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Sequencing-based assays (Page 87)
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GSE123759: RNA-seq Analysis of Pancreatic Epithelium and Mesenchyme from Wild Type and Pbx-mutant Embryos
The surrounding microenvironment plays a crucial role in pancreas formation and differentiation. Nev...
GSE130389: NFIA differentially controls adipogenic andmyogenic gene program through distinct pathways to ensure adipocyte differentiation [RNA-seq]
The transcription factor nuclear factor I-A (NFIA) is a regulator of brown adipocyte differentiation...
GSE130363: Transcriptional changes in the breast cancer cell line MCF7 rendered resistant to the cationic drug siramesine
Repurpusing cationic amphiphilic drugs (CADs) may be enhance the effect of chemotherapy in cancer tr...
GSE130970: Gene expression predicts histological severity and reveals distinct molecular profiles of nonalcoholic fatty liver disease
Transcriptomic analysis of liver biopsies that cover the spectrum of nonalcoholic fatty liver diseas...
GSE81534: Uridylation-mediated RNA quality control pathway in mammalian cytoplasm [RNA-Seq]
Uridylation of various cellular RNA species at the 3 end has been generally linked to RNA degradatio...
GSE132217: Choroid Plexus Releases miR-204 Regulating the Number of Neural Stem Cells in the Adult Brain
We compared transcriptomes changes in murine quescent neural stem cells after the interference with ...
GSE131881: MBOAT7 loss of function in clear cell Renal Carcinoma (ccRCC)
We demonstrated an increase in MBOAT7 and downstream phosphatidylinositol products in ccRCC. This RN...
GSE134422: HNF4 nuclear localization correlates with the clinical progression of terminal hepatic failure in humans
HNF4 is a transcription factor that plays a critical role in terminal hepatocyte failure. HNF4-based...
GSE131877: Retinal Organoids derived from AIPL1-LCA Patient iPSCs Maintain Retinal Cytoarchitecture under Reduced AIPL1 Levels
In this study, we generated three-dimensional (3D) retinal organoids (ROs) from induced pluripotent ...
GSE130381: Total RNA sequencing of a time course treatment of human embryonic stem cells with CHIR99021, recombinant Wnt3a, and a time course activation of constitutively active beta-catenin expression
Here we analysed the transcriptomic response of human embryonic stem cell line H9 to sustained activ...
GSE122043: Single-cell analysis RNA sequencing of whole mouse skin at embryonic day 13.5 and 14.5
A major challenge in delineating molecular and cellular events that precede appendage morphogenesis ...
GSE130898 (mouse): The RNA hairpin binder TRIM71 modulates alternative splicing by repressing Mbnl1 [RNA-seq & Ribo-seq]
We demonstrate that global effects of TRIM71 on the cellular transcriptome of mouse embryonic stem c...
GSE120708: mRNA sequencing analysis of transcripts from hippocampus of Wt1 mice
Purpose: Study the differentially expressed genes in the hippocampus of mice, comparing Wt1 mice wit...
GSE130686: RNA-seq of triple knockout (TKO) mouse embryonic stem cells: Dnmt1-/-, Dnmt3a-/-, Dnmt3b-/-.
TKO mouse embryonic stem cells were cultured in serum/LIF and 2i/LIF in order to investigate the rol...
GSE132207: Epigenetic remodelling of enhancers in response to estrogen deprivation and re-stimulation [RNA-Seq]
Estrogen hormones are implicated in a majority of breast cancers and estrogen receptor alpha (ER) or...
GSE121884: RNA-Seq analysis of the pancreatic islets from 6-week-old Paupar WT and KO mice
Transcriptional analysis of the pancreatic islets of adult Paupar KO mice versus Paupar WT mice. Tot...
GSE130955: Global skin gene expression profile of early diffuse cutaneous systemic sclerosis shows a prominent innate and adaptive immunity profile
RNA from skin biopsies from 48 patients in the Prospective Registry for Early Systemic Sclerosis (PR...
GSE120958: High Phosphate Diet Induces Exercise Intolerance and Impairs Fatty Acid Metabolism in Mice
Inorganic phosphate (Pi) is used extensively as a preservative and a flavor enhancer in the Western ...
GSE129508: Impact of a pre-operative exercise intervention on breast cancer proliferation and gene expression
RNAseq analysis of primary breast cancer samples SOURCE: Rinath Jeselsohn (rinath_jeselsohn@dfci.har...
GSE131039: Adaptable durable human endothelial cells for organogenesis and tumorigenesis
ETV2 resets endothelial cells' fate, confering them with vascular mallebility, which results in long...
GSE140077: Transcriptome analysis of human pancreatic cancer cell lines and gemcitabine-resistant pancreatic cancer cell lines
Gemcitabine (GEM) alone and GEM-based chemotherapy are the preferred regimens for treating advanced ...
GSE122345: Transcriptomic profile of brain endothelial cells after stroke w/o chronic stress
Our previous studies demonstrate that chronic stress leads to worse stroke outcome with increased br...
GSE121001: Thrombopoietin metabolically primes hematopoietic stem cells to megakaryocyte lineage differentiation
During acute myelosuppression or thrombocytopenia, bone marrow (BM) hematopoietic cells respond rapi...
GSE130394: Next Generation Sequencing of Wild Type and Mice Knocked Out for Known Methionine Sulfoxide Reducatases
Methionine sulfoxide reductase (Msr) is an important antioxidant enzyme. The mammalian Msr family ha...
GSE132268: Characterization of Slfn3KO mice
RNA sequencing was performed on intestinal mucosa from male and female Slfn3KO mice to determine gen...
GSE131887: Analysis of gene expression from TC3 cells of Rip-Tag2 PanNET mouse model upon miR-137 and miR-23b cluster doxycycline (DOX) induction
Using cross-species analysis, we have previously shown that the miR-137 and the miR-23b microRNA clu...
GSE130597: Obesity Remodels Activity and Transcriptional State of a Lateral Hypothalamic Brake on Feeding
We demonstrate that high fat diet (HFD)-induced obesity alters the transcriptional state of lateral ...
GSE137078: Transcriptional profiling of neurons in the midbrain of a Lhx5-TRAP (DT154) mouse line
TRAP translational profiling is a method that allows investigators to genetically characterize speci...
GSE121009: RNA-seq in Prdm16 KO duodenal crypts
The adult intestinal epithelium is maintained by a continuous replacement of differentiated cells fr...
GSE130715: Budesonide induced transcriptional activity in control and Gs-knockdown human airway smooth muscle cells
Budesonide alter cell function through gene expression changes that occur via activation of ubiquito...
GSE133127: Distinct transcriptional responses across tissue-resident macrophages to short-term and long-term metabolic challenge
The innate immune system safeguards the organism from both pathogenic and environmental stressors. E...
GSE133254: Effect of ZIKV on pre-implantation embryos
To determine the effect of Zika virus infection on pre-implantation embryonic development, we perfor...
GSE133492: A transcriptional switch in a novel non-canonical, catenin dependent Wnt pathway controls axon midline decisions
During the establishment of neuronal connections, axons must correctly navigate long pathways to fin...
GSE124560: Liver Single-Cell Transcriptome Analysis of Cell-specific Dysregulation of Liver Cell Biology Following Intravenous Administration of AAV Vectors
Zhu et al. report the application of single-cell RNA-sequencing technology for profiling the cell-sp...
GSE121033: Maintenance of nucleolar homeostasis by PC2 alleviates senescence and osteoarthritis
Polycomb 2 protein (PC2), a component of polycomb repressive complex 1 (PRC1), plays important roles...
GSE130229 (human): EZHIP constrains Polycomb Repressive Complex 2 activity in germ cells (RNA-Seq)
We identified a novel cofactor of PRC2, expressed predominantly in the gonad, that limits PRC2 enzym...
GSE157089: Loss of UTX/KDM6A and the activation of FGFR3 converge to regulate differentiation gene expression programs in bladder cancer [RNA-seq]
Bladder cancer prognosis is closely linked to the underlying differentiation state of the tumor, ran...
GSE133174: Ascending colon-derived mucin-type O-glycans form key mucus layers encapsulating microbiota in the colon (RNA-seq)
The colon contains a dense metabolically potent microbiota. The colonic O-glycan-rich mucus has been...
GSE131895: RNA analysis of Nr4a1 and Nr4a1-knockout mammary tumor cells from MMTV-PyVT transgenic mice
MMTV-PyVT Mammary tumors were harvested from PyVT-wild-type (WT), PyVT-Nr4a1 knockout (KO) litterma...
GSE132602: Dissecting the regulatory strategies of NFkB RelA target genes in the inflammatory response reveals differential transactivation logics [caRNAseq]
NFkB RelA is the potent transcriptional activator of inflammatory response genes. We stringently def...
GSE157103: Large-scale Multi-omic Analysis of COVID-19 Severity
Using RNA-seq and high-resolution mass spectrometry we performed a comprehensive systems analysis on...
GSE133123: Transcriptomic analysis of 5637 bladder cancer cell line transfected with MAT1A plamid, 48 hours post transfection
Transcriptomic analysis of 5637 bladder cancer cell line transfected with MAT1A plamid, 48 hours pos...
GSE120954: Loss of primary cilia drives switching from Hedgehog to Ras/MAPK pathway
Basal cell carcinomas (BCCs) rely on Hedgehog (HH) pathway growth signal amplification by the microt...
GSE139665: HDAC3 maintains oocyte meiosis arrest by repressing amphiregulin expression before the LH surge [oocyte-transcriptome]
It is known that granulosa cells (GCs) mediate gonadotropin-induced oocyte meiosis resumption by rel...
GSE120960: Setd5 haploinsufficiency alters neuronal network connectivity and leads to autistic-like behaviors in mice [single cell]
SETD5, a gene linked to intellectual disability (ID) and autism spectrum disorder (ASD), is a member...
GSE129542: RNA-seq based transcriptomic profiling of GBM44 glioma cell line with BAT1 shRNA knockdown
Purpose: We found that BAT1 plays key role in the regulation of immune related factors, we aim to ch...
GSE129402: Targeted deletion of Tcf7l2 in adipocytes promotes adipocyte hypertrophy and impaired gluose metabolism [HFD]
We generated a Tcf7l2 F/F mouse and harvested preadipocytes from these mice, immortalized them, and ...
GSE121069: RNAseq of fluidically isolated human and mouse motor neuron somas and axons in vitro
Spinal motor axons traverse large distances to innervate target muscle, and thus require local contr...
GSE134085: Transcriptome analysis of valosin-containing protein effect on cardiac hypertrophy and dysfunction
This sstudy was designed to investigate the gene netweork regulated by valosin-containing protein (V...
GSE141737: SOAT1 knock-out downregulates the expression of mevalonate pathway genes in PDAC organoids
One of the emerging cancer vulnerabilities is altered metabolism, and several metabolic pathways hav...
GSE132883: B cell humoral response and differentiation is regulated by non-canonical poly(A) polymerase TENT5C.
Purpose: The goal of this study was to assess changes in the activated B cells transcriptome upon TE...
GSE135283: The Polycomb-Associated Factor Phf19 Controls Hematopoietic Stem Cell Status and Differentiation
Adult hematopoietic stem cells (HSCs) are rare, multipotent cells in bone marrow that are responsibl...
GSE129698: Resistance mechanisms to SYK inhibition in AML
Targeted therapy studies with small molecules against kinases, such as spleen tyrosine kinase (SYK),...
GSE130864: RNA-Seq of whole kidneys of inducible TFAP2B KO mice (b-actinCreERT2+TFAP2Bfl/fl) mice and control littermates
RNA-Seq of kidneys lacking the gene TFAP2B in the nephron; knockdown at 6 weeks of age; assessed at ...
GSE124554: Axonogenesis is coordinated by alternative splicing programming and splicing regulator PTBP2
How a neuron acquires an axon is a fundamental question. Piecemeal identification of many axonogenes...
GSE123958: RNA-binding chromatin modifier MTA1 regulates mitotic transition and tumorigenesis by orchestrating mitotic mRNA processing [Synchronized RNA-seq]
The processing of RNAs by chromatin-associated proteins (CAPs) is highlighted by the latest findings...
GSE131917: Intersection of ARID1A, EZH2 RNA-seq in OVCA429 cells with IFN treatment
Whether cancer driver mutation(s) directly drives cancer immune phenotype and immune tolerance remai...
GSE135634: Analysis of the Clustered Protocadherin (cPcdh) Locus in Human Pluripotent Stem and Derived Cells [scRNA-seq]
In the mammalian genome, the clustered protocadherin (cPcdh) locus is a paradigm of stochastic gene ...
GSE131903: RNA-Seq analysis of Harlequin Ichrthyosis skin, HI 3D model ABCA12 CRISPR-Cas9 KO cell line
The biology of Harlequin Ichthyosis (HI), a devastating skin disorder, caused by loss of function mu...
GSE132287: ADAR1 overexpression in MDA-MB-231 cells
Abstract: RNA editing has emerged as novel mechanisms involved in cancer progression. Despite the ph...
GSE124580: DDX18 safeguards rDNA epigenetic landscape by counteracting PRC2 and maintains ESC identity
Here we have RNA binding protein DDX18 connecting rRNA transcription to early embryo development and...
GSE132930: Transcriptional profiling reveals running promotes cerebrovascular remodeling in young but not aged mice
We report that running at a young age showed ECM-related changes as well as angiogenesis-related pat...
GSE141728: Sonoselective Transfection of Cerebral Vasculature without Blood-Brain Barrier Disruption - Bulk RNA seq
Treatment of many pathologies of the brain could be improved markedly by the development of non-inva...
GSE136641: CXCR5+PD-1+CD8+ T cells are a novel T helper cell sublineage and are negatively regulated by Stat5 [scRNA-Seq]
Many autoimmune diseases are characterized by the production of autoantibodies. The current view is ...
GSE135685: Effect of EGCG treatment on MDSC
This study is set out to identify EGCG transcriptional targets in 4T1 breast cancer mediated myeloid...
GSE133495: Transcriptomic profile of Calu-3 airway epithelial cells in response to flagellin
The purpose of the study is to compare the transcriptomic profile of the airway epithelial cell line...
GSE130115: Allelic histone-to-DNA methylation switch establishes secondary DMR to maintain noncanonical imprinting
Faithful maintenance of genomic imprinting is essential for mammalian development. While germline D...
GSE129582: Subcellular RNA fractions of HSV-1 infected primary human fibroblasts including infection with delta-Vhs mutant
Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain...
GSE130538: Distruption of TOX and TOX2 transcription factors in CAR T cells limits T cell exhaustion [RNA-Seq]
We comapre mRNA expression level TOX and TOX2 CAR TILS and WT CAR TILs SOURCE: Anjana Rao (arao@lji....
GSE140066: Caco2 response to methotrexate, lactoferrin, and methotrexate-lactoferrin co-exposure
bulk sequencing outputs of Caco2 cells after exposure to permeability modifying and permeability res...
GSE141740: Nrf2-mediated enhancer activation ameliorates oxidative stress and cystogenesis in autosomal dominant polycystic kidney disease [RNA-seq]
Oxidative stress is emerging as a crucial contributor to the pathogenesis of autosomal dominant poly...
GSE135582: Tissue-resident memory T cells mediate immune homeostasis in the human pancreas through the PD-1/PD-L1 pathway
We investigated the distinct state of pancreas resident memory T cells (TRM) by whole transcriptome ...
GSE131927: 499 GRKO vs WT Single Cell Seq
Interferon-gamma (IFNG) augments immune function yet promotes T cell exhaustion through PDL1. How th...
GSE132925: Comprehensive transcriptome analysis of cochlear spiral ganglion neurons at multiple ages
The inner ear spiral ganglion neurons (SGNs) transmit sound information to brainstem. Although recen...
GSE135557: RNA-seq analyses of wild-type and PML KO mESCs
Promyelocytic leukemia (PML) body is a phase-separated nuclear structure composed of various protein...
GSE124561: Epithelial endoplasmic reticulum stress orchestrates a protective IgA response I
Immunoglobulin A (IgA) is the major secretory immunoglobulin isotype at mucosal surfaces where it re...
GSE130435: Macrophages in eutopic endometrium endometriosis
Comparison of macrophages M1 (M1) and M2 (M2) from eutopic endometrium from women with and without e...
GSE131934: Global transcriptional profiling changes upon knockout of USP22 in human Non-small cell lung cancer cells
The experiment was designed to display differential gene expression profiling changes in two human n...
GSE130706: Chromatin Assembly Factor 1 (CAF-1) facilitates the establishment of facultative heterochromatin during pluripotency exit
Establishment and subsequent maintenance of distinct chromatin domains during embryonic stem cell (E...
GSE130665: Differential expression of genes in HCMV-infected fibroblasts regulated by the purinergic receptor P2Y2.
We studied changes in a whole transcriptome during HCMV infection. SOURCE: Thomas Shenk Princeton Un...
GSE135733: Effect of DSS Colitis on Meninges
The Meninges of mice which were treated with DSS to induce colitus were compared to control mice. SO...
GSE132961: RNA-seq to identify targets of integrin alpha2 in breast cancer
Knockdown of ITGA2 was done in MDA-MB-231 cells and RNA-seq results were compared to control cells. ...
GSE137126: Genome-wide maping of chromatin state and gene exoression in hematopoietic stem and progenitor cells.
We report the application of H3K27me3 ChI-seq assays in hematopoietic stem and progenitors cells (HS...
GSE129782: ARID1A and PI3-Kinase pathway mutations in the endometrium drive epithelial transdifferentiation and collective invasion [12Z_RNA-seq]
ARID1A and PI3-Kinase (PI3K) pathway alterations are common in neoplasms originating from the uterin...
GSE124687: Identification of murine gammaherpesvirus 68 miRNA-mRNA hybrids reveals miRNA target conservation among gammaherpesviruses including host translation and protein modification machinery
Gammaherpesviruses, including the human pathogens Epstein-Barr virus and Kaposis sarcoma-associated ...
GSE132306 (human): N6-methyladenosine (m6A) profiling of EndoC-bH1 cell line and RNA seq of Mettl14 knockout mice beta cell
In type 2 diabetes, pancreatic beta-cells fail to compensate for the presence of insulin resistance ...
GSE130416: Hominid-specific transposable elements and KRAB-ZFPs facilitate human embryonic genome activation andtranscription in nave hESCs [RNA-seq]
Transposable elements (TEs) are key to the evolutionary turnover of regulatory sequences. How they c...
GSE141756: Gene expression profiles of active and restricted R/G-HIV+ primary human fetal astrocytes
The gene expression patterns of astrocyte harboring active vs restricted LTRs were similar, and that...
GSE131946: Transcriptome of P1 wild-type and RykSL/SL mutant lungs
Transcriptomic analysis between P1 wild-type and RykSL/SL mutant lungs (Left lobs) SOURCE: Stefan Gü...
GSE136654: KSHV Requires vCyc to Overcome Replicative Senescence in Primary Human Lymphatic Endothelial Cells
We performed high throughput RNA-sequencing on KSHV-infected blood and lymphatic HMVECs at 48hpi as ...
GSE129846: A genome-wide CRISPR screen reveals a role for the non-canonical nucleosome remodeling BAF complex in Foxp3 expression and regulatory T cell function
Regulatory T cells (Treg) play a pivotal role in suppressing auto-reactive T cells and maintaining i...
GSE121144: Kinetics of Xist-induced gene silencing depends on combinations of epigenetic and genomic features
To initiate X-chromosome inactivation (XCI), the long non-coding RNA Xist mediates chromosome-wide g...
GSE135683: Transcriptome analysis of adipocyte differentiation (3T3-L1 WT and MIGA2 perturbed/overexpressed)
RNA-Seq of 3T3-L1 WT and MIGA2 perturbed/overexpressed adipocyte differentiation SOURCE: giancarlo r...
GSE121166: Early response to loss of Argonaute proteins in embryonic stem cells activates the Tgf-/Smad Transcriptional Network [mRNA-Seq: DicerDgcr8_KOs]
Argonaute (Ago) proteins, which act in post-transcriptional gene regulation directed by small RNAs, ...
GSE123421: Taggera Swiss army knife for multiomics to dissect cell type-specific mechanisms of gene expression in mice [TU-Tag-RNA-seq]
We developed a knock-in mouse line that combines four enrichment tools to study gene regulatory netw...
GSE136325: In vivo atlas of RNA secondary structures recognized by ADARs [irCLASH-seq&hiCLIP-seq]
We performed irCLASH and HiCLIP for ADAR1-3 in HEK293 cells. In addition, we performed mRNA-seq in A...
GSE130567: IFN- selectively suppresses a subset of TLR4-activated genes and enhancers to potentiate M1-like macrophage polarization [RNA-seq II]
Complete polarization of macrophages towards an M1-like proinflammatory and antimicrobial state requ...
GSE123124: The emergent landscape of the mouse gut endoderm at single-cell resolution
To comprehensively delineate the ontogeny of an organ system, we generated 112,217 single- cell tran...
GSE131942: Inactivation of Bap1 Cooperates with Losses of Nf2 and Cdkn2a to Drive the Development of Pleural Malignant Mesothelioma in Conditional Mouse Models
Mutations/deletions of BAP1, CDKN2A, and NF2 are the most frequent genetic lesions in human MM. We i...
GSE130100: Comparative gene expression profiling of telomerase-reverse transcriptase (TERT)-immortalised BJ fibroblasts transduced with pBabe empty vector control or HRASG12V
We use RNA-seq to characterise the transcriptional programs of proliferating BJ-TERT fibroblasts ver...