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Sequencing-based assays (Page 63)
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GSE109226: Dysregulation of RNA splicing in tauopathies
Pathological aggregation of RNA binding proteins (RBPs) has emerged as an important driver of multip...
GSE108775: Graded arrays of spinal and supraspinal V2a interneuron subtypes underlie forelimb and hindlimb motor control [RNA-seq]
The spinal cord contains neural networks that enable regionally-distinct motor outputs along the bod...
GSE108068: Replacing reprogramming factors with antibodies selected from autocrine antibody libraries
Identification of antibodies with reprogramming activity from combinatorial libraries SOURCE: Kristi...
GSE110672: Glucagon contributes to liver zonation in mice [Gcg KO]
Liver zonation characterizes the separation of metabolic pathways along the lobules and is required ...
GSE108491: Id1 in mutant KRAS lung adenocarcinoma
Analysis of global gene expression changes in mutant KRAS lung adenocarcinoma cells upon Id1 inhibit...
GSE101898: A single TCF transcription factor, regardless of its activation capacity, is sufficient for effective trilineage differentiation of ES cells
Co-expression and cross-regulation of the four TCF/LEFs render their redundant and unique functions ...
GSE117382: Human muscle-derived CLEC14A-positive cells regenerate muscle independent of PAX7
Skeletal muscle stem cells, called satellite cells, are responsible for postnatal muscle growth, hom...
GSE112607: To determine the potential molecular mechanisms by which STAT5 signaling controls colonic crypt homeostasis, we isolated total RNA from ileal intact crypts of STAT5+/+, STAT5DIEC-/- and STAT5DIEC+++ mice and performed RNA sequencing (RNA-seq).
Reads were aligned to the mm10 genome with annotations provided by Ensembl. Transcripts were filter...
GSE109315: Gene expression analysis of mouse brain regions after chronic social defeat stress (CSDS)
Chronic psychosocial stress is a risk factor for psychiatric disorders, and genetic factors interact...
GSE114312: A distinct lineage of origin reveals heterogeneity of plasmacytoid dendritic cells I
Plasmacytoid dendritic cells (pDCs) are an immune subset devoted to the production of high amounts o...
GSE115232: The 3' end processing factor PCF11 regulates gene expression based on gene size and intronic polyadenylation
Genes with different sizes have distinct expression patterns and functions. Here we show that the 3'...
GSE112381: Diverse reprogramming codes for neuronal identity
The transcriptional programs that establish neuronal identity evolved to produce a rich diversity of...
GSE100601: Id proteins suppress E2A-driven iNKT cell development prior to TCR selection [RNA-seq_new]
Id proteins have been shown to promote the differentiation of conventional and T cells, and to supp...
GSE114151: PRMT5 regulated transcriptome in prostate cancer cells
Compared to intensely studied DNA methylation, protein methylation is less studied. PRMT5 is the maj...
GSE108304: Transcriptome Analysis Reveals a Role for Myc in Constitutive and Antiestrogen-resistant Proliferation of Breast Cancer Cells Expressing ERY537S and ERD538G Mutations
Approximately 30% of metastatic breast cancers harbor estrogen receptor (ER/ESR1) mutations that ar...
GSE140732: A Highly Phenotyped Open Access Repository of Alpha-1 Antitrypsin Deficiency Pluripotent Stem Cells
We profiled the global transcriptomes of 10 featured AATD-patient specific iPSC that underwent direc...
GSE110685: Low density granulocytes and their gene signature associate with vascular inflammation and coronary atheroclerosis in systemic lupus erythematosus patients
Patients with systemic lupus erythematosus (SLE) display an increased risk of cardiovascular disease...
GSE112412: Combinatorial knockout of RAR, RAR, and RAR completely abrogates transcriptional responses to retinoic acid in murine embryonic stem cells
All-trans retinoic acid (ATRA) alters gene expression in CCE WT embryonic stem cells, but has no eff...
GSE137524: Integrated single cell and bulk gene expression and ATAC-seq reveals heterogeneity and early changes in pathways associated with resistance to cetuximab in HNSCC sensitive cell lines (scRNA-Seq)
The identification of the potential mechanisms of resistance while tumor cells still respond to ther...
GSE112222: BAZ2A safeguards genome architecture of ground-state pluripotent stem cells
Chromosomes have an intrinsic tendency to segregate into compartments, forming long-distance contact...
GSE100607: Pigment producing melanocytes as the cells of origin of BRAFV600E-induced mouse cutaneous melanoma
To investigate whether cutaneous melanoma originates from a resident adult melanocyte stem cell (MSC...
GSE116073: Specific modulation of HIV RNA splicing and upregulation of anti-inflammatory miR-124 by the new drug candidate ABX464
Purpose: To ensure that ABX464 acted specifically on HIV splicing and did not significantly or globa...
GSE128466: Eomes and Brachyury control pluripotency exit and germ-layer segregation by changing the chromatin state
We aimed to elucidate molecular mechanisms of first lineage decision in the mouse pluripotent epibla...
GSE106406: Transcription factor Etv6 controls functional differentiation of cross-presenting classical dendritic cells [RNA-Seq]
An IRF8-dependent subset of classical dendritic cells (cDCs), termed DC1, effectively cross-primes C...
GSE110684: Identification and characterization of HIV-specific resident memory CD8+ T cells in human lymphoid tissue
We investigate the role of resident memory T cells in protective immunity in HIV infection; ; Fundin...
GSE109533: Blocking IFNRA1 inhibits Multiple Myeloma-driven regulatory T-cell expansion and immunosuppression
Despite significant advances in the treatment of multiple myeloma (MM), most patients succumb to dis...
GSE116225: Regulation of brown fat homeostasis by H19 lincRNA [I]
Increases in organismal energy expenditure, as during cold exposure or exercise training, can improv...
GSE107998: Transcriptome (RNA-seq) of statin-treated human primary myotubes
Statin-induced myopathy is a common side-effect but its mechanisms in human skeletal muscle have nev...
GSE109167: EZH2 Reduction Is an Essential Mechanoresponse for the Maintenance of Super-enhancer Polarization
Despite the ubiquitous mechanical cues at both spatial and temporal dimensions, cell identities and ...
GSE104478: scRNAseq reveals heterogeneity among mouse bone marrow Ly6Chi monocytes produced by GMPs and MDPs
Granulocyte-monocyte progenitors (GMPs) and monocyte-dendritic cell progenitors (MDPs) produce monoc...
GSE111723: RNA-seq in Smchd1 control and Smchd1 deleted male and female neural stem cells.
We sought to examine whether the non-canonical SMC protein Smchd1 plays a role in chromosome conform...
GSE110341: RNA-seq of control and Lmna -/- mice heart samples
RNA-sequencing analysis from whole heart ribosome depleted RNA from the 2-week old WT and Lmna-/- ...
GSE111138: RNA-Seq of CD8+ T cells expressing different levels of Runx3 in during LCMV infection (in vivo)
T cell receptor (TCR) stimulation of nave CD8+ T cells initiates reprogramming of cis-regulatory lan...
GSE109161: Comparison of transcriptional changes after CD28/CD3z and 4-1BB/CD3z chimeric antigen receptor ligation
The adoptive transfer of chimeric antigen receptor- (CAR) modified T cells is revolutionizing the tr...
GSE130885: Transcriptomic alterations of stromal cells during ageing
The hematopoietic microenviroment plays a pivotal role in erythropoiesis. Here we compare the transc...
GSE117570: Reprogramming of Tumor-infiltrating Immune Cells in Early Stage of NSCLC
Comparing the relative proportions of immune cells in tumor and adjacent normal tissue from NSCLC pa...
GSE100674: Subset- and tissue-defined STAT5 thresholds control homeostasis and function of innate lymphoid cells
Innate lymphoid cells (ILCs) patrol environmental interfaces to defend against infection and protect...
GSE109491: LKB1, Salt-Inducible Kinases, and MEF2C are linked dependencies in acute myeloid leukemia (RNA-Seq)
Transcriptome analysis by high throughput sequencing SOURCE: Yusuke Tarumoto (ytarumot@cshl.edu) - ...
GSE116279: Dynamic BAF chromatin remodeling complex subunit inclusion promotes temporally distinct gene expression programs in cardiogenesis [RNA-Seq III]
We compared differential gene expression between WT and BAF60c KO and between WT and BAF170 KO card...
GSE102072: Hepatic transcriptome by Next Generation Sequencing of WT and clock mutant mice fed a HFD ad libitum or time-restricted feeding.
Increased susceptibility of circadian clock mutant mice to metabolic diseases has led to the underst...
GSE111696: Circadian Rhythms in Bmal1-/- Mouse Fibroblast Cells and Liver Tissue
Circadian clocks exist in almost all levels of living organisms and play elementary roles in the per...
GSE138581: The molecular and stromal landscape of salivary duct carcinoma reveals new therapeutic opportunities
Purpose: RNA-sequencing data was used to determine the main molecular pathways invovled in SDC and d...
GSE100820: Genetic deletion or small molecule inhibition of the arginine methyltransferase PRMT5 exhibit anti-tumoral activity in mouse models of MLL-rearranged AML
The hematological malignancies classified as Mixed Lineage leukemias (MLL) harbor fusions of the MLL...
GSE107943: Integrative molecular and clinical analysis of intrahepatic cholangiocarcinoma reveals two prognostic subclassees
Intrahepatic cholangiocarcioma has two molecular classification of intrahepatic CCA with distinct cl...
GSE140445: Transcriptome analysis of nave or stimulated WT and TRIM28 KO CD4 T cells (RNA-seq)
Critical role for TRIM28 and HP1b/g in the epigenetic control of T cell metabolic reprogramming and ...
GSE116283: Human Treg IFNg/IL-10 subpopulations
Human Tregs isolated from PBMCs were sorted into 4 different subpopulations based on IFNg and IL-10 ...
GSE109546: Loss of adrenergic nerves in bone marrow drives hematopoietic stem cell niche aging
Aging of hematopoietic stem cells (HSCs) is associated with the decline of their regenerative capaci...
GSE108863: An integrative network biology analysis identifies miR-508-3p as the determinant and a prognosis biomarker of the mesenchymal subtype ovarian cancer
Recently, several research groups have identified the mesenchymal subtype of serous OvCa on the basi...
GSE112174: RNA-seq for MP, AML and MEFs from mice that carry a "knock-in" allele of the mutant splicing factor, U2af1(S34F), with or without homozygous deletion of the transcription factor, Runx1
We have generated mice that carry Cre-dependent "knock-in" alleles (MGS34F and IES34F) of U2af1(S34F...
GSE100685: Dynamic methylome remodeling throughout mammalian fetal development
Genetic studies have revealed an essential role for cytosine DNA methylation in gene regulation. How...
GSE111007: RNA-Seq profiling of iPSC-derived ventricular and atrial cardiomyocytes
We profiled RNA expression in human iPSC-derived ventricular and atrial cardiomyocytes SOURCE: Gabri...
GSE115266: Virus Infection Induces Expression of Novel RNAs in Human Cells
Innate antiviral immune responses are driven by virus-induced changes in host gene expression. In t...
GSE109965: Analysis of genetically diverse macrophages reveals local and domain-wide mechanisms that control transcription factor binding and function
Non-coding genetic variation is a major driver of phenotypic diversity and allows investigation of m...
GSE110608: RNA sequencing analysis of human embryonic stem cells and axial progenitors
We analysed the transcriptomes of human embryonic stem cells (hESCs) and in vitro derived axial prog...
GSE102963: The E3 ubiquitin ligase Siah1 regulates adrenal gland organization and hyperaldosteronism
Primary and secondary hypertension are major risk factors for cardiovascular disease. Elevated secre...
GSE109288: Impaired immunosurveillance by the simultaneous loss of both atypical PKCs drives serrated intestinal cancer
The serrated adenocarcinoma subtype accounts for 15-30% of all colorectal cancers (CRCs) and is aggr...
GSE108188: Immune-Responsive Gene 1 expression in myeloid cells prevents neutrophil mediated immunopathology during Mycobacterium tuberculosis infection [macrophage]
Immune-Responsive Gene 1 (Irg1) is a mitochondrial enzyme that produces itaconate under inflammatory...
GSE109485: Anti-PD-1/anti-CTLA-4 efficacy in melanoma brain metastases depends on extracranial disease and augmentation of CD8+ T cell trafficking
Intracranial B16 melanoma tumors isolated from C57Bl6 mice were analyzed by mRNAseq. Four experiment...
GSE110725: Estrogen Receptor Drives Pro-Resilient Transcription in Mouse Models of Depression
Most people exposed to stress do not develop depression. Animal models have shown that stress resili...
GSE112686: Effect of hyperfractionated irradiation (HFRT) of prostate primary basal cells (PrEPs) on the transcriptome
We irradiated PrEPs derived from four patients undergoing radical prostatectomy according to a HFRT ...
GSE109586: IL-15 Complex-Stimulated NK cells Protect Mice from Cerebral Malaria
We report a comparison of purified mouse NK cells from mice treated in vivo with either IL-2 cytokin...
GSE113154: RNA Sequencing Facilitates Quantitative Analysis of Wild Type and HRD1-/- liver Transcriptomes
Screen the differential genes of Wild Type and HRD1-/- liver under fasted and refed condition SOURCE...
GSE108020: Single-cell RNA-seq of mouse dopaminergic neurons informs candidate gene selection for sporadic Parkinson's disease
Genetic variation modulating risk of sporadic Parkinsons disease (PD) has been primarily explored th...
GSE112715: Loss of Neurological Disease HSAN-I-Associated Gene SPTLC2 Impairs CD8+ T Cell Responses to Infection by Inhibiting T Cell Metabolic Fitness
Hereditary sensory and autonomic neuropathy type I (HSAN-I) is neurological disorder characterized b...
GSE102727: Accelerated and Improved Differentiation of Retinal Organoids from Mouse Pluripotent Stem Cells in Rotating-Wall Bioreactors
Pluripotent stem cells can be differentiated into three-dimensional (3D) retinal organoids, with maj...
GSE113604: BET bromodomain dependency in EWS/ETS driven Ewing Sarcoma
The pathognomonic EWS/ETS fusion transcription factors drive Ewing sarcoma (EWS) by orchestrating an...
GSE111011: Integrative analysis of mRNA and lncRNA profiles identified pathogenetic lncRNAs in esophageal squamous cell carcinoma
Systems biology approaches can help understand pathogenesis of complex human diseases like cancers f...
GSE109519: Genome-wide transcriptional response to random aneuploidy in human cells
Previous studies on transcriptional response to aneuploidy have focused on comparing model cell line...
GSE84432: Analysis of active enhancers and direct androgen receptor target genes in VCaP prostate cancer cells
Androgen receptor (AR) is typically overexpressed in castration-resistant prostate cancer (CRPC). CR...
GSE109556: Transcriptional profiling of pre- and post-natal glutamatergic progenitors and nascent neurons by single cell RNA sequencing
Purpose: We labeled synchronous cohorts of prenatal and postnatal glutamatergic progenitors to study...
GSE113182: Characterisation of the myeloid differentiation process of human hematopoietic stem cells
Hematopoietic stem cells (HSCs) can self-renew and/or differentiate into various functionally diverg...
GSE111157: Modulating Immune Cells to Prevent Breast Cancer Lung Metastasis
Current lack of insight into mechanisms governing breast cancer metastasis has precluded development...
GSE117713: Transcriptome analysis of murine B cell and CLL samples
Transcriptional profiling revealed that murine VH11 and non-VH11 CLL differed in the upregulation of...
GSE121232: Mir-146a wild-type 3' sequence identity is dispensable for proper innate immune function in vivo (RNA-Seq)
A long-prevailing model has held that the seed region (nucleotides 2-8) of a microRNA is typically s...
GSE110051: GRNs driving cartilage and bone formation interact via averaging and synergism during cartilage maturation
Transcriptional control of any biological process occurs through the action of one to many gene regu...
GSE109467: Developmental analysis of bone marrow neutrophil reveals populations specialised in expansion, trafficking and effector functions
RNAseq was performed on bone marrow GMP and neutrophil subsets to understand the difference in their...
GSE100732: LRPPRC-mediated folding of the mitochondrial transcriptome [RNA-seq]
The roles of RNA-binding proteins as chaperones in the lifecycles of mRNAs are not well understood. ...
GSE111024: Hypomethylated enhancer DNA confers memory for embryonic gene reactivation
To understand how dynamics of enhancer features correlates with gene expression in adult tissue and ...
GSE109328: Epigenetic Rescue of Autism-like Social Deficits in Shank3-Deficient Mouse Models
To determine whether histone deacetylase (HDAC) inhibition has genome-wide effects on gene expressio...
GSE110713: PTHrP overexpression in MCF7 cells
A PTHrP construct expressing full-length secreted PTHrP (-36-139aa) was stably expressed in MCF7 cel...
GSE110219 (human): JAK1/2 inhibitor therapy-associated lymphomas in myelofibrosis arising from a pre-existing B-cell clone
In this study, we elucidated differential gene expression between transformed and untransformed muri...
GSE102935: The lncRNA Hand2os1/Uph locus orchestrates heart development through regulation of precise expression HAND2
Exploration and dissection of potential actions and effects of long noncoding RNA (lncRNA) in animal...
GSE111753: Gene expression profiling of neural crest cells from E10.5 mouse embryos with basal p53 or activated p53
To investigate the mechanisms by which p53 activation triggers developmental defects, we generated a...
GSE110694: Transcriptome profiling of normal and transformed mouse urothelial cells
Transcriptome analysis of urothelial KRT5-traced and KRT8-traced YFP-sorted cells with and without c...
GSE110404: BONE MORPHOGENETIC PROTEIN 8B (BMP8B) IN NON-ALCOHOLIC STEATOHEPATITIS (NASH) AND ACUTE HEPATIC DAMAGE
TGF/BMP family member Bone Morphogenetic Protein 8b (Bmp8b) is upregulated in NASH (Western Diet -WD...
GSE119598: Supraphysiological Androgens Repress Prostate Cancer Growth and Induce DNA Damage Augmented by PARP Inhibition
Prostate cancer (PC) is initially dependent on androgen receptor (AR) signaling for survival and gro...
GSE101801: ZBTB2 as a novel reader for unmethylated DNA [RNA-seq]
DNA methylation is a dynamic epigenetic modification that plays a key role in various cellular proce...
GSE108537: Far upstream element-binding protein 1 regulates LSD1 alternative splicing to promote terminal differentiation of neural progenitors
Analysis of mouse neural progenitors with non targeting or FUBP1 targeting shRNA in proliferation an...
GSE100874: Temporal Layering of Signaling Effectors Drives Chromatin Remodeling during Hair Follicle Stem Cell Lineage Progression [RNA-seq]
Tissue regeneration relies on resident stem cells (SCs), whose activity and lineage choices are infl...
GSE108541: Immortalized breast epithelial cell lines from normal breast with luminal and intrinsic subtypes enriched gene expression
The cell-type origin has long been suspected to determine molecular features of tumors but has prove...
GSE100906: Mouse lt-hsc single cells - 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...
GSE116364: Analysis of the IFNgamma induced pathways in murine macrophages
Macrophages derived from the CH3 mice were treated with the increasing concentrations of the IFNgamm...
GSE109429: Next Generation Sequencing Facilitates Quantitative Analysis of Ter cells Transcriptomes
Purpose:The purpose of this study is to detect genes Ter-119+CD45Lin cells sorted from spleen of tum...
GSE109378: MicroRNA (miR)-211 loss promotes metabolic vulnerability and BRAF inhibitor sensitivity in melanoma
We report that miR-211 loss-of-function in the pigmented melanoma cell line SKMEL-28 slowed growth ...
GSE111801: Kidney-resident CD8 T cells downregulate IL-18R during maturation
Using the expression of IL-18 receptor (CD218) as a surface marker, CD69+ kidney-resident CD8 T cell...
GSE112499: RNA-seq analysis of FACS-sorted control and Tsc2-deleted nociceptors
The goals of this study are to compare the transcriptomes of control heterozygous and Tuberous scler...
GSE116354: Genetic models reveal cis and trans immune-regulatory activities for lincRNA-Cox2 in vivo (lungs and spleens)
Here we compare gene expression profiles between lungs and spleens following LPS in vivo injection i...
GSE133097 (mouse): Identification of ALPPL2 as a novel specific and functional surface marker for nave pluripotency
We report ALPPL2 as a prominently specific and functional surface marker for nave pluripotency. By p...
GSE109709: Insm1 induces neural progenitor delamination in developing neocortex via down-regulation of the adherens junction belt-specific protein Plekha7
Delamination of neural progenitor cells (NPCs) from the ventricular surface is a crucial prerequisit...
GSE100887: PARP14 controls the nuclear accumulation of a subset of type I Interferon-inducible proteins [RNA-seq2]
The enzymes of the poly-ADP-ribose polymerase (PARP) super-family control many relevant cellular pro...