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Sequencing-based assays page 106
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GSE135180: Dynamic cohesin is required for lineage specific distal gene regulation
The cohesin complex plays essential roles in sister chromatin cohesin, chromosome organization and g...
GSE145068: Pharmacological blockade of high-risk MYCN driven neuroblastoma using an orally-bioavailable CDK2/9 inhibitor
The undruggable nature of oncogenic Myc transcription factors poses a therapeutic challenge in neuro...
GSE148701: RNA sequencing of human marcrophages treated with lipopolysaccharide (LPS) for 8 hours, with or without BCAT1 inhibitor (ERG240)
Branched-chain aminotransferases (BCAT) are enzymes that initiate the catabolism of branched-chain ...
GSE144654: RNA sequencing analysis of WT- and Tet2-/-G17VRHOA-CD4 splenocytes
Angioimmunoblastic T-cell lymphoma, a subtype of T-cell lymphoma, is a disease with relative poor ou...
GSE139378: Pharmacological activation of pyruvate kinase M2 (PKM2) inhibits CD4+ T cell pathogenicity and suppresses autoimmunity
Pyruvate kinase (PK) catalyzes the conversion of phosphoenolpyruvate to pyruvate during glycolysis. ...
GSE143743: Knocking out C9ORF72 exacerbates axonal trafficking defects associated with hexanucleotide repeat expansion and reduces levels of heat shock proteins I
iPSCs with mutant C9ORF72 were edited using CRISPR/Cas9 (1) to knockout C9ORF72 or, alternatively, (...
GSE149275: Elevated EGFR signals in epithelial cells delay mammary gland development and skew organoids away from stem cell signatures
During puberty, robust morphogenesis occurs in the mammary gland and mammary stem- and progenitor- c...
GSE144323: Dual RNA 3 end processing of H2A.X messenger RNA maintains DNA damage repair throughout the cell cycle
Replication-dependent (RD) histone mRNA are the only non-polyadenylated protein coding transcripts i...
GSE132155: beta-glucan-induced trained immunity protects against Leishmania braziliensis infection: a crucial role for IL-32
We reported the first definitive characterization of the role of IL-32 in the trained phenotype, the...
GSE148667: Culturing C2C12 myotubes on micromolded gelatin hydrogels accelerates myotube maturation
We report that differentiation of the C2C12 myoblast line on patterened hydrogels results in the inc...
GSE136993: GM-CSF-transduced proliferating myeloid cells represent cell cycle related gene signature
We previously established a method to generate myeloid lineage cells with proliferation capacity fro...
GSE136948: FoxO Transcription Factors Are Critical Regulators of Diabetes-Related Muscle Atrophy
Insulin deficiency and uncontrolled diabetes lead to a catabolic state with decreased muscle strengt...
GSE144335: Transcriptomics analysis of lineage-restricted Dendritic-cell (DC) progenitor cells in obesity
The overall goal of the project is to understand transcript-level changes in DC-progenitors from bon...
GSE148758: Tnfaip2/Exoc3 driven lipid metabolism is essential for stem cell differentiation & organ homeostasis [Mus musculus, 2]
Lipid metabolism is recognized as a key process for stem cell maintenance and differentiation but ge...
GSE136572: Polymorphic immune mechanisms regulate commensal repertoire
Environmental influences such as infections and dietary changes strongly affect a hosts microbiota. ...
GSE142441: Integrating Next Generation Sequencing with Morphology Improves Prognostic and Biologic Classification of Spitz Neoplasms [RNA-Seq]
The newest WHO classification suggests eliminating cases with BRAF and NRAS mutations from the categ...
GSE94696: POLR3G Dependent PolyA+ and smallRNA Transcriptomes in Human Pluripotent Stem Cells
POLR3G is expressed at high levels in human pluripotent stem cells (hPSCs) and is required for maint...
GSE95227: Gene expression profiling of ISWI chromatin remodeler mutants before and after DNA damage
Gene expression profiling of ISWI chromatin remodeler mutants before and after DNA damage BAZ1A is a...
GSE144357: Clonal maintenance of transcriptional and epigenetic states in cancer cells.
We performed single-cell transcriptome analysis (using MARS-seq and 10x) of four human cell lines, a...
GSE137187: Klf6 protects -cells against insulin resistance-induced dedifferentiation
In the pathogenesis of type 2 diabetes development of insulin resistance triggers an increase in pan...
GSE152972: Blockade of the G-CSFR or C5 in a murine model of unilateral warm renal ischemia-reperfusion injury (IRI).
Purpose: Understand gene transcriptional changes in kidney cell populations after ischemia-reperfusi...
GSE145163: Modulation of Wnt and Activin/Nodal supports efficient derivation, cloning and suspension expansion of human pluripotent stem cells
Various culture systems have been used to derive and maintain human pluripotent stem cells (hPSCs), ...
GSE135868: Heme metabolism confronts urinary pathogens at the urothelium
The kidney and bladder expresses a variety of powerful defense mechanisms to limit urinary infection...
GSE142499: Viral-Induced Alternative Splicing of Host Genes Promotes Influenza Replication
Competition and interplay between host and viral gene expression programs is a critical determinant ...
GSE142582: High-throughput transcriptome analysis of clinical psoriasis
Purpose: The present study is aiming to understand transcriptome changes during psoriatic changes us...
GSE142526: Single cell transcriptomic comparison of human fetal retina, hPSC-derived retinal organoids, and long-term retinal cultures.
To study the development of human retina, we used single cell RNAseq at key fetal stages and followe...
GSE97541: A Unique B-cell Regulome links Notch to Downstream Oncogenic Pathways in Small B-cell Lymphoma
We perform integrative analysis of Notch-dependent transcripts, genome-wide binding of Notch transcr...
GSE149311: RNAseq analysis of distinct small intestinal cell populations isolated from Lgr5-EGFP C57BL/6 mice treated with NRG1
Purpose: The goal of the study was to investigate the effect of Neuregulin 1 (NRG1) on intestinal cr...
GSE135276: RNA-seq-based identification of StAR upregulation by islet amyloid formation
Aggregation of islet amyloid polypeptide (IAPP) into islet amyloid results in -cell toxicity in huma...
GSE143741: TP53 c.1000G>C; p.G334R is an Ashkenazi Jewish predominant mutation associated with a low penetrance Li-Fraumeni Syndrome
Multiple family members with cancer or individuals with multiple primary cancers are indicative of p...
GSE151200: Division of labor between YAP and TAZ in non-small cell lung cancer [RNA]
The paralogous transcriptional cofactors Yes-associated protein (YAP) and transcriptional co-activat...
GSE145053: Cortical kidney bulk RNA Sequencing in the reversible unilateral ureter obstruction model.
The kidney has limited capacity to regenerate following injury and preferentially repairs chronic in...
GSE148709: Interferons disrupt lung epithelial repair during recovery from respiratory infection [RN19197]
Respiratory viral infections cause lung epithelial damage, barrier dysfunction and severe disease. T...
GSE145145: Targets of EOMES in mouse CD4+ T cells
To gain mechanistic insights into how EOMES regulates CD4+ T-cell differentiation and function, we p...
GSE149257: Generation of Inner Ear Hair Cells by Direct Lineage Conversion of Primary Somatic Cells [RNA-seq]
We purified seven different cell populations and performed RNA sequencing to profile transcriptional...
GSE97395: Transcriptomic insights into human decidual and peripheral blood CD4 T cells
We performed the analysis of transcriptional and alternative splicing landscapes for paired decidual...
GSE145815: The transcriptional landscape of Venezuelan equine encephalitis virus infection
No vaccines or antivirals are approved against Venezuelan equine encephalitis virus (VEEV) infection...
GSE151090: Verteporfin treatment controls morphology, phenotype, and global gene expression for cells of the human nucleus pulposus
Purpose: It has been observed that the drug verteporfin (VP), a known disruptor of YAP-TEAD signalin...
GSE143758: Single nuclei RNA-seq of brain of mouse Alzheimer's disease model
Here we report single nucleus RNA-seq shows in 5xFAD mouse model of AD and WT, showing changes in t...
GSE142609: NFIA differentially controls adipogenic andmyogenic gene program through distinct pathways to ensure adipocyte differentiation [ingSVF RNA-seq]
The transcription factor nuclear factor I-A (NFIA) is a regulator of brown adipocyte differentiation...
GSE142580: Impaired phagocytic function in CX3CR1+ tissue-resident skeletal muscle macrophages prevents muscle recovery after influenza A virus-induced pneumonia in aged mice
Skeletal muscle dysfunction in survivors of pneumonia is a major cause of lasting morbidity that dis...
GSE145964: Genome-wide R-loop landscapes during epigenetic programming and reprogramming
The role of R-loops, three-stranded nucleic acid structures harboring DNA:RNA hybrids, in regulating...
GSE149104: ALC1 and PARP activities coordinate chromatin accessibility and viability in homologous recombination deficient cells (RNA-seq)
The response to Poly (ADP-ribose) polymerase inhibitors (PARPi) is dictated by homologous recombina...
GSE145502: ZipSeq : Barcoding for Real-time Mapping of Single Cell Transcriptomes
single cell RNA Sequencing runs for various models linking transcriptomes with regional position usi...
GSE147043: Distinct immune microenvironments between primary and paired metastatic tumors in gastric cancer patients
We performed RNA-seq to investigate the differences in the gene expression profiles between primary ...
GSE146508: Transcriptome and open chromatin analysis of 5-month mouse liver and blood by the TaRGET II consortium
The TaRGET (Toxicant Exposures and Responses by Genomic and Epigenomic Regulators of Transcription) ...
GSE135278: The transcription factor Bhlhe40 programs mitochondrial regulation of resident CD8+ T cell fitness and functionality
Tissue-resident memory CD8+ T cells (Trm) share characteristics and core residency gene programs wit...
GSE149189: RNA-Seq of human fetal and adult scalp hair follicle dermal papilla (DP), dermal sheath cup (DSC), and interfollicular dermal (IFD) cells
Much is still unknown about the molecular regulatory networks which govern the dermal papillas (DP) ...
GSE134700: Cell cycle-dependent YTHDF2 promotes mitotic entry by repressing WEE1
The m6A modification regulates mRNA stability and translation. Here we show that transcriptomic m6A ...
GSE151113: Effects on imidazoacridinone C-1311 on the transcriptomic profile in prostate cancer cell depending on their AR status.
Human prostate cancer cells, LNCaP (AR+) and DU-145 (AR-), were treated with C-1311 to identify the ...
GSE148767: TGF- treatment of human melanoma cell lines
To analyse whether the activation of TGF- signalling (recombinant hTGF-, 5 ng/mL; PeproTech) is able...
GSE149167: Craniofacial periosteum-derived cells as source for bone tissue engineering
The development of alternatives for autologous bone grafts is a major focus of bone tissue engineeri...
GSE135224: An ontogenetic switch in the positive and negative selection of B cells [bone marrow and fetal liver]
Developing B cells can differentiate into a variety of different subsets, but the mechanisms that de...
GSE147744: Zeb2 regulates myogenic differentiation in pluripotent stem cells
Zinc finger E-box-binding homeobox 2 (ZEB2, also known as SMAD interacting protein 1 or Zfhx1b) prot...
GSE148556: Repression of the B cell identity factor Pax5 is not required for plasma cell development
B cell and plasma cell fates are controlled by different transcriptional networks, as exemplified by...
GSE143685: Neuroinflammation and EIF2 signaling persist despite antiretroviral treatment in an HiPSC tri-culture model of HIV infection [bulk RNA-seq]
HIV-Associated Neurocognitive Disorders (HAND) affect over half of HIV-infected individuals, despit...
GSE136441: Single-cell analysis RNA sequencing of prenatal and neonatal gonads/ovaries at E11.5, E12.5, E14.5, E16.5, E18.5, P1 and P5
We sequenced more than 52,500 single cells from E11.5 to P5 gonads to analyze primordial follicles a...
GSE147111: The LIM protein Ajuba promotes a metastatic phenotype in colon cancer cells
RNA-seq of Colon cancer cell line Sw480 with Ajuba OE and KD.Colon cancer, along with its potential ...
GSE152050: ARID1A deficiency weakens BRG1-RAD21 interaction that jeopardizes chromatin compactness and drives HCC metastasis [RNA-seq]
ARID1A, encoding a subunit of SWI/SNF chromatin remodeling complex, is widely recognized as a tumor ...
GSE151154: Global analysis of kidney gene expression by RNA-Seq of aged CTRP1-deficient mice on high-fat diet
Aging and obesity profoundly influence organ system health by altering circulating levels of hormone...
GSE141851: Massively parallel, time-resolved single-cell RNA sequencing with scNT-seq
Single-cell RNA sequencing offers snapshots of whole transcriptomes but obscures the temporal dynami...
GSE143698: Hyperactive platelets promote aberrant Tfh cell response and disrupt immune homeostasis
We unexpectedly found that platelet specific PTEN deletion mice exhibited spontaneous severe lymphad...
GSE38770: Histone variant H2A.Bbd is associated with active transcription and mRNA processing in human cells [RNA-Seq]
Variation in chromatin composition and organization often reflects differences in genome function. H...
GSE145907: Characterization of the chromatin accessibility in an Alzheimers disease (AD) mouse model (RNA-Seq)
The assay for transposase-accessible chromatin by sequencing (ATAC-seq) was used to investigate the ...
GSE145486: RNA-Sequencing of LPS-stimulated TLR4 HEK293 cells edited at an immune-response trans-eQTL locus
In order to investigate the genetic effect of an IRF1-associated immune-response trans-eQTL, we used...
GSE46665: Identification of differentially expressed transcripts and pathways one week and six months following implant of left ventricular devices
A specific set of genes involved in regulating cellular immune response, antigen presentation, and T...
GSE148803 (mouse): Gene expression regulation by the Chromodomain Helicase DNA-binding protein 9 (CHD9) chromatin remodeler is dispensable for murine development
Purpose: Chromodomain helicase DNA-binding (CHD) chromatin remodelers regulate transcription and DNA...
GSE146731 (human): Histone H3.3G34-mutant interneuron progenitors co-opt PDGFRA for gliomagenesis
Histone H3.3 glycine 34 to arginine/valine (H3.3G34R/V) mutations occur in deadly hemispheric high-g...
GSE17312: BI Human Reference Epigenome Mapping Project
The NIH Roadmap Epigenomics Mapping Consortium aims to produce a public resource of epigenomic maps ...
GSE26880: PARP1- and CTCF-mediated interactions between active and repressed chromatin at the lamina promote oscillating transcription
Transcriptionally active and inactive chromatin domains tend to segregate into separate sub-nuclear ...
GSE136627: Gene regulation in gastrocnemius muscle of denervated mouse with HDAC4 inducible knockout or class IIa HDAC inhibitior NVS-HD1 treatment
Our class IIa HDAC inhibitor, NVS-HD1, inhibited HDAC4 with less than 1 nM potency while exhibiting ...
GSE147183: maternal microbiome modulation of fetal brain development and sensory behavior
Dysbiosis" of the maternal gut microbiome, in response to environmental challenges such as infection...
GSE148791: Single Cell RNA-sequencing of mammary gland epithelial cells
The mammary gland epithelium is composed of basal cells (BC) and luminal cells (LC). Lineage tracing...
GSE136978: Long-term programming of CD8 T cell immunity by perinatal exposure to stress hormone [RNA-seq]
Early life environmental exposure, particularly during perinatal period, can have a lifelong impact ...
GSE143749: Tuft cell formation reflects epithelial plasticity in pancreatic injury; implications for modeling human pancreatitis
We performed RNA-seq on pancreatic tuft cells and non-tuft epithelial cells in caerulein-induced pan...
GSE152978: Identification of 3 Endotypes In Pediatric ARDS Using Nasal Transcriptomics-Standard Input
This study used nasal transcriptomic profiling of the inferior turbinate in control and pediatric AR...
GSE146694: KRAS drives immune evasion in a genetic model of pancreatic cancer [bulk RNA-seq]
Immune evasion is a hallmark of KRAS-driven cancers, but underlying mechanism and clinical implicati...
GSE144361: RNA-Seq for transcriptome analysis of germinal center B cells upon GSK3 inhibition
To compare transcriptional changes of germinal center B cells upon GSK3 inhibition, induced GC B cel...
GSE148529: bT87Q-globin gene therapy reduces sickle hemoglobin production, allowing for ex vivo anti-sickling activity in human erythroid cells
We performed RNA-seq analysis on immortalized human erythroid cell line (HUDEP-2), that had been eng...
GSE149313: Molecular signatures of inflammatory profile and B-cell function in SFTS patients
Severe fever with thrombocytopenia syndrome banyangvirus (SFTSV) induces immunopathogenic disease wi...
GSE136584: Parallel PRC2/cPRC1 and vPRC1 pathways silence lineage-specific genes and maintain self-renewal in mouse embryonic stem cells
The transcriptional repressors Polycomb Repressive Complex 1 (PRC1) and PRC2 are required to maintai...
GSE136593: RNA sequencing of aortic tissue of Klotho knock-out mice treated with a minimal and a high magnesium diet
Klotho knock-out mice are an important model for CKD-induced calcification. In CKD, serum magnesium ...
GSE148222: Next Generation Sequencing of expression profile from synchronized WT and BRD4 KO MEFs cells at different time point
Brd4f/f ERT2Cre MEFs are a type of fibroblast prepared from Brd4f/f ERT2Cre/- mouse embryo. MEFs ar...
GSE137001: Excluding Oct4 from Yamanaka cocktail unleashes the developmental potential of iPSCs
Oct4 is widely considered the most important among the four Yamanaka reprogramming factors. Here we ...
GSE149280: Genetic screening for single-cell variability modulators driving therapy resistance
We present the transcriptome of WM989 melanona cells without or without inhibition of DOT1L. Differe...
GSE144633: Tissue responses to Shiga toxin in human intestinal organoids
Intestinal tissue responses to protein synthesis inhibition by Shiga toxin are complex. Organoid mo...
GSE147191: Single Cell Transcriptomics Reveals Dysregulated Cellular and Molecular Networks in a Fragile X Syndrome Model
Despite advances in understanding the pathophysiology of Fragile X syndrome (FXS), its molecular bas...
GSE146304: RNA-Seq Analysis of FACS-sorted GFP-expressing and skeletal stem cells (SSC) from the bone marrow of mice with S1P ablation in the Osterix (Osx)-lineage (Cko)
Comparison of the transcriptome of GFP-expressing cells from the bone marrow compartment of Cko mice...
GSE144353: Untargeted transcriptomic profiling of activated primary human CD4+ T cells treated with metformin and 2-deoxyglucose
Purpose: To investigate the effects of metabolic inhibitors metformin and 2-deoxyglucose on the glob...
GSE144864: NRF2 Activates Growth Factor Genes and Downstream AKT Signaling to Induce Mouse and Human Hepatomegaly (RNA-seq dataset 2)
The goal of this study is to provide the liver metabolic changes in the liver specific constitutivel...
GSE150708: scRNA profiles on hESC-derived lung cells and lung-macrophage co-cultured cells
Study transcriptomes on the lung cells and macrophages derived from hESC SOURCE: Joyce Chen (joycech...
GSE147206: Hair-bearing human skin generated entirely from pluripotent stem cells
In this study, we defined a differentiation approach for guiding human pluripotent stem cells in to ...
GSE135235: Light-entrained and brain-tuned circadian circuits regulate ILC3 and gut homeostasis
Group 3 innate lymphoid cells (ILC3) are major regulators of inflammation, infection, microbiota com...
GSE149294: RNA-seq of in vitro differentiated human abdominal and gluteal adipocyte cell lines following doxycycline induced RSPO3-knockdown
GWAS studies and our own work have identified RSPO3 as a gene modulating human body fat distribution...
GSE147978: Knockdown of transcription factor Creb3l1 in anterior pituitary mouse corticotroph cell line AtT20
Transcription factor Creb3l1 is a non-classical ER stress molecule that is emerging as an important ...
GSE145945: Keap1 deficiency results in a genotype-specific dependency on Slc33a1
Approximately 20-30% of human lung adenocarcinomas (LUAD) harbor loss-of-function (LOF) mutations in...
GSE78213: SPOP mutation confers intrinsic BET inhibitor resistance in prostate cancer (BRD4_JQ1_RNA-seq)
Bromodomain and extraterminal domain (BET) protein inhibitors are emerging as promising therapeutics...
GSE144705: Distinct signature, origin and dynamics of macrophages in the peripheral and central nervous system (bulk)
We performed ontogenic, transcriptomic and spatial characterization of sciatic nerve Macs (snMacs). ...
GSE145357: Regulatory T Cells Play a Central Role in a Subset of Idiopathic Preterm Birth and Adverse Neonatal Outcomes
Regulatory T cells (Tregs) have been exhaustively investigated during early pregnancy; however, thei...
GSE137299: Characterization of cochlear development at the single cell level
The organ of Corti, located in the floor of the scala media of the cochlea, acts as the primary sens...