting a...
GSE104096: Epidermal growth factor receptor expression licenses T helper-2 cells to function in a T cell receptor-independent fashion
Gastro-intestinal helminth infections trigger the release of interleukin-33 (IL-33), which induces t...
GSE108223: DNA and Histone Methyltransferase Inhibitors Cooperate to Increase Viral Mimicry in Ovarian Cancer Cells
Total RNA sequenceing method was used to compare the differential expression of genes in A2780, CAOV...
GSE104976: Physiologic expression of Srsf2(P95H) causes myeloid expansion, impaired competitive stem cell function and initiates the myeloproliferative/myelodysplastic syndrome in vivo [RNA-seq2]
Mutations in the RNA splicing complex member SRSF2 are found frequently in myelodysplastic syndrome ...
GSE103666: Human primary macrophages derived in vitro from circulating monocytes comprise adherent and non-adherent subsets with differential expression of Siglec-1 and CD4 and permissiveness to HIV-1 infection
Macrophages are a major target for human immunodeficiency virus type 1 (HIV-1) infection. However, m...
GSE103841: Next Generation Sequencing of WT and DM1 mutant muscle stem cell and its differentiated cells Transcriptomes
In order to decipher the mechanisms of DM1 disease, we generated new DM1 mouse model and found the k...
GSE98287: Manipulation of the gut microbiome as a strategy to treat the osteoarthritis of obesity
Obesity is a risk factor for Osteoarthritis (OA), the greatest cause of disability in the US. The i...
GSE108726: Vascular organoids differentiation from human induced pluripotent stem cells (iPSC)
We have established a vascular organoid culture system with self-assembled endothelial networks that...
GSE94791: TDRD6 mediates early steps of spliceosome maturation in primary spermatocytes
Very little is known about splicing and its regulation in germ cells, particularly during meiosis. T...
GSE107045: Tafazzin Regulates Cell State by Modulating Phosphatidylethanolamine and Phosphatidylserine levels
Inhibiting tafazzin a cardiolipin remodeling enzyme reduces stemness of AML by modulating the level ...
GSE108773: Role of SETMAR in gene expression in U2OS cells
ChIP-exo of Flag-SETMAR in U2OS-SMF cell line, RNA-seq in duplicates for the U2OS control cell line,...
GSE128749: RNA sequencing data of human prostate cancer cells treated with androgen
To analyse and understand the differentially expressed genes following treatment with synthetic andr...
GSE129307: Studying the selectivity of a targeted small molecule degrading a hypoxia-associated non-coding RNA
Small molecule targeted recruitment of nucleases to RNA is a powerful method to affect RNA biology. ...
GSE94688: A non-catalytic role of TET3 promotes open chromatin and enhances global transcription
The methylcytosine dioxygenase Tet3 is highly expressed as a specific isoform in oocytes and zygotes...
GSE103719: Transcriptome-wide profiling of poly(A)-tail length, translation efficiency and mRNA stability using TED-seq, mRNA-seq, Ribo-seq and PRO-seq in ER stress conditions
We report systematical profiling of translation efficiency and mRNA stability dependent on the dynam...
GSE94774: Next generation sequencing of RNA expression on total splenic B cells from NOD mice fed variable diets
Purpose: The goals of this study is to examine if feeding NOD mice with diets supplemented with SCF...
GSE109002: Calorie restriction governs intestinal epithelial regeneration through cell autonomous regulation of mTORC1 in reserve stem cells
Here, we show that CR enhances regenerative capacity of the intestinal epithelium as a result of inc...
GSE104821: RNA-seq analysis of murine gastric tissue from Lats1/2-knockout mice
YAP and TAZ play oncogenic roles in various organs, but the role of YAP/TAZ activation in gastric ca...
GSE126230: HIV-1 SortSeq identifies HIV-1-infected cells from HIV-1-infected individuals
Using HIV-1 SortSeq, we identified HIV-1-infected cells containing inducible HIV-1 for RNAseq from r...
GSE111483: RNA-seq of MLLT3-overexpressing cultued HSPC, compared to non-overexpressing and uncutured FL-HSPC [RNAseq_MLLT3_OE]
MLLT3 preserves the FL-HSPC gene expression signature in culture SOURCE: Vincenzo Calvanese (vincalv...
GSE105094: RNA sequencing of HCT116 and HKE3 colorectal cancer cell lines before and after stimulation with TGF-alpha
RNA sequencing was performed on HCT116 and HKE3 colorectal cancer cell lines before stimulation and ...
GSE130005: Effect of miRNA-30e-5p on innate immunity during viral infection.
Comparative transcriptomic analysis of A549 cell after overexpression of miRNA-30e-5p revealed that ...
GSE94842: Vertical sleeve gastrectomy reverses diet-induced gene-regulatory changes impacting lipid metabolism
Vertical sleeve gastrectomy (VSG) produces sustainable weight loss, remission of type 2 diabetes (T2...
GSE95138: An orchestrated intron retention program in meiosis controls timely usage of transcripts during germ cell differentiation (RNA-Seq)
Alternative splicing (AS) represents a powerful resource to amplify the coding potential of eukaryot...
GSE105161: Glutaminolysis is a metabolic dependency in FLT3 ITD Acute Myeloid Leukemia unmasked by FLT3 Tyrosine Kinase Inhibition
FLT3ITD are common mutations in Acute Myeloid Leukemia (AML) and carry a particularly bad prognosis....
GSE104766: New insights into diagnosis and therapeutic options for proliferative hepatoblastoma
Surgery and cisplatin-based treatment of hepatoblastoma (HB) currently guarantee the survival of 70-...
GSE110179: Next Generation Sequencing Facilitated Differential Transcriptome Study of melanoma cells transduced with Notch 1 Intracellular Domain (NICD)
Transcriptome profiling (mRNA-seq) of melanoma cells overexpressing NICD SOURCE: Vijayasaradhi Setal...
GSE111559: Modulation of dietary methionine intake elicits potent, but distinct, anticancer effects on primary vs metastatic tumors
Methionine concentration in diet influences the growth rate of metastatic cells in vivo SOURCE: Kyle...
GSE112316: Synergistic Axrivation of the Cardiac Enhancer Lanscape during Caridac Reprogramming (RNA-seq data set)
Fibroblasts can be directly reprogrammed toward a cardiac fate by introducing cardiogenic transcript...
GSE104664: Characterization of transcriptomics landscape in HUVEC cells exposed to oxidative stress (Total RNA)
The aim of the project was to characterize the transcriptional landscape of human HUVEC cells expose...