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Sequencing-based assays page 29
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GSE50590: A role for H3K4 mono-methylation in facultative heterochromatin assembly and partitioning of chromatin readers
Mono-methylation of lysine 4 on histone H3 (H3K4me1) is a well-established feature of enhancers and ...
GSE55005: mRNA profiling reveals determinants of trastuzumab efficiency in HER2-positive breast cancer
The intention was to detect genes that are determining trastuzumab efficiency in HER2-positive breas...
GSE115146: A Novel Class of MicroRNA Recognition Elements That Function Only in Open Reading Frames
MicroRNA (miRNA) are well known to target 3 untranslated regions (3UTR) in mRNAs to silence gene exp...
GSE118119: Inverse data-driven modelling and multiomics analysis reveals PHGDH as a metabolic signature of M2 macrophages
RNAseq data from C57BL/6 bone marrow-derived macrophages that were stimulated with IL-4 in the prese...
GSE57423: Expression data from embryonic day 15.5 atrioventricular canal regions were isolated from Scx-/- and Scx+/+ mice.
Purpose: Our lab has previously shown that Scleraxis (Scx) is require for proper valve development i...
GSE35510: Isl1-Lhx3 fusion specifies motor neuron fate by inducing motor neuron genes and concomitantly suppressing the interneuron programs
Combinatorial transcription codes generate the myriad of cell types during development, and thus lik...
GSE52594: Antioxidants Accelerate Lung Cancer Progression in Mice
Antioxidants are widely used to protect cells from damage induced by reactive oxygen species (ROS). ...
GSE126217: RNAseq analysis of glomerular transcriptome of wild-type vs. Podocyte Cosmc knockout
Cosmc is an obligate chaperone for C1GalT1 T transferase necessary for generating mature mucin-type ...
GSE57926: RBFox2 regulates a broad RNA program and is required for genome-wide targeting of polycomb complex
Increasing evidence suggests that diverse RNA binding proteins interact with regulatory RNAs to regu...
GSE58345: Activation of a SOX2-dependent transcriptional regulatory circuit drives glioblastoma.
Overexpression of the transcription factor SRY-related box 2 (SOX2) is characteristic of Glioblastom...
GSE52854: Inhibition of MEK and PI3K alone or in combination alters the transcriptome of the lung during TGF-induced pulmonary fibrosis
Pulmonary fibrosis is often triggered by an epithelial injury resulting in the formation of fibrotic...
GSE58286: Transcriptome comparison of pancreatic islets of Urocortin3 null islets and wild type controls.
The peptide hormone Urocortin3 (Ucn3) is abundantly expressed by mature beta cells, yet its physiolo...
GSE58089: Altering the intestinal microbiota during a critical developmental window has lasting metabolic consequences [RNA-Seq]
Acquisition of the intestinal microbiota begins at birth, and a stable microbial community develops ...
GSE58371: Gene profile of Wt and miR-155-/- Tfh cells
Differential gene expression profile of Tfh and non-Tfh cells from both Wt and miR-155-/- mice splee...
GSE57998: Ataxin-2 modulates mRNA levels of proteins in ribosomal large and small subunit and in translation initiation complex
Spinocerebellar ataxia type 2 (SCA2) is a neurodegenerative disorder, caused by an unstable CAG-repe...
GSE63679: Mesenchymal tumors can derive from pericytes.
We demonstrated that deletion of the p53 tumor suppressor gene in NG2 expressing cells resulted in t...
GSE65518: Dynamic regulation of the histone variant H1.0 contributes to intratumor epigenetic and functional heterogeneity [RNA-Seq]
Identification of genes regulated by the histone variant H1.0 by RNA-seq analysis of cell lines expr...
GSE94554: Functional activity of RNA-binding protein binding sites drives 3 UTR evolution
Protein bound segments of mammalian 3 UTRs are GC rich, folded in vivo, rapidly evolving, and reduce...
GSE58357: Transcriptome sequencing of GRK6 knockout HSCs and CLPs
WT and GRK6-/- Lin-c-kit+sca-1+ cells (hereafter referred to as HSC) as well as CLP (Lin-c-kit+sca-1...
GSE86507: Next Generation Sequencing Facilitates Quantitative Analysis of either Pkd1f/f, Pkd1f/f:HoxB7-Cre mice or Pkd2f/f, Pkd2f/f:HoxB7-Cre mice transcriptome [RNA-seq]
Purpose: To reveal the cystogenesis regulatory mechanism by miRNA and miRNA targeted genes in ADPKD ...
GSE97036: Effects of arsenic and Pseudomonas aeruginosa infection on gene expression in human airway epithelial cells
Purpose: To determine effects of arsenic on gene expression in polarized primary human bronchial epi...
GSE55338: Dicer-microRNA-Myc circuit promotes transcription of hundreds of long noncoding RNAs
Long noncoding RNAs (lncRNAs) are important regulators of cell fate, and their mis-expression has be...
GSE129666: RNA sequence data in whole cell extracts of differentiated human podocytes
RNA from Ctrl and SMPDL3b OE podocytes was isolated and analyzed for differences in the mRNA express...
GSE60545: Hybrid mice reveal parent-of-origin and cis- and trans-regulatory effects in the retina
A fundamental challenge in genomics is to map DNA sequence variants onto changes in gene expression....
GSE58387: The human skeletal muscle transcriptome sex differences, alternative splicing and tissue homogeneity assessed with RNA sequencing
The amount of RNA sequencing data on skeletal muscle is very limited. We have analyzed a large set o...
GSE57945: Core Ileal Transcriptome in Pediatric Crohn Disease
We report the global pattern of ileal gene expression in a cohort of 359 treatment-nave pediatric Cr...
GSE97464: Developmental high binge ethanol exposure does not alter the transcriptome of visual cortical microglia as determined by mature mRNA RNA sequencing
This RNA-seq data was generated to determine the effects of developmental ethanol exposure on the mi...
GSE38842: Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros (RNA-seq: sorted proB cell Hardy Fractions B and C+C')
The C2H2 zinc finger is the most prevalent DNA-binding motif in the mammalian proteome, with DNA-bin...
GSE60569: Sustained expression of activated beta-catenin in dermal fibroblasts causes skin fibrosis
Forced expression of activated beta-catenin in mouse dermal fibroblasts is sufficient to cause spont...
GSE62378: Regulatory RNA Apela Is a Component of a Negative Feedback Loop Regulating p53-Mediated Apoptosis in Embryonic Stem Cells (III)
The goal is to identify RNAs that bind to Hnrnpl (hnRNP L) using RNA immunoprecipitation (RIP) assay...
GSE58398: The histone lysine demethylase Kdm6b is required for activity-dependent preconditioning of hippocampal neuronal survival
We profiled basal and bicuculline+4-AP inducible mRNA expression in cultured mouse hippocampal neuro...
GSE54443: Mutant Huntingtin promotes neuronal death through cell autonomous microglial activation via myeloid lineage- determining factors
Huntington's Disease (HD) is a fatal neurodegenerative disorder caused by an extended polyglutamine ...
GSE93325: Proteogenomic characterization of developmental defects in the forebrain resulting from hyperactivated mTOR signaling
Hyperactivated mTOR signaling in the developing brain has been implicated in multiple forms of patho...
GSE60808: Jarid2 regulates hematopoietic stem cell function by acting with Polycomb Repressive Complex 2
Polycomb Repressive Complex 2 (PRC2) has been shown to play a key role in hematopoietic stem and pro...
GSE58971: RNAseq data from in vitro-stimulated (6 hours) murine relfl/flCD19-Cre and CD19-Cre splenic B cells purified by magnetic cell separation (REL6)
RNAseq analysis of CD40 + IgM in vitro-stimulated (6 hours) murine relfl/flCD19-Cre (furtheron desig...
GSE62098: RNA-Seq of the corpus callosum from 12 individuals
We performed RNA-Seq for the corpus callosum sampled from 12 individuals. The samples were dissected...
GSE124761: The study of the role of POU3F2 in response to UVB treatment
siRNA KD of POU3F2 directly effect DNA-damage repair and apoptosis genes SOURCE: Pakavarin Louphrasi...
GSE55282: Characterization of distinct classes of differential gene expression in osteoblast cultures from non-syndromic craniosynostosis bone
We report on explant osteoblast cultures from human patients, demonstrating that there are at least ...
GSE60590: Dynamics of the human skeletal muscle transcriptome in response to exercise training - part 1
A total of 23 participants (data available in present submission and in GSE58608) completed three mo...
GSE58365: The BCL6 RD2 domain governs commitment of activated B-cells to form germinal centers
Our data demonstrated that Bcl6 directly binds and represses trafficking receptors S1pr1 and Grp183 ...
GSE97309: Nucleobindin-2 controls insulin-sensitivity in obesity without impacting food intake and adiposity
We performed whole transcriptome profiling on sorted tissue macrophages from adipose of wild-type or...
GSE117543: Low cytosolic folate cycling is a hallmark of U251 glioblastoma cells reprogramming towards pluripotency [RNA-seq]
we report that U251 glioblastoma tumor spheres exhibit low cytosolic folate cycle and a reprogrammme...
GSE60837: BCL9/9L--catenin Signaling is Associated With Poor Outcome in Colorectal Cancer
Canonical Wnt signaling output is mediated by -catenin, which interacts with LEF/TCF transcription f...
GSE120601: RNA sequencing of CFU-GM derived from CD34+ cells expressing PRR14L shRNA or a scramble control
Here we are using RNA-Seq to study the effect of PRR14L knockdown on transcriptome of hematopoietic ...
GSE30567: ENCODE Cold Spring Harbor Labs Long RNA-seq (hg19)
This data was generated by ENCODE. If you have questions about the data, contact the submitting labo...
GSE97462: Transcriptional deregulation in EZH2-deficient lymphocyte progenitors
This goal of this study was to identify genes that are deregulated in the absence of EZH2 in early l...
GSE56762: Histone variant H3.3 is an essential maternal factor for oocyte reprogramming
Mature oocyte cytoplasm can reprogram somatic cell nuclei to the pluripotent state through a series ...
GSE58973: RNAseq data from in vitro-stimulated (24 hours) murine relfl/flCD19-Cre and CD19-Cre splenic B cells purified by magnetic cell separation.
RNAseq analysis of CD40 + IgM in vitro-stimulated (24 hours) murine relfl/flCD19-Cre (furtheron desi...
GSE60883: RNA-seq of young and quiescent MRC-5 human fibroblasts
Quiescent MRC-5 fibroblasts were compared to young fibroblasts SOURCE: Steffen Priebe (steffen.prieb...
GSE60219: Transcriptional landscape of different brain regions in a Rett syndrome mouse model
We propose to investigate differential gene expression in Hippocampus and Frontal cortex of MeCP2 kn...
GSE103495: RNA seq with AML (NB4) cells upon FTO inhibition
To determine the potential targets of FTO and identify treatment significance of FTO inhibition in A...
GSE117933: Effect of Menin cKO on MLL-AF9 transformed cells
We determined the effect of conditional deletion of Menin in MLL-AF9 transformed leukemia cells SOUR...
GSE58018: Gene silencing triggers Polycomb Repressive Complex 2 recruitment to CpG islands genome-wide [iTC-seq_drugs]
Polycomb group (PcG) proteins are required for normal differentiation and development, and their act...
GSE125737: Niche-specific factors dynamically regulate sebaceous gland stem cells during skin homeostasis and aging
We deleted different Notch pathway components in different sub-compartments of mouse skin, and perfo...
GSE56613: RNAseq analysis of murine ITPKB deficient versus wild type LT-HSC
Tight regulation of hematopoietic stem cell (HSC) homeostasis is essential for life-long hematopoies...
GSE59318: Neural gene expression in Pten knock-in mice at 6-weeks of age
The goal of this study was to assess the changes in the neural transcriptome of Ptenm3m4 mice, in or...
GSE36871: Nascent-Seq Reveals Novel Features of Mouse Circadian Transcriptional Regulation [RNA-Seq]
Over the past decade, genome-wide assays have underscored the broad sweep of circadian gene expressi...
GSE74762: Sequencing analysis of proliferative heterogeneity in squamous cell carcinomas
ChIP-seq, ATAC-seq and RNA-seq analyses were integrated to define direct, transcriptional Tgf target...
GSE37646: Distinct STAT5 concentrations uniquely control establishment and differentiation of mammary epithelium during pregnancy
To dissect regulatory processes of cell proliferation and differentiation we generated mouse strains...
GSE59383: RNA-seq data: Baf60c homozygous deletion vs. WT at two time points in cardiac differentiation
This project compares Baf60c homozygous deletions to WT at two time points during cardiac differenti...
GSE57170: Suppression of pervasive noncoding transcription in embryonic stem cells by esBAF
Approximately 75% of the human genome is transcribed, the majority of which does not encode protein....
GSE58996: The CNS-Heart Axis is a Source of Cardiac Dysfunction in Mouse Models of Huntingtons Disease
Purpose: Transcriptome profiling (RNA-seq) to microarray to evaluate transcriptional changes in the ...
GSE119007: Prostaglandin E2 inhibits pro-fibrotic function of human pulmonary fibroblasts by disrupting Ca2+-signaling
Purpose: Identification of gene expression in human lung fibroblasts, including analysis of impact o...
GSE56636: Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) Analysis Uncovers Broad Changes in Chromatin Structure Resulting from Hexavalent Chromium Exposure
The ability of chromatin to switch back and forth from open euchromatin to closed heterochromatin is...
GSE124729: Transcriptomes of E16 neocortical tissue knockout from Nfia, Nfib and Nfix knockout mice
Here, we generated transcriptomes of microdissected neocortex of Nfix knockout and wildtype litterma...
GSE120663: Transcriptome Analysis of PBMCs in peripheral blood of patients with hepatocellular carcinoma
The aim of this study was to analyze the expression profile of circRNAs in PBMCs in peripheral blood...
GSE42509: Transcriptome-profiling (RNA-seq) and Ribosome-profiling (Ribo-seq) in proliferation, quiescence, senescence and transformed states.
We applied in parallel RNA-Seq and Ribosome-profiling analyses to immortalized human primary BJ fibr...
GSE59020: ETS1 is a genome-wide effector of RAS/ERK signaling in epithelial cells (RNA-Seq)
ETS1 and RAS/ERK regulate a common gene expression program in establishing enviroment suitable for p...
GSE61329: Role of Tet3 and DNA replication in zygotic demethylation of both paternal and maternal genomes [RNA-seq]
With the exception of imprinted genes and certain repeats, DNA methylation is globally erased during...
GSE59463: Polycomb PRC2 antagonizes de novo DNA methylation at the maternal Gtl2-Rian-Mirg locus [Next-Gen Sequence Data]
Wild-type mouse embryonic stem cells are compared with mutants for components of PRC2 including Ezh...
GSE60441: Ebf2 is a selective marker of brown and beige adipogenic precursor cells (RNA-seq)
Brown adipocytes, muscle and dorsal dermis descend from precursor cells in the dermomyotome, but the...
GSE59813: Transcriptional Pause Release Is a Rate-Limiting Step for Somatic Cell Reprogramming (RNA-seq)
Reactivation of the pluripotency network during somatic cell reprogramming by exogenous transcriptio...
GSE127344: Transcriptomic profile of human embryonic renal corpuscles
In order to characterize and benchmark the podocytes-like cells generated through human ES cell diff...
GSE60243: Tristetraprolin (TTP) regulated splenic transcriptome in "Triple KO" mice
Tristetraprolin (TTP) binds to specific AU-rich elements in the 3'UTR of certain transcripts and re...
GSE116390: Single-cell RNA-seq of sorted CD8+ T cells from B16 melanoma tumors
CD8 T cells are the main effectors of the adaptive immune response against intracellular pathogens a...
GSE57776: Transcriptome of Smooth Muscle Cells, Interstitial Cells of Cajal and PDGFR+ Cells
Genome scale expression data on absolute numbers of gene isoforms offer essential clues for cellular...
GSE60296: Comparison of total and cytoplasmic mRNA reveals global regulation by nuclear retention and miRNAs
We extracted RNA from whole cells and RNA from the cytoplasm and performed RNA sequening to compare ...
GSE56122: A dual cis-regulatory code links IRF8 to constitutive and inducible gene expression in macrophages.
IThe transcription factor (TF) interferon regulatory factor 8 (IRF8) controls both developmental and...
GSE74928: XX-650-23, an inhibitor of CREB-CBP interaction, effect on acute myeloid leukemia cell line
Analysis of acute myeloid leukemia KG1 cells treated with XX-650-23 (5 mM) for 12hrs. XX-650-23 inhi...
GSE59987: TET1 regulates hypoxia-induced epithelial-mesenchymal transition through DNA demethylation (RNA-Seq)
In order to explore the status of DNA methylation in hypoxia response, we show that TET1, a DNA diox...
GSE59483: Transcriptomic analysis of an archived bladder cancer cohort
Establishment and application of RNAseq based transcriptome analayis on an archivaed bladder cancer ...
GSE60391: Global Regulation of Alternative Internal Exon Usage by mRNA 3' End Formation Factors [RNA-Seq]
RNA-seq analysis of samples from Non-silencing, RBFOX2 and CPSF2 knockdown cells SOURCE: Ashish Misr...
GSE58514: Opposing roles for the lncRNA Haunt and its genomic locus in regulating HOXA gene activation during embryonic stem cell differentiation
Long noncoding RNAs (lncRNAs) have been implicated in controlling various aspects of embryonic stem ...
GSE58206: Pontin functions as an essential coactivator for Oct4 target genes and lincRNAs in embryonic stem cells.
The actions of transcription factors, chromatin modifiers, and noncoding RNAs are crucial for the pr...
GSE60334: DNA methylation analysis and expression profiling during murine embryogenesis and in embryos deficient for DNMT3A or DNMT3B
We quantified the targets and kinetics of DNA methylation acquisition in mouse embryos, and determin...
GSE134637: Comparison of cortisol metrics and total RNA profiles from Healthy Individuals
The study seeks to identify transcripts whose expression levels are significantly correlated with be...
GSE62633: Transcription Factors GATA4 and HNF4A Control Distinct Aspects of Intestinal Homeostasis in Conjunction With the Transcription Factor CDX2
To determine whether the intestine-restricted transcription factor (TF) CDX2 functionally interacts ...
GSE46433: Promoter directionality is controlled by U1 snRNP and polyadenylation signals
Transcription of the mammalian genome is pervasive, but productive transcription outside of protein-...
GSE111322: Macrophage microRNA-150 promotes pathological angiogenesis as seen in age-related macular degeneration: part II
We identified that microRNA-150 is upregulated in aged macrophages of diverse origins and therefore ...
GSE65506: Graded Expression Changes Determine Phenotype Severity In Mouse Models of CRX-Associated Retinopathy
Background: Mutations in the cone-rod-homeobox protein CRX are typically associated with dominant bl...
GSE60482: Stretch-Enhancers Delineate Disease-Associated Regulatory Nodes in T Cells
T Cell stretch-enhancers are vulnerable to Jak inhibitor tofacitinib SOURCE: Golnaz VahediLymphocyte...
GSE56175: KRAS and YAP1 converge to regulate EMT and tumor survival
Cancer cells that express oncogenic alleles of RAS typically require sustained expression of the mut...
GSE60548: A rapid and robust approach for inducing neurogenesis in human stem cells
Advances in cellular reprogramming and stem cell differentiation now enable ex vivo studies of human...
GSE60426 (human): mRNA destabilization is the dominant effect of mammalian microRNAs by the time substantial repression ensues (sequencing)
MicroRNAs (miRNAs) regulate target mRNAs through a combination of translational repression and mRNA ...
GSE59598: mRNA expression in human DAOY cells
We generate ZNF423 knockdown and control DAOY cells with lentivirus that co-expressed the fluorescen...
GSE60373: A relative shift in cloacal location repositions external genitalia in amniote evolution
Comparative RNA-seq profiling of mouse and anole lizard developing limbs and external genitalia, to ...
GSE60570: Aneuploidy-induced cellular stresses limit autophagic degradation.
An unbalanced karyotype, a condition known as aneuploidy, has a profound impact on cellular physiolo...
GSE88987: Dynamic changes in chromatin accessibility in CD8+ T cells responding to viral infection
In response to acute infection, naive CD8+ T cells expand, differentiate into effector cells and the...
GSE45159: Genetic regulation of human adipose microRNA expression and its consequences for metabolic traits
The genetics of messenger RNA expression has been extensively studied in humans and other organisms,...
GSE126074: Simultaneous profiling of transcriptome and chromatin accessibility in single nucleus
Here we describe SNARE-seq, a droplet-based method to simultaneously profile gene expression and chr...