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Sequencing-based assays page 43
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GSE80207: Transcriptome analysis in a radiosensitive and a radioresistant cell line after ionizing radiation
Differential gene expression profiling was performed in two lymphoblastoid cell lines with different...
GSE84476: Transcriptomic Differences Associated with TSC2 Gene Expression Loss in Lymphangioleiomyomatosis [human cells]
Pulmonary Lymphangioleiomyomatosis (LAM), a rare lung disease that affects predominantly women, is c...
GSE81441: Mutant p53 R270H induces invasion and metastasis of mouse intestinal tumor organoids through gain-of-function mechanism
Apc(D716) mutant mice develop benign intestinal adenoma, while Apc(D716) and p53 R270H compound muta...
GSE79903: The transcription factor Zeb2 regulates development of conventional and plasmacytoid DCs by repressing Id2
Plasmacytoid dendritic cells (pDCs) develop from pre-pDCs, while two lineages of conventional DCs (c...
GSE75417: mRNA-seq analysis of B3 pre-B cell line from STATegra Project
The main goal of the project is to develop a new generation of bioinformatics resources for the inte...
GSE78984: MNase titration reveals differences between nucleosome occupancy and chromatin accessibility
Chromatin accessibility plays a fundamental role in gene regulation. One mechanism to regulate acces...
GSE116234: Bloodstream infection in leukemia
We examine the role of the gastrointestinal lymphatic tissue (GALT) in the formation of bloodstream ...
GSE74055: Histone H3 lysine 4 monomethylation modulates longrange chromatin interactions at enhancers
Long-range chromatin interactions between enhancers and promoters are essential for transcription of...
GSE86602: Comparison of gene expression profiles between SCD1 knockdown and vector control of Huh7 cells and PLC/PRF/5 cells by RNA-sequencing
The purpose of this experiment is to search for the downstream target of SCD1 SOURCE: Chi Ho Lin (ni...
GSE94098: FTO regulates adult neurogenesis through modulating the dynamics of N6-methyladenosine
Fat mass and obesity-associated gene (FTO) is a member of the Fe (II) and oxoglutarate-dependent Alk...
GSE110481: DNMT1 in Six2 progenitor cells is essential for transposable element silencing and kidney development
Cytosine methylation (5mC) plays a key role in maintaining progenitor cell self-renewal and differen...
GSE79702: USP15 regulates type I interferon response in vivo and is required for pathogenesis of microbial and autoimmune neuroinflammation
Genes and pathways in which inactivation dampens tissue inflammation present new opportunities for u...
GSE137628: RNA-seq of mouse testis samples from different treatment groups
The aim of this project was to explore the role of muscarinic receptors (M1, M3, and M5) in spermato...
GSE84405: ARID1A-mutated ovarian cancers depend on HDAC6 activity
ARID1A, encoding a subunit of the SWI/SNF chromatin remodeling complex, is the most mutated epigenet...
GSE129480: Targeting the CBM signalosome induces Treg to prime the tumor environment for effective immune checkpoint therapy
We report here the transcriptome analysis on resting and activated mature Treg cells from mice with ...
GSE80597: Fetal and adult progenitors give rise to unique populations of CD8+ T cells
Neonatal CD8+ T cells are unable to form long-lived memory cells in response to infection due to cel...
GSE80732 (human): Global transcriptional analysis of human extended pluripotent stem cells, human primed pluripotent stem cells, mouse extended pluripotent stem cells, and mouse embryonic stem cells by RNA-seq
All mammals develop from embryonic founder cells with the ability to generate all of the differentia...
GSE79252: Microglia self-renewal comprises context-dependent random or clonal expansion.
Microglia constitute a highly specialized network of tissue resident immune cells that is important ...
GSE81803: RNA-sequencing in WT and Fmr1-/- (KO) neurons treated with Jq1 and THZ
Widespread epigenetic disruptions in FXS mice leads to transcriptional changes that likely contribut...
GSE90983: Transcriptome Data of Peritoneal Macrophages Isolated from ApoE-/-/Ch25h-/- Mice
Cholesterol 25-hydroxylase (Ch25h) has been previously demonstrated to be required for anti-inflamma...
GSE79426: Direct GR binding sites potentiate clusters of TF binding across the human genome [3]
The glucocorticoid receptor (GR) binds the human genome at >10,000 sites, but only regulates the exp...
GSE147227: Effect of Particulate Matter (PM10) on innate immunity upon H5N1 infection
Comparative transcriptomic analysis of A549 cell after H5N1 infection alone and H5N1 infection with ...
GSE84812: Profiling of AKVPL vs AKVPSL derived tumor cells (Mouse)
RNA was isolated from fluorescence activated cell sorted (FACS) Lgr5-GFP+ and Lgr5-GFP- from aged ma...
GSE81420: Gene expression analysis of murine FLT3ITD induced acute leukemias
FLT3-ITD mutations are found in 30% of acute myeloid leukemia (AML) and portend a poor prognosis. Pa...
GSE91087: Comparing gene expression in iPSC derived RPE from control and AMD donors
iPSC-RPE cells derived from a patient with AMD, whom harboured the Y402H mutation were compared to h...
GSE79174: RNAseq of pre-T cells from control and Zfp36l1, Zfp36l2 double conditional knockout mice.
Purpose: Conditional knockout of Zfp36l1 Zfp36l2 early in lymphocyte development leads to a bypass o...
GSE80673: Comprehensive transcriptomes of mouse pancreatic islet delta, beta, and alpha cells
Rodent models are widely used to study diabetes. Yet, significant gaps remain in our understanding o...
GSE144725: RNA sequencing in ALS patient fibroblasts with a mutation in CHCHD10
Purpose: Comparing patient and rescue (Pat-OE) cells SOURCE: Isabella Straub (isabella.straub@mail.m...
GSE80953 (human): Temporal comparison of transcriptomic alterations in human, mouse and rat primary B lymphocytes exposed to 2,3,7,8-tetrachlorodibenzo-p-dioxin (TCDD)
RNA-Seq was used to analyze and compare temporal TCDD-induced gene expression changes in primary hum...
GSE81439: Identification of an NKX3.1-G9a-UTY regulatory network that controls prostate differentiation (Human_RWPE1_RNA-Seq)
Analysis of transcriptome of human RWPE1 cells over-expressing wild type NKX3.1 and mutant NKX3.1 (T...
GSE85161: DHX9 suppresses spurious RNA processing defects originating from the Alu invasion of the human genome [RNA-Seq]
Transposable elements increase genetic diversity thus making them an important part of evolution and...
GSE74176: Activating Mutation in STAT5 Is Sufficient To Drive PTCL peripheral T-Cell Lymphoma (PTCL)
Recurrent gain-of-function mutations in the transcription factor STAT5 have been detected in PTCL, a...
GSE79577: High throughput characterization of the m6A demethylase FTO by CLIP and RNAseq
We performed the CLIP-seq analysis of RNAs bound by 3xFLAG-tagged FTO protein stably expressed in hu...
GSE81095: RNA Sequencing Data in differentiating mouse embryonic stem cells [day2 and 2.5 in differentiation]
ES cell lines were established from mouse embryos, which were homozygous for the Trim33-flox allele ...
GSE109353: Astrocyte-derived Interleukin-33 promotes microglial synapse engulfment and neural circuit development II
Neuronal synapse formation and remodeling is essential to central nervous system (CNS) development a...
GSE74178: RNA binding protein SYNCRIP regulates the leukemia stem cell program [RNA-Seq]
RNA binding proteins (RBPs) tightly control mRNA abundance, stability and translation while mutation...
GSE80812: Klf5 regulates muscle differentiation via directly targeted muscle-specific genes in cooperation with MyoD
Deletion of Klf5 in satellite cells impaired muscle regeneration due to a failure of differentiation...
GSE81466: SOX7 supresses the expression of RUNX1 target genes during EHT
The molecular mechanisms regulating endothelial to hematopoietic transition (EHT) of hemogenic endot...
GSE154121: Investigating the Mechanism of Adherent-Invasive E. coli Induced Mitochondrial Fission in the Intestinal Epithelium (Exp. 1)
RNA-seq was performed to interogate the transcriptional changes in response to infection with Adhere...
GSE79993: Transcriptome changes in cultured mouse cortical neurons infected with lentivirus expressing shMeCP2
Illumina RNA sequencing technology was used to determine transcriptome changes in cultured mouse cor...
GSE80682: Lineage-specific genes are prominent DNA damage hotspots during leukemic transformation of B-cell precursors
In human leukemia, lineage-specific genes represent predominant targets of deletion, with lymphoid-s...
GSE80237: RNA-seq analysis reveals profound changes in transcript profiles between siCon- and siH19-transfected EVT cells
We used high throughput sequencing to analyze the transcriptional profiling of EVT. By comparing the...
GSE80810: Paternal X inactivation is fully Xist-dependent with strain-specific kinetics revealed by single cell embryo profiling
In Mammals, the difference in sex-chromosome constitution between males (XY) and females (XX) has le...
GSE144980: Single cell RNA-seq of mouse dorsal raphe Pet1 neurons
Here we use high-throughput and DR subdomain-targeted single-cell transcriptomics and intersectional...
GSE79452: Janus kinase 1 is essential for inflammatory cytokine signaling and mammary gland remodeling
Jak1 is a ubiquitously expressed tyrosine kinase that transduces extracellular signals from a variet...
GSE79580: Role of H3.3 residues in chromatin assembly and cell fate at the maternal-to-embryo transition
HISRainbow mice were used to obtain mosaic ovaries for transcriptome analysis of MII eggs expressing...
GSE106338: Gene expression profiling study by RNA-seq in PDX model based diffuse type gastric cancers.
We established PDX lines from diffuse type gastric cancers (DGCs). Using these cells, we carried out...
GSE76205: Integration of RNA-seq transcriptomics with metabolomics in mouse model of cigarette smoke exposure
Chronic obstructive pulmonary disease (COPD), a leading cause of morbidity and mortality, is primari...
GSE80264: Transcriptome analysis of H9 hESC derived cerebral organoids
RNA-seq was utilized to characterize the transcriptome of human embryonic stem cells-derived 3D cere...
GSE80336: Transcriptome profiling of the human dorsal striatum in bipolar disorder
Bipolar disorder (BD) is a highly heritable and heterogeneous mental illness whose manifestations of...
GSE80268: Active and inactive enhancers co-operate to exert localized and long-range control of gene regulation [RNA-seq]
We report that in developing B cells individual enhancers of Igk make up super-enhancer cluster wher...
GSE80960: Dynamic DNA methylation landscape defines brown and white cell specificity during adipogenesis (RNA-Seq)
We depicted a genome-wide integrative view of DNA methylome by reduced representation bisulfite sequ...
GSE96818: Analysis of WT and IRF1-deficient Th9 cell transcriptomes in the presence of IFN-gamma
Goal of this study was to compare transcriptional changes in IFN-gamma-treated WT compared to IRF1-d...
GSE78708: Not All H3K4 methylations are Created Equal: Mll2/COMPASS Dependency in Primordial Germ Cell Specification
The spatiotemporal regulation of gene expression is central for cell-lineage specification during em...
GSE81817: Glutamine Deficiency Occurs in Regions of Solid Tumours and Promotes Dedifferentiation through Inhibition of Histone Demethylation
We sequenced mRNA from the core regions and the peripheral regions of melanoma xenograft tumors SOU...
GSE106158: Comparative gene expression profiling of mouse pXEN, XEN, ES, and rat XENP cells
We derived and describe a novel mouse cell type that we name primitive XEN (pXEN) cells, and compare...
GSE107617: Gene expression in islets from control (WT) or transgenic (MYC) animals
We report changes in gene expression in mouse islets that express c-MYC in pancreatic beta cells as ...
GSE149838: In vivo CRISPR screening identifies Fli1 as transcriptional safeguard that restrains effector CD8 T cell differentiation [RNA-seq]
Genetic deletion of Fl1 enhanced CD8 Effector responses SOURCE: E,JOHN,WHERRY University of Pennsylv...
GSE80346: Transcriptional regulatory dynamics set the stage for a coordinated metabolic and neural response to social threat in mice [RNA-Seq data set]
Agonistic encounters with conspecifics are powerful effectors of future behavior that evoke strong a...
GSE82099: RNA-Seq of mouse E12.5 brain regions
Investigations into the roles for Pbx1 and its transcriptional network in dopaminergic neuron develo...
GSE111168: Next Generation Sequencing Facilitates Quantitative Analysis of Retinoblastoma Transcriptomes
Methods: mRNA profiles of retinoblastoma samples and para-tumor were generated by deep sequencing, ...
GSE80128: Evidence for two protein coding transcripts at the Igf2as locus
The insulin-like growth factor 2 antisense (Igf2as) gene is part of the Ins-Igf2-H19 imprinted gene ...
GSE79403: IL-31 regulation of transcripts in skin
Interleukin-31 (IL-31), a T cells derived cytokine which is mainly produced by CD4+ T cells skewed t...
GSE80963: Gene expression changes upon NUSAP1 over- or under-expression in PC-3 or DU145 cells.
By transcriptome (RNA-Seq) analysis of PC-3 or DU145 prostate cancer cell lines over- or under-expre...
GSE80284: Differential expression of Hdc-/- VS WT hematopoietic stem and progenitor cells (HSPC) from bone marrow.
The gene expression of bone marrow Hdc-/- and WT (LSK, Lin-c-kit+Sca-1+) hematopoetic stem and pro...
GSE146833: Transcriptional profiling of mouse pancreatic tumor cells II
RNA-seq analysis of sorted WT and Kdm3a-KO 6419c5 and 6694c2 mouse pancreatic tumor cells from subcu...
GSE134567: Gene expression profiling via RNA sequencing of patient brain tumors cultured in 3D bioengineered cultures
Using pediatric ependymoma and adult glioblastoma (GBM) as examples, it was shown that the 3D brain ...
GSE99246: Interleukins 12 and 15 induce cytotoxicity and early natural killer cell differentiation in type 3 innate lymphoid cells
Type 3 innate lymphoid cells (ILC3s) fulfill protective functions at mucosal surfaces via cytokine p...
GSE84450: ER stress increases alternative splicing of SRFS3s poison exon.
Mouse fibroblasts stressed with 1mM dithiothreitol for 4 hours were interogated for stress-induced a...
GSE85723: The ubiquitin ligase HUWE1 regulates hematopoietic stem cell maintenance and lymphoid commitment [high-throughput sequencing]
We identified the ubiquitin ligase Huwe1 as a crucial regulator of hematopoietic stem cell (HSC) fun...
GSE83381: Immune-restricted epigenetic reader SP140 maintains macrophage identity and activation states critical to intestinal homeostasis [RNA-seq]
Introduction: SP140 is a bromodomain/plant homeo domain (PHD)-containing reader with immune-restrict...
GSE78183: Molecular phenotyping of multiple mouse strains under metabolic challenge uncovers Elovl2 as a novel regulator of glucose-induced insulin secretion
Defective insulin secretion by pancreatic cells underlies the development of type 2 diabetes (T2D)....
GSE80160: Role of transcriptional coregulator GRIP1 in control of macrophage polarization and metabolic homeostasis
Diet-induced obesity is characterized by macrophage (M) infiltration and low-grade chronic inflammat...
GSE139270: AIB1D4 role in early breast cancer progression
We report the role of AIB1D4 in early stage breast cancer progression. Using CRISPR editing, we gene...
GSE76514 (mouse): Laser-capture microscopy coupled with Smart-seq2 (LCM-seq) for robust and efficient transcriptomic profiling of mouse and human tissues
Generally, when LCM is used in diverse transcriptomic analyses, several hundred, if not thousands, o...
GSE75842: Screening microRNA-196 targets in 11q23-translocation acute myeloid leukemia reveal mechanisms maintaining leukemia stemness with therapeutic potential [RNA-seq]
microRNA are aberrantly expressed in acute myeloid leukemia (AML), and clinically may have diagnosti...
GSE124922 (mouse): TET1 contributes to allergic airway inflammation and regulates interferon and aryl hydrocarbon receptor signaling pathways in bronchial epithelial cells
RNA-seq analysis to understand the regulation of genes by TET1 in mouse lungs and human bronchial ep...
GSE77846: Dnmt3a haploinsufficiency transforms Flt3-ITD myeloproliferative disease into a rapid, spontaneous, and fully-penetrant acute myeloid leukemia (Bulk RNA-Seq)
Cytogenetically normal acute myeloid leukemia (CN-AML) represents nearly 50% of human acute myeloid ...
GSE80304: RNA Sequencing Facilitates Quantitative Analysis of Primary Microglia Transcriptomes II
Using RNA-seq, we report here that primary microglia (PM) cells have a distinct transcriptomic signa...
GSE81130: Analysis of miR-203 transient over-expression on stemness potential of pluripotent cells
The balance between pluripotency and differentiation is critical during development and regeneration...
GSE81470: BTBD18 licenses piRNA-generating loci to support mouse germ cell development
PIWI-interacting RNAs (piRNAs) are small non-coding RNAs essential for animal germ cell development....
GSE80537: Next Generation Sequencing Analysis of ADHFE1 and vector control Transcriptomes in breast cancer cells
Our study represents a detailed analysis of MCF10A and MCF7 transcriptomes, with biologic replicates...
GSE87419 (human): Enhancer Remodeling During Adaptive Bypass to MEK Inhibition Is Attenuated by Pharmacological Targeting of the P-TEFb Complex (RNA-seq)
Targeting the dysregulated BRaf-MEK-ERK pathway in cancer has increasingly emerged in clinical trial...
GSE81885: Impact of Runx3 deficiency on mature CD8 T cell responses [RNA-seq]
Comparison of transcriptome between control and Runx3-deficient CD8 effector T cells SOURCE: Hai-Hui...
GSE135775: Gene expression analysis of mesenchymal stem cells at different stages of differentiation in to adipocytes
Mechanisms involved in adipose tissue expansion is of great interest in development of obesity and a...
GSE87808: Impaired Amino Acid Transport at the Blood Brain Barrier Is a Cause of Autism Spectrum Disorder
Autism spectrum disorders (ASD) are a group of genetic disorders often overlapping with other neurol...
GSE106529: Translatome analysis of the ribosomal protein L10 R98S mutation reveals altered serine metabolism in acute lymphoblastic leukemia [Ribo-seq]
Somatic ribosomal protein defects have recently been described in cancer, yet their impact on cellul...
GSE80382: Pioneering function of Isl1 in the epigenetic control of cardiomyocyte cell fate [Baf60c_RNA-seq]
Generation of widely differing and specialized cell types from a single totipotent zygote involves l...
GSE96815: Enhancement of Arterial Specification in Human Pluripotent Stem Cell Cultures Promotes Definitive Hematoendothelial Program with Broad Myelolymphoid Potential
Identification of the regulators that lead to arterial specification with definitive hematopoietic p...
GSE115434: Transcription profile analysis of wild type and Irf9-/- bone marrow derived macrophages in response to type I and type II interferons
Host defense by the innate immune system requires the establishment of antimicrobial states allowing...
GSE84293: Identification of transcriptomic drivers of squamous cell carcinoma development through a preneoplastic intermediate [human RNA-Seq]
Cutaneous squamous cell carcinoma (cuSCC) comprises 15-20% of all skin cancers, accounting for over ...
GSE126757: RNA-seq profiling of the human neutrophil genome during PMA- and E. coli encounter-induced activation
Human neutrophil genome during PMA- and E. coli encounter-induced activation SOURCE: Matthew Denholt...
GSE80958: Sonic hedgehog signaling promotes basal radial glia and 1 intermediate progenitor cell
The unique mental abilities of humans are rooted in the immensely expanded and folded neocortex, whi...
GSE80397: Global transcriptome analysis in the MYCN-amplified neuroblastoma cell line IMR5-75 upon inducible MYCN-knockdown
Inducible MYCN-knockdown, followed by RNA-seq analysis in the MYCN-amplified neuroblastoma cell line...
GSE99248: Comparsion of the transcriptome profiles in normal and age-related macular degneration in retina and RPE-Choroid-Scleral (RCS) tissues
Analysis of retinal and RCS tissues revealed a significant differential expression of noncoding RNA ...
GSE81476: PTEN-deficient synovial sarcoma
Transcriptome comparisons by RNAseq of genetically engineered mouse models of synovial sarcoma, expr...
GSE96661: Chd2 knockout effect on chromatin remodelling and the expression of developmental genes in mouse embryonic stem cells (RNA-Seq)
We demonstrate that chromodomain helicase DNA-binding domain 2 (Chd2) is required to maintain the di...
GSE74549: Dynamic Changes in Histone Modifications Precede de novo DNA Methylation in Oocytes
Erasure and subsequent re-instatement of DNA methylation in the germline, especially at imprinted Cp...
GSE97278: Genome-wide mRNA expression profiling of WT MEFs and NSD2 KO MEFs
NSD2 (also known as Whsc1, MMSET) play a role in H3K36 methyl transferase. Here we showed that 199 I...
GSE80365: Genomic agonism and phenotypic antagonism between estrogen and progesterone receptors in breast cancer. [tumor samples RNA-seq]
Transcriptomic changes and estrogen and progesterone receptor binding in multiple ER+/PR+ models (ei...