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Sequencing-based assays page 23
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GSE98599: BCG reprogramming of hematopoietic stem cells generates protective innate immunity against tuberculosis (RNA-Seq)
The dogma that adaptive immunity is the only arm of the immune response with memory capacity has bee...
GSE106275: Alteration of the transcriptional program in dendritic cells by GOLPH2
To explore the immune functions of GOLPH2 in dendritic cells in a comprehensive way, we performed gl...
GSE141228: Sporadic activation of an oxidative stress-dependent NRF2p53 signaling network in breast epithelial spheroids and premalignancies
Breastmammary epithelial cells experience different local environments during tissue development and...
GSE97060: Argonaute CLIP defines a deregulated miR-122 bound transcriptome that predicts patient survival in human liver cancer (Mouse RNA-Seq)
MicroRNA-122, an abundant and conserved liver-specific miRNA, regulates hepatic metabolism and funct...
GSE124620 (mouse): Virus-specific memory T cells populate tumors and can be repurposed for tumor immunotherapy
Improvements in cancer immunotherapy are needed. The immunosuppressive tumor microenvironment limits...
GSE113628: A fast PAR-CLIP variant using phenolic extractions
We performed PAR-CLIP in three variants using ELAVL1 (HuR) as example. SOURCE: Benedikt,M,Beckmann (...
GSE99409: Plagl1/Zac1 regulates extracellular matrix genes and the imprinted gene network
In order to determine the targets of the imprinted transcription factor Zac1, we compared wild type ...
GSE138889: Dysregulation of different classes of tRNA fragments in chronic lymphocytic leukemia
We analyzed small RNA sequencing data from CD5+/CD19+ B cells of a cohort of indolent and aggressive...
GSE87043: The Dynamic Epigenetic Landscape of the Retina During Development, Reprogramming, and Tumorigenesis [RNA-Seq_Mm]
In the developing retina, as in many other regions of the central nervous system, multipotent neural...
GSE97770: Inactivation of transcription factor HNF-1 with CRISPR/Cas9 induces epithelial-mesenchymal transition
Hepatocyte nuclear factor-1 (HNF-1) is a tissue-specific transcription factor that is essential for ...
GSE87069: Single-cell RNA Sequencing Uncovers A Close Relationship Between Differentiating Dopamine and Subthalamic Nucleus Neuronal Lineages
Stem cell engineering and grafting of mesencephalic dopamine (mesDA) neurons provides a promising st...
GSE100265: Loss of a CDR1as, a conserved mammalian circRNA, causes miRNA de-regulation and a psychiatric phenotype [rRNA-depleted RNA-Seq]
Circular RNAs (circRNAs) are highly expressed in mammalian brains, with oftentimes conserved express...
GSE96917: Splicing Modulators Act at the Branch Point Adenosine Binding Pocket Defined by the PHF5A-SF3b Complex
Developing small-molecule splicing modulators represents a promising therapeutic approach for variou...
GSE97223: Expression profiles of genetically engineered mouse model tumors (GNA11 Q209L and GNA11 Q209L Bap1 KO)
RNA-seq of end-point tumors harvested from genetically engineered mouse melanoma model SOURCE: Yu Ch...
GSE97941: Single cell analysis of atherosclerosis baseline and regression macrophages-surgical model
CD45+ CD11b+ F4/80+ macrophages were isolated using the BD FACS Aria IIu SORP from pre-transplant ba...
GSE138121: scRNAseq of human iPSC-derived motor neurons from control and ALS patients.
We compare single cell transcriptomic profiles of motor neurons differentiated in vitro from human i...
GSE85520: IRF8 transcription factor controls survival and function of terminally differentiated conventional and plasmacytoid dendritic cells respectively
Interferon regulatory factor-8 (IRF8) has been proposed to be essential for development of monocytes...
GSE95315: Transcriptome analysis of single cells from the mouse dentate gyrus [10X]
RNA sequencing was performed on 5454 single cells from dentate gyrus of CD-1 mice, sampled at postna...
GSE97184: Intestinal epithelial and intraepithelial T cell crosstalk mediates a dynamic response to infection
Oral infection of mice with Salmonella Typhimurium leads to rapid changes in small intestinal TCRgd ...
GSE98027: Changes in gene expression due to alpha-crystallin mutations cryaa-R49C and cryab-R120G in mutant knock-in mouse lenses
To investigate the relationship between histones, chaperone function, and cataracts, we performed RN...
GSE98030: Sequencing of ponatinib-resistant LC-2/ad derivatives (PR1 and PR2) and parental LC-2/ad cells
Sequencing of ponatinib-resistant LC-2/ad derivatives (PR1 and PR2) and parental LC-2/ad cells was p...
GSE100469: 4sU-seq of HFF exposed to salt and heat stress
Primary human foreskin fibroblasts (HFF) were exposed to either salt stress (80mM KCl) or heat stres...
GSE100449: Within-cell-type heterogeneity mediates parallel hippocampal output
Here, we profile gene expression from subiculum pyramidal cells in the mouse. SOURCE: Mark,Steven,Ce...
GSE96568: Single cell RNA-seq reveals expansion of IGRP-reactive CD4+ T cells in recent onset type I diabetes (single-cell RNA-seq of CD4+ pooled islet antigen-reactive T cells)
Islet-reactive T cells found in peripheral blood of type 1 diabetes (T1D) subjects are thought to be...
GSE85513: Genome structure and organization in mouse CD8 T cells [RNA-seq]
Our experiments aimed to investigate the landscape of enhancers and super-enhancers in nave, effecto...
GSE95401: The cerebrovascular response to injury and disease
RNAseq of purified CNS endothelial cells from health and disease. SOURCE: Gladstone Bioinformatics G...
GSE97204: Effect of selective glucocorticoid receptor modulation (SGRM) on gene expression in human prostate cancer cell lines
Human prostate cancer cell lines treated with androgen receptor (AR) agonists/antagonists and concur...
GSE111247: RNA sequencing of LNZ308 glioma cells treated under differential conditions including monotherapies, dual therapy and synergistic triple regimen employing -irradiation, temozolomide and oncolytic measles virus.
The synergistic regimen CT-VT-RT triggers proinflammatory antiviral signalling with activation of ap...
GSE139883: RNA sequencing of sorted immune cells from WT and CD4Cre-Yapfloxed mice from tumors and tumor-draining lymph nodes
We report the effect of T cell lineage-specific Yap deletion on tumor immunity in the B16F10 melanom...
GSE97930: Integrative single-cell analysis of transcriptional and epigenetic states in the human adult brain [snDrop-seq]
Detailed characterization of the cell types in the human brain requires scalable experimental approa...
GSE98086: Transcriptome profiling of Peyers patch naive and germinal center B cells
Germinal center (CD19+Fas+GL7+) and naive (CD19+Fas-GL7-) B cells were sorted from Peyer's patches o...
GSE93909: Type I interferon signaling attenuates Regulatory T cells function in LCMV infection
Regulatory T cells (Tregs) play a cardinal role in the immune system by suppressing detrimental auto...
GSE132684: A mouse mutation that dysregulates neighboring Galnt17 and Auts2 genes is associated with phenotypes related to the human AUTS2 syndrome
AUTS2 was originally discovered as the gene disrupted by a translocation in human twins with Autism ...
GSE113609: MPTAC determines APP fragmentation via sensing sulfur amino acid catabolism
The data from the analysis of transcripts of metabolic enzymes suggested the metabolic pathways that...
GSE116516: Effect of ALOXE3 overexpression on primary murine hepatocyte gene expression profiles
We demonstrate the effects of ALOXE3 overexpression on primary murine hepatocyte gene expression by ...
GSE114260: Effect of estrogen (E2) treatment on the C4-12 relative to the MCF7 cells
To confirm the effect of estrogen, through the estrogen receptor, on cell cycle progression and to i...
GSE96619: Interferon receptor signaling pathways regulating PD-L1 and PD-L2 expression
We studied the molecules involved in downstream signaling induced by interferons to regulate PD- L1 ...
GSE116538: Hypoxia serum starved Flt-1 wild type and Flt-1 heterozygote BMDMs
The goal is to identify differential gene expression between hypoxia serum starved (for 6 hours) Flt...
GSE98580: High capacity of the endoplasmic reticulum to prevent secretion and aggregation of amyloidgenic proteins
Protein aggregation is associated with neurodegeneration and various other pathologies. How specific...
GSE98212: A third generation therapeutic vaccine for human visceral leishmaniasis and post kala azar dermal leishmaniasis: first-in-human trial of ChAd63-KH
Whole blood transcriptomic profiling indicated that CHAd63-KH induced innate immune responses chara...
GSE110097: Analysis of Th17 gene signature in the presence of CD28 costimulation in human CD4 nave T cells
We determined differentially regulated gene expression profile in CD4 nave T cells cultured in prese...
GSE86225: Single-cell transcriptomic analyses reveal distinct dorsal/ventral pancreatic programs
The pancreas of vertebrates is separately derived from both the dorsal and ventral endodermal domain...
GSE97645: Dnmt2 mediates intergenerational transmission of paternally acquired metabolic disorders through sperm small non-coding RNAs
The discovery of RNAs (e.g. mRNAs, non-coding RNAs) in sperm has opened the possibility that sperm m...
GSE114528: Endovascular progenitors invade melanoma tumors and differentiate towards a variety of vascular beds to promote tumor metastasis
Tumors have the capacity to trigger the formation of blood vessels allowing them to spread to other ...
GSE95386: TRIM24 is an oncogenic transcriptional co-activator of STAT3 in glioblastoma
Aberrant amplication and mutations of epidermal growth factor receptor (EGFR) are the most common on...
GSE130017: Analysis of the expression profile of skin fibroblasts FACS-sorted from mice overexpressing activin and/or oncogenes of human papilloma virus 8 in keratinocytes.
Overexpression of activin by keratinocytes promotes HPV8-induced skin tumorigenesis in mice. Activin...
GSE85512: TSHZ3 deletion causes an autism syndrome and defects in cortical projection neurons
TSHZ3, which encodes a zinc-finger transcription factor, was recently positioned as a hub gene in a ...
GSE114285: Next Generation Sequencing Facilitates Quantitative Analysis of ES, pMN, MN, and IN Transcriptomes
In this experiment, we sought to identification the stage specific lncRNAs from the transcriptome of...
GSE94343: ATF4 inhibition by p62 represses stromal metabolic reprogramming and tumorigenesis
Tumors often undergo stress and need to reprogram their metabolism to survive and grow under nutrien...
GSE100687: RNA-Seq analysis of breast cancer cells after shikonin treatment
We performed RNA-seq analysis using differnt breast cancer cell lines (MCF-7, SK-BR-3 and MDA-MB-231...
GSE97443: RNA-seq in acute myeloid leukemia (AML) cells with and without knockdown of METTL14
To dissect the mechanism underlying the oncogenic function of METTL14 in AML, we performed deep sequ...
GSE94367: ATF4 inhibition by p62 represses stromal metabolic reprogramming and tumorigenesis II
Tumors often undergo stress and need to reprogram their metabolism to survive and grow under nutrien...
GSE87093: Identification of Klf9-regulated genes in HT22 tissue culture cells [RNA-Seq]
Krueppel-like factor 9 (Klf9) is a DNA-binding transcription factor that has been implicated in neur...
GSE114417: RNA-seq single cells analysis of 2 tumors from KPC (KrasLSL-G12D/+; Trp53LSL-R172H/+; Pdx1-Cre) mice
We investigated the RNA expression levels of NF-kB ligands and their receptors in epithelial cancer ...
GSE113616: Stromal Fibroblasts Drive Single Cell Heterogeneity in Pancreatic Cancer
To understand the interplay between cancer and stroma, we performed single cell RNA-sequencing of PD...
GSE116620: RNA-seq analysis of LSK from Oga(Vav-Cre) mice compared to wildtype
In order to define HSC dysfunction in Oga mutant mice, we examined transcriptional deregulation in L...
GSE116566: Expression data from WT and Trim24-deficient tumor-associated macrophage(TAM) sorted from B16 bearing mouse
We conducted gene expression profile analysis by using CD45+ CD11b+ F4/80+ TAM sorted from WT or Tri...
GSE114814: Next Generation Sequencing for Quantitative Transcriptomic Profiling of TLR7 deficiency in Neurons
The goal of this study is to compare gene expression of mouse cultured cortical and hippocampal neur...
GSE114502: Altered mRNA splicing by mutant p53 activates oncogenic RAS in pancreatic cancer
Integrating transcriptomic analyses of both clinical PDAC and PDAC models, we identified that the mo...
GSE113848: Transcriptome sequencing after MAGOHB knockdown in MAGOH-deleted or non-deleted cancer cells
Transcriptome profiling was performed after knocking down MAGOHB in ChagoK1 cells or ChagoK1 cells w...
GSE142895: Robust partitioning of microRNA targets from downstream regulatory changes [RNA-seq]
The biological impact of microRNAs is determined by their targets, and robustly identifying direct m...
GSE92699: Distinct mesenchymal lineages and niches promote epithelial self-renewal and myofibrogenesis in the lung
Using flourescence activated cell sorting, we gated on cells negative for CD45, CD326 and CD31, from...
GSE123153: Gene expression comparison of exhausted CD8 T cells after PD-L1 blockade alone or PD-L1 blockade combined with LPS
CD8 T cells after combined treatment exhibit a distinct molecular signature SOURCE: Pablo Penaloza-M...
GSE127205: RNA-seq to compare gene expression profiles between Asf1a WT and Asf1a KO cells
KrasG12D/P53-/-(KP)-Cas9 single clone was transfected with ctrl vector, ctrl sgRNA-1, ctrl-sgRNA-2 o...
GSE115322: Combined phosphoproteome and transcriptome analysis of the macrophage response to mycobacterial cord factor reveals a dichotomy of MINCLE-dependent and -independent signaling
Immune sensing of Mycobacterium tuberculosis relies on recognition by macrophages. Mycobacterial cor...
GSE97275: Genome-wide mRNA expression profiling of ZMYND11 crispr KO in NIH3T3 cells upon IFN treatment.
ZMYND11 is a reader protein, which specifically recognizes H3.3K36me3 and regulate RNA polymerase II...
GSE115077: The novel lncRNA lnc-NR2F1 is pro-neurogenic and mutated in human neurodevelopmental disorders [RNA-seq]
The goal is to examine the global transcriptomic changes upon lnc-Nr2f1 overexpression in both Contr...
GSE96981 (human): Multilineage communication regulates human liver bud self-organization from pluripotency II
Conventional 2-D differentiation from pluripotency fails to recapitulate cell interactions occurring...
GSE94673: RNA-sequencing of brain ECs isolated at P8 from mice with EC-specific deletion of YAP/TAZ
To investigate the role of Hippo-YAP signaling in angiogenesis, we performed RNA-sequencing by using...
GSE98729: Cortical gene expression of WT, Grin1 knockdown, and Grin1 Cre rescue mice
The purpose of the study was to compare cortical transcript abundance between WT mice and Grin1 knoc...
GSE119248: PatchSeq analysis of Pthlh expressing cells of the mouse dorsolateral striatum
In order to investigate how electrophysiological properties vary within the Pthlh population in the ...
GSE109805: Comparison of gene expression profiles of ex vivo sorted Common Lymphoid Progenitors (CLPs) and in vitro cultured cCLPs.
A common lymphoid progenitor cell culture system was established, maintaining a multipotent, prolife...
GSE96729: Conditional p120ctn deletion in pancreatic ductal cells
These experiments aimed to determine the global gene expression patterns in p120WT, p120HET, and p12...
GSE94636: Effects of FTY720 on B cells in experimental autoimmune encephalomyelitis (EAE)
MP4-induced experimental autoimmune encephalomyelitis (EAE) is a B cell-dependent mouse model of mul...
GSE112711: Host and genetic viral adaptations enable development of an immunocompetent mouse model of Zika virus infection
Host and genetic viral adaptations enable development of an immunocompetent mouse model of Zika viru...
GSE99559: SQSTM1/p62-directed metabolic reprogramming is essential for normal neurodifferentiation
Neurodegenerative disorders are an increasingly common and irreversible burden on society, often aff...
GSE97440 (mouse): RNA-sequencing of human leukemia cells and mouse hematopoietic progenitors
human leukemia cells treated with vitamin C for 12 and 72hrs and mouse hematopoietic progenitor cell...
GSE95635: RNA Helicase DDX1 Converts RNA G-Quadruplex Structures into R-Loops to Promote IgH Class Switch Recombination
We performed high-throughput sequencing of chromatin-associated RNA from CH12 cells depleted of Ddx1...
GSE100706: Identification of genes associated with TGF-beta/Smad3-mediated macrophage-myofibroblast transition (MMT) by single-cell RNA sequencing
In this study, we conducted single-cell RNA sequencing (scRNA-Seq) to identify the Smad3-dependent t...
GSE96061: The Quantitative Analysis of Transcriptomes Derived From Ezh2- or Ezh1/2-Deleted Leukemia Stem Cells of Murine Acute Myloid Leukemia
We report dual genetic delstion of Ezh1/2 in murine AML model induced cell cyle progression of quies...
GSE98177: Transcriptome-wide analysis of IL2RA enhancer activation by CRISPRa
We previously performed a tiling CRISPR activation (CRISPRa) screen in Jurkat T cells to discover en...
GSE112345: Viral shRNA Knockdown of INS Promotor Activity in EndoC-H1 Cells
To inhibit INS expression, we used shRNA to target the INS promoter. We find that knocking down INS ...
GSE110449: Catalytic subunits switch drives resistance to EZH2 inhibitors in ARID1A-mutated cells [RNA-seq]
The SWI/SNF chromatin remodeling complex is altered in ~20% of human cancers. ARID1A, a component o...
GSE111945: AComparison of theSexually Dimorphic Pravastatin TranscriptomeinMouse CerebralCortical EmbryonicNeuralStemCells
We used RNA-Seq analysis to identify thesexually dimorphic pravastatin regulated gene expression pro...
GSE102190: Electrophilic stress induced by dimethyl itaconate regulates IkB-zeta-mediated inflammatory responses
Interplay between metabolic state of the cell and its ability to undergo immunological activation ha...
GSE94387: RNA editing is the essential function of ADAR1 and, in the absence of MDA5, is dispensable for normal adult homeostasis [RNAseq (Adult Brain)]
Adenosine-to-Inosine (A-to-I) editing of dsRNA by ADAR proteins is a pervasive feature of the epitra...
GSE99522: The effect of Tmem135 overexpression on the mouse heart
Transgenic mice overexpressing a novel regulator of mitochondrial dynamics, transmembrane protein 13...
GSE113436: A transcriptomic analysis reveals increased complexity of the alternative splicing landscape by Nsmce1 overexpression in mouse hippocampal neuronal cell
Nsmce1 (NSE1 Homolog, SMC5-SMC6 Complex Component) is a Protein Coding gene, it was reported to func...
GSE142826: Up-regulation of JAK-STAT pathway promotes maturation of human stem cell-derived cardiomyocytes
hPSC-CM has been used to model cardiac-related disease phenotypes. However, the immaturity of hPSC-C...
GSE84681: PRC2 represses transcriptionally competent genes on the inactive X-chromosome
Polycomb repressive complex 2 (PRC2) catalyzes histone H3K27me3, which characterizes many silenced g...
GSE115390: Differences in tissue immune cell populations following hematopoietic stem cell transplantation in Crohns disease patients
Treatment of severely refractory Crohns disease (CD) patients remains a clinical challenge. Recent s...
GSE107240: Dynamic EBF1 occupancy directs sequential epigenetic and transcriptional events in B cell programming [RNA-Seq-Cre]
EBF1 is essential for B cell specification and commitment. To explore the dynamics of EBF1 initiated...
GSE115121: TAF1 is critical for AE driven leukemogenesis [RNA-seq]
TAF1 is essential for AE driven leukemogenesis. Depletion of TAF1 impairs the recruitment of AE to i...
GSE96064: H3K4ox-Mediated Chromatin Condensation Protects Breast Cancer Cells from the DNA Damage Repair Machinery
Using an H3K4ox-specific antibody, we determined that the H3K4ox modification is enriched in triple-...
GSE107678: Loss of microRNA-128 promotes cardiomyocyte proliferation and heart regeneration [RNA-seq]
To identify the potential microRNAs (miRNAs) involved in the regulation of cardiomyocyte (CM) prolif...
GSE114342: Alpha-ketoglutarate links p53 to cell fate during tumor suppression
The tumor suppressor TP53 is mutated in the majority of human cancers, including over 70% of pancrea...
GSE95424: Transcriptome analysis of liver tissue in HBV - associated liver fibrosis mice
Purpose:Next-generation sequencing (NGS) were performed to investigate the differentially expressed ...
GSE117621: Differential expression data between E15.5 outflow tracts of Gata4 G295S mutant embryos and littermate controls
E15.5 embryos were micro-disscted from Gata4 G295S mutant mice and littermate controls, RNA was isol...
GSE97471 (human): Differentially expressed genes from RNA-Seq and functional enrichment results are affected by the choice of single-end versus paired-end reads and stranded versus non-stranded protocols
We undertook four mammalian transcriptomics experiments to compare the effect of read mapping, featu...
GSE101772: Fibroblast-specific genetic dissection of TGF-Smad2/3 signaling in cardiac fibrosis
Overall goal: To elucidate fibroblast-specific role of TGF-Smad2/3 signaling in fibroblast activatio...