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Sequencing-based assays (Page 139)
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GSE130590: Gene expression profiling in two dimensional and extracellular matrix based three-dimensional cultures of lung and breast cancer cells
A549 and MDA-MB-231 cells were cultured in 2D and Matrigel based 3D culture for 4 days. Total RNA wa...
GSE128669: RNA-seq (PolyA) of RNA from Tet-inducible SaOS2-p21 cells
RNA was extracted from SaOS2 cells harboring a tet-inducible p21 expression vector. 3 replicates fro...
GSE127274: RNA Sequencing Analysis of human glioblastoma derived cells and xenograft derived primary cells
RNA sequencing was performed on cultured human glioblastoma cells from patient directly or from the ...
GSE128529: Targeting the scaffolding role of LSD1(KDM1A) poises acute myeloid leukemia cells for Retinoic Acid induced differentiation [RNA-seq]
The histone demethylase LSD1 is deregulated in several tumors, including leukemias, providing the ra...
GSE131257: RNA Helicase DDX5, a Negative Regulator of Wnt Activation and Hepatocyte Reprogramming in Hepatitis B Virus-associated Hepatocellular Carcinoma
We demonstrate that HBV infection induces expression of the proto-oncogenic miR17~92 and miR106b~25 ...
GSE132204: Phenotypic and functional characterization of corneal endothelial cells during in vitro expansion
The advent of cell culture-based methods for the establishment and expansion of human corneal endoth...
GSE133663: Transcriptional profile of CAOV2 primary and CAOV2 recurrent cells
We performed RNAseq to study the transcriptional changes of human CAOV2 recurrent vs CAOV2 primary o...
GSE127298: A novel Menin-MLL inhibitor induces specific chromatin changes and eradicates disease in models of MLL-rearranged leukemia
Inhibition of the Menin (encoded by MEN1) and MLL1 (KMT2A) protein-protein interaction has been prop...
GSE128626: Prediction of bacterial infection outcome using single cell RNA-seq analysis of human immune cells [sorted population Bulk RNA-seq]
During host-pathogen encounters, the complex interactions between different immune cell-types can de...
GSE128840: Neuronal deletion of Gtf2i, associated with Williams syndrome, causes behavioural and myelin alterations rescuable by a remyelinating drug [human]
Williams syndrome (WS), caused by a heterozygous microdeletion in 7q11.23, is a neurodevelopmental d...
GSE133857: Transcriptome of control and FTO-knockdown HOC313 cells
N6-methyladenosine (m6A) modification is the major post-transcriptional modification present in mamm...
GSE128860: Identification of FMRP targets in human neural progenitors and neurons
We identified FMRP-bound RNAs in hPSC (human pluripotent stem cells)-differentiated forebrain neurop...
GSE132624: MITF controls the TCA cycle to modulate the melanoma hypoxia response
In response to the dynamic intra-tumor microenvironment, melanoma cells adopt different phenotypic s...
GSE130637: mRNA expression profiling in MDA-MB-231 (LM1) cells with a tet-incible MBD2 or p66 knock down, or treated with MBD2-targeting small molecule ABA or APC
The goal of this study is to compare mRNA expression profiles among wild type, MBD2 knock down, p66 ...
GSE131770: Human CD4+CD103+ cutaneous resident memory T cells are found in the circulation of healthy subjects
Tissue-resident memory T cells (TRM) persist locally in non-lymphoid tissues where they provide fron...
GSE138518: Transcriptome Profiling Reveals the key genes and pathways involved in polycystic ovary syndrome [RNA-seq]
Aberration in miRNA expression or DNA methylation is a causal factor for numerous pathological condi...
GSE129002: Gene expression regulated by CSA and CSB in neuroblastoma cell line
Mutations in the CSA and CSB genes are causative of Cockayne syndrome neurological disorder. Since t...
GSE129310: Transcriptome analysis of neural progenitor cells derived from Lowe Syndrome induced pluripotent stem cells
Lowe Syndrome (LS) is caused by loss-of-function mutations in the X-linked gene OCRL that codes for ...
GSE131809: Control of human hemoglobin switching by LIN28B-mediated regulation of BCL11A translation (Ribo-seq, RNA-seq)
While BCL11A protein is not well synthesized at these earlier stages of development, its mRNA curiou...
GSE135460: Colorectal cancer cell lines with SETDB1 depletion [RNA-seq]
We performed RNA sequencing analysis of three colorectal cancer cell lines (Caco2, HCT116, SW480) wi...
GSE129058: Phenotypic variation between stromal cells differentially impacts engineered cardiac tissue function
Understanding the relationship between parenchymal and supporting cell populations is paramount to r...
GSE128836: The hematopoietic master transcription factor PU.1 requires its interaction with the SWI/SNF remodeler to access chromatin de novo [RNA-seq]
PU.1 is a prototype master transcription factor (TF) of hematopoietic cell differentiation with dive...
GSE128717: Human Embryonic Stem Cell-derived Expandable Hepatic Organoids Enable Pathophysiological Model of Alcoholic Liver Injury
We report the generation of human pluripotent-stem-cell-derived (hPSC), expandable hepatic organoids...
GSE131823: Dynamic induction of drug resistance through a stress-responsive enhancer in acute myeloid leukemia [RNA-seq]
The drug efflux pump ABCB1 is a key driver of chemoresistance, and high expression predicts for trea...
GSE127514: UTX/KDM6A suppresses AP-1 and a gliogenesis program during neural differentiation of human pluripotent stem cells[RNA-seq]
UTX/KDM6A is known to promote open chromatin structure to facilitate gene activation. Although UTX ...
GSE127266: Inducible knock-out of BCL6 in lymphoma cells results in tumor stasis
Diffuse large B-cell lymphoma (DLBCL) is the most common type of non-Hodgkin lymphomas worldwide and...
GSE131916: RNA-seq in ARID1A WT, KO OVCA429 Cells after IFN treatment
Whether cancer driver mutation(s) directly drives cancer immune phenotype and immune tolerance remai...
GSE127492: FLT3-N676K drives acute myeloid leukemia in a xenograft model of KMT2A-MLLT3 leukemogenesis
Activating signaling mutations are common in acute leukemia with KMT2A (previously MLL) rearrangemen...
GSE127559: A Novel Role for the Tumor Suppressor Gene ITF2 in Tumorigenesis and Chemotherapy Response [RNA-seq]
Despite often leading to platinum resistance, platinum-based chemotherapy continues to be the standa...
GSE130313: Epigenetic activation and memory at a TGFB2 enhancer in systemic sclerosis
Epigenetic activation of an enhancer for TGFB2 locks SSc patient fibroblasts into a pro-fibrotic syn...
GSE131758: Transcriptome analysis of bFGF and WNT3A treated stem cells isolated from human exfoliated deciduous teeth
bFGF regulated stemness maintenance and cell differentiation in stem cells isolated from human exfol...
GSE127750: Bacteria boost mammalian host NAD metabolism by engaging the deamidated biosynthesis pathway
Nicotinamide adenine dinucleotide (NAD), a cofactor for hundreds of metabolic reactions in all cell ...
GSE128730: RNAseq of parental and neratinib resistant 5637 and OVCAR8 cells with or withour neratinib treatment
Pan-HER TKI neratinib has demonstrated clinical activity in patients with HER2-mutant cancers. Howev...
GSE138485: Retrospective gene expression analysis of human RNA samples from Hepatocellular Carcinoma in relation with survival
The aim of this study is to identify by Next Generation Sequencing - RNA-seq profiling a molecular s...
GSE134441: Error-free and error-prone DNA repair gene expression through reprogramming and passage in human iPS cells
Medical applications of human iPS cells(hiPSC) are evolving, but detailed elucidation of the mechani...
GSE127855: 4sU-seq of EV vs PRL3 expressing melanoma cells
We report the use of 4sU-seq to determine the role of PRL3 in transcriptional processivity in human ...
GSE128728 (human): Alkylating Agent-Induced ER Stress Overcomes Microenvironmental Resistance to Lymphoma Therapy
Compartment-specific resistance to cancer therapy remains poorly understood. We utilized orthotopic ...
GSE134076: High-depth RNA sequencing of isogenic wild-type, PIK3CA-WT/H1047R and PIK3CA-H1047R/H1047R human iPSCs
We used CRISPR/Cas9 to knock in the cancer "hotspot" mutation PIK3CA-H1047R into one or both alleles...
GSE127964: RNA sequencing to compare gene expession in control and PF228-treated hepatic stellate cells
Primary human hepatic stellate cells (HSCs) isolated from healthy donors were purchased from Science...
GSE131841: Generating Patterned Kidney Organoids for Studying Development and Diseases [bulk RNA-Seq]
Human pluripotent stem cells (hPSCs)-derived kidney organoids recapitulate complex developmental pro...
GSE134080: RNASeq whole blood of Dutch 500FG cohort
Expression levels from bulk whole blood from 96 individuals within the 500FG cohort. The aim of the...
GSE137351: Global changes in human neutrophil transcriptome profile during Filifactor alocis challenge
Periodontitis is a multifactorial chronic inflammatory infectious disease with a high prevalence in ...
GSE132228: Social network architecture of human immune cells in ZIKV-infected patients highlights a unique role of plasmacytoid dendritic cells
Zika virus (ZIKV)is an emerging mosquito-borne pathogen with increasing public health significance. ...
GSE128718: Genetic disarray follows mutant KLF1-E325K expression in a congenital dyserythropoietic anemia patient
Congenital dyserythropoietic anemia (CDA) type IV is caused by a heterozygous mutation, Glu325Lys (E...
GSE130038: Elevated colonic mucin expression correlates with extended time to surgery for ulcerative colitis patients
Background: Ulcerative colitis (UC) develops from chronic inflammation of the colon. Most patients r...
GSE130361: Induction of human hemogenesis in adult fibroblasts by defined factors and hematopoietic co-culture
Previous work demonstrates an induction of definitive hematopoiesis from human dermal fibroblasts (H...
GSE130368: Innate, non-cytolytic CD8+ T cell-mediated suppression of HIV replication by MHC-independent inhibition of virus transcription
MHC-I-restricted, virus-specific cytotoxic CD8+ T cells control HIV/SIV replication via the recognit...
GSE138611: Extracellular matrix hydrogel derived from decellularized tissues enables endoderm organoids culture
Organoids have extensive therapeutic potential and are increasingly opening up new avenues within re...
GSE130564: Overexpression of poly(rC) binding protein 2 by alternative cleavage and polyadenylation promotes breast cancer progression via regulating UFD1 and NT5E
Alternative cleavage and polyadenylation (APA) is an important post-transcriptional regulatory mecha...
GSE133447: shRNA-mediated knockdown of ETV4 and MED25 in the prostate cell line PC3 reveals set of genes potentially coregulated by MED25 and ETV4
Our in vitro binding studies support a model whereby MED25 exhibits multivalent interactions with a ...
GSE128898: PLIN2 knockdown alters the genome-wide gene transcription profile of leiomyoma cells
Purpose: To investigate the function of PLIN2 in human uterine leiomyoma tumorigenesis, we generated...
GSE128940 (human): IL-11 neutralising therapies for the treatment of nonalcoholic steatohepatitis
Background and aims: Here we investigate the role of IL-11 signalling in the pathogenesis of nonalco...
GSE129075: Functional Comparison of the HGF/Met and MSP/Ron Systems in a Pancreatic Cancer Model
Pancreatic cancer is an aggressive disease with a poor prognosis for which current standard chemothe...
GSE130891: MeRIP-seq for host response to Flaviviridae infection
The modification N6-methyladenosine (m6A) affects rates of translation and degradation of mRNA trans...
GSE134908: RNA Sequencing Facilitates Quantitative Analysis of Transcriptomes of H1 derived cells with or without SB431542 treatment at Day8 after human early hematopoietic differentiation .
Purpose: The goals of this study are to verify the inhibition of TGFb signaling is suffice to surpre...
GSE136661: Molecular profiling predicts meningioma recurrence and reveals loss of DREAM complex repression in aggressive tumors
Meningiomas account for roughly one-third of all primary brain tumors. Although typically benign, ab...
GSE133996: GATA2 promotes hematopoietic development and represses cardiac differentiation of human mesoderm
In vertebrates, GATA2 is a master regulator of hematopoiesis and is expressed throughout embryo deve...
GSE130309: Effect of BTAF1 downregulation on gene expressions of TBP 3X-WT and TBP 3X-T114A Hela cell lines
In eukaryotes, gene expression is performed by three RNA polymerases that are targeted to promoters ...
GSE134045: Improving drug discovery using image-based multiparametric analysis of the epigenetic landscape
With the advent of automatic cell imaging and machine learning, high-content phenotypic screening ha...
GSE130636: Single-cell RNA-Seq Investigation of Foveal and Peripheral Expression in the Human Retina
Purpose: Single-cell RNA sequencing has revolutionized cell-type specific gene expression analysis. ...
GSE131876: The miR-146 family connects stem cell identity with cellular metabolism and pharmacological resistance in breast cancer
Although ectopic overexpression of miRNAs can influence mammary normal and cancer stem cells (SCs/CS...
GSE129570: Transcriptomically-guided mesendoderm induction of human pluripotent stem cells using a systematically defined culture scheme
Human pluripotent stem cells (hPSCs) are an essential cell source in tissue engineering, studies of ...
GSE130219: Expansion, in vivo-ex vivo cycling and genetic manipulation of primary human hepatocytes
Primary human hepatocytes (PHH) are an essential tool for modeling drug metabolism and liver disease...
GSE129076: miR-450a acts as a tumor suppressor in ovarian cancer by readjusting energy metabolism
Dysregulation of miRNA expression is associated with multiple diseases, including cancers where they...
GSE129182: H2A.Z overexpression suppresses senescence and chemosensitivity in pancreatic ductal adenocarcinoma
Pancreatic ductal adenocarcinoma is one of the most intractable and devastating of all malignant tum...
GSE141711: Characterization of glyceollins as novel aryl hydrocarbon receptor ligands and their role in cell migration
This study is to investigate the effects of glycellin I (GI) and glyceollin II (GII), a aryl hydorca...
GSE129534: Frailty in middle age is associated with race-specific changes to the transcriptome.
Frailty is an aging-associated syndrome resulting from diminished capacity to respond to stressors, ...
GSE134074: Genome-wide CRISPR-Cas9 screen identifies SLC1A3 as a key contributor to L-asparaginase Resistance in Solid tumors
L-asparaginase (ASNase) has been incorporated in the treatment of acute lymphoblastic leukemia for d...
GSE135537: TPR Knockdown Frac-Seq
How splicing regulates the nuclear export of mRNAs has been a source of much debate. While splicing ...
GSE130742: Effect of ILF3 on translation during homeostasis and the antiviral response
Upon detection of viral infections, cells activate the expression of type I interferons (IFNs) and p...
GSE138512: Next Generation Sequencing Facilitates Quantitative Analysis of LAP2 deficient cells and control cells
Purpose: The goals of this study are to compare the mRNA profiles of LAP2 deficient human adipose-de...
GSE129270: Mycobacterium tuberculosis hijacks an evolutionary recent IFN-CEBP-IL6 axis linked to monocyte development and disease severity in humans
Monocyte counts are increased during human tuberculosis (TB) but it has not been determined whether ...
GSE131921: Molecular characterization of a toxicological tipping point in human induced pluripotent stem cell (hiPSC)-derived endoderm exposed to all-trans retinoic acid (ATRA)
Embryonic development commences with the formation of three germ layers from the primitive streak du...
GSE129381 (human): An evolutionarily conserved function of polycomb silences the MHC class I antigen presentation pathway and enables immune evasion in cancer [RNA-Seq]
Loss of MHC class I (MHC-I) antigen presentation in cancer cells can lead to immunotherapy resistanc...
GSE137454: Long noncoding RNA INCA1 regulates tumor interferon signaling
Tumor interferon signaling regulates the expression of immunosuppressive molecules and promotes canc...
GSE131948: Wnt signaling inhibition in human colon cancer cell lines (SW480 and SW620) drives changes in gene programs for cell adhesion, mobility, and cell junction
Overactive Wnt signaling has been found to be a significant driver in colon cancer carcinogenesis ta...
GSE130866: Nuclear RNA-seq of siRNA-mediated METTL3 knockdown
To identify changes in splicing patterns following METTL3 knockdown, RNA-sequencing was performed on...
GSE138604: Response of expanded human conventional and regulatory T cells to CD28 or TNFR2 costimulation [Exp2]
Immune responses depend on a dynamic balance between the opposing activities of conventional (Tconv)...
GSE132288: ADAR1 role on transcriptome stability
Abstract: RNA editing has emerged as novel mechanisms involved in cancer progression. Despite the ph...
GSE132291: SMARCA4 Rescue Profiling [RNA]
Mutations in SMARCA4, a central ATPase of the human BAF/PBAF chromatin remodeling complexes, cause d...
GSE131990: Deconvolution of myeloid cell cytokine specific transcriptional profiles during tuberculosis and cancer identifies neutrophil activation as a prognostic feature
The cytokine environment and cellular infiltrate during an inflammatory response may contain prognos...
GSE131308: The RNA-binding protein ATXN2 controls cellular processes during megakaryopoiesis.
Megakaryocytes accumulate mRNA during their maturation, which is required for the correct spatio-tem...
GSE134577: Clonally expanded CD8 T cells patrol Alzheimer's cerebrospinal fluid [CSF]
Alzheimers disease (AD) is an age-related neurodegenerative disorder in which neuroinflammation play...
GSE130442: CXCR4 is a host factor that regulates Plasmodium development in hepatocytes
The liver stage of the etiological agent of malaria, Plasmodium, is obligatory for successful infect...
GSE138638: Stop Codon Context Influences Genome-Wide Stimulation of Termination Codon Readthrough by Aminoglycosides [Dataset 1]
Stop codon readthrough (SCR) occurs when the ribosome miscodes at a stop codon. Such readthrough eve...
GSE129829: Integrated Metabolomic and Transcriptomic Profiling Reveals Novel Activation Induced Metabolic networks in Human T cells
Targeting metabolic pathways is emerging as an exciting new approach for modulating immune cell func...
GSE129944: Drug combination of 17-AAG and Belinostat on MDA-MB-231 breast cancer cells
Breast cancer is the most common cancer that threatens women's health. While the strategy of drug co...
GSE130817: Transcriptional profiling of CART19 cells exposed to WT and BIDko Nalm6 cells
Cellular immunotherapy using T cells engineered to express chimeric antigen receptors targeting CD19...
GSE130768: Oncogene regulated release of extracellular vesicles
Oncogenes reprogram multiple metabolic phenotypes of cancer cells including the balance between anab...
GSE130501: Transcriptome-wide analysis of wild-type and SRSF3-knockout glioma stem-like cells
Purpose: The splicing factor SRSF3 is a member of serine- and arginine-rich proteins, which is frequ...
GSE138606: Long non-coding RNA RP11-19E11.1 is an E2F1 target required for tumor cell proliferation and survival in basal breast cancer
Long non-coding RNAs (lncRNAs) play key roles in the regulation of breast cancer initiation and prog...
GSE132053: Epigenetic Pathways of HDAC Inhibitor Resistance in Cutaneous T Cell Lymphoma
Epigenetic changes deregulate gene expression to drive oncogenesis. The reversible nature of these c...
GSE135023: H3K79me2/3 controls enhancer promoter interactions and activation of the pan-cancer stem cell marker PROM1/CD133 in MLL-AF4 leukemia cells (RNA-seq)
MLL gene rearrangements (MLLr) are a common cause of aggressive, incurable acute lymphoblastic leuke...
GSE132062: Alternative splicing of LSD1+8a is mediated by SRRM4 in Neuroendocrine Prostate Cancer
Neuroendocrine prostate cancer (NEPC) is the most virulent subtype. Currently, there is an urgent ne...
GSE132836: A variant erythroferrone disrupts iron homeostasis in SF3B1-mutated myelodysplastic syndrome (RNA-Seq)
Myelodysplastic syndromes (MDS) with ring sideroblasts are hematopoietic stem celldisorders with ery...
GSE130905: An improved method for circular RNA purification that efficiently removes linear RNAs containing G-quadruplexes or structured 3 ends
Thousands of eukaryotic protein-coding genes generate circular RNAs that have covalently linked ends...
GSE130977: Isolated fiber-type transcriptional profiles in human skeletal muscle
Skeletal muscle is a complex heterogeneous tissue comprised of diverse muscle fiber and non-fiber ce...
GSE138621: AUF-1 affected genes in human skin cells
This study aims to evaluate the effect of AUF-1 knokdown on the function and global gene expression ...
GSE132065: Sampling time-dependent artifacts in single-cell genomics studies
Robust protocols and automation now enable large-scale single-cell RNA and ATAC sequencing experimen...
GSE138622: Effect of Ephrin-A5 DNA Nanocalipers stimulation of EphA2 receptor signaling in U3013 cell line
Ligand binding induces extensive spatial reorganization and clustering of the EphA2 receptor at the ...