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Sequencing-based assays page 3
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GSE60641: Active repression of Sox9 by Jag1 is required for silencing the default chondrogenic fate of the vascular smooth muscle wall [set 1]
Acquisition and maintenance of vascular smooth muscle fate is essential for the morphogenesis and fu...
GSE53249: Transcriptomics analysis of gene expression in normal and FTO, METTL3 deficient Mouse embryo fibroblast 3T3-L1 pre-adipocytes
RNA was isolated from control and FTO,METTL3 deficient mouse 3T3-L1 cells using the TRIzol (Invitrog...
GSE135600: Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells [RNA-Seq]
Transcriptional regulatory network controlling the ontogeny of hematopoietic stem cells SOURCE: Kai ...
GSE76381 (mouse): Single Cell RNA-seq Study of Midbrain and Dopaminergic Neuron Development in Mouse, Human, and Stem Cells
In order to get a better molecular understanding of human midbrain development, this study defines c...
GSE49949: Loss of Sip1 leads to migration defects and retention of ectodermal markers during lens development
We report the application of RNA-sequencing technology for the high-throughput profiling of mammali...
GSE54619: RNA-seq analysis of the transcriptomes of Piwi-deficient iPSCs
genome wide RNA-seq analysis of the transcriptomes of iPSCs that are derived from Miwi(-/-), Mili(-/...
GSE54982: Probing In vivo Brachyury Function with Tc mouse model
To identify Brachyury target genes in vivo and elucidate how Brachyury-mediated regulation contribut...
GSE53398: Barx2 and Pax7 have antagonistic functions in regulation of Wnt signaling and satellite cell differentiation
The canonical Wnt signaling pathway is critical for myogenesis and can induce muscle progenitors to ...
GSE47496: Selective Functions of Individual Zinc Fingers Within the DNA-Binding Domain of Ikaros (RNA-seq: sorted DP thymocytes)
The C2H2 zinc finger is the most prevalent DNA-binding motif in the mammalian proteome, with DNA-bin...
GSE54569: Oct6 promotes neural commitment via activation of neural lineage genes and inhibition of BMP/Wnt signals
The neural fate commitment of pluripotent stem cells requires repression of extrinsic inhibitory sig...
GSE55090: SRF is required for neutrophil migration in response to inflammation
RNA expression in Srf wildtype and knockout primary bone marrow derived mature neutrophils was deter...
GSE60691: Disrupting SUMOylation potentiates transactivation function and ameliorates polyglutamine AR-mediated disease
Our findings demonstrate beneficial effects of enhancing transactivation function of the ligand-acti...
GSE127856: Identification of Atrial Fibrillation associated genes and functional non-coding variants
Expression analysis of whole tissue and cardiomyocytes of fetal and adult atrial free wall SOURCE: V...
GSE54640: Serpinb3a contributes to early skin inflammation following allergen exposure
Serpinb3a knockout mice show attenuated Transepidermal Water Loss (TEWL) and S100A8 expression (an e...
GSE55291: Noncoding RNA transcriptome analysis during cellular reprogramming
We report the application of single-cell and bulk RNA sequencing technology to examine the noncoding...
GSE56545: mRNA profiling of Hepatocellular carcinoma (HCC)
We did mRNA profiling and showed that an interferon-inducible gene's deletion and under-expression ...
GSE134408: Transcriptome analysis of naive B cells from CD19Cre and CD19Cre_STAT6vt mice
To investigate how activated STAT6 modulates B cells development and function in vivo, we characteri...
GSE54729 (human): Transcriptome profiling of a mouse model of alveolar soft part sarcoma
In order to dtermine how well a mouse genetic model of alveolar soft part sarcoma (ASPS) mimics the ...
GSE58261: RNA sequencing (RNA-SEQ) of Dnmt1 and Dnmt3a conditional knockout mice
Purpose: Epigenetic regulation contributes to pathogenesis of neurondegenerative disease. We found ...
GSE53942: RNA-seq of poly(A)-/ribo- or poly(A)+ RNAs from mouse and rhesus ES cells
We have used RNA-seq to examine circular RNAs from RNase R treated poly(A)-/ribo- RNAs in human embr...
GSE54795: RNA-SEQ profiling of dopaminergic neurons from the mid-brain of mice that received intraperitoneal injections of MPTP
RNA-SEQ of dopaminergic neurons from the mid-brain of mice that received one daily intraperitoneal i...
GSE53190: Hydroxymethylcytosine in mouse intestinal differentiation [RNA-Seq]
The discovery of cytosine hydroxymethylation (5-hmC) as a mechanism that potentially controls DNA me...
GSE65422: Gene expression profiling and mutation analysis of B cell lymphomas arising in mice expressing NIK and BCL6 transgenes
In this study, by RNA sequencing we generated the gene expression profile (GEP) of each mouse lympho...
GSE54308: Transcriptome Sequencing from Diverse Human Populations Reveals Differentiated Regulatory Architecture
To understand the full range of expression variation, alternative splicing, and the genetics of regu...
GSE52616: Effect of LMP7 and MECL1-immunoproteasome subunits deficiency on the transcriptome of mouse bone marrow-derived dendritic cells
As regulators of protein degradation, proteasomes regulate practically all cellular functions. It is...
GSE66817: Diabetes Enhances the Proliferation of Adult Pancreatic Multipotent Progenitor Cells and Biases Their Differentiation to More Beta-Cell Production
Endogenous pancreatic multipotent progenitors (PMPs) are ideal candidates for regenerative approache...
GSE55790: Next Generation Sequencing of Wild-Type FVB/NJ Mouse Cardiac Polyadenylated RNA
Purpose: Next-generation sequencing (NGS) provides for quantitation of RNA abundances and comparison...
GSE54574: Direct Conversion from Mouse Fibroblasts Informs the Identification of Hemogenic Precursor Cells In Vivo
Definitive hematopoiesis emerges via an endothelial-to-hematopoietic transition in the aorta-gonad-m...
GSE52234: Consequences of beta-PDGFR deletion on hepatic stellate cells during hepatic regeneration
Purpose: The goal of this study was to determine biological consequences during liver regeneration f...
GSE62974 (mouse): RNA sequencing (RNA-SEQ) of EPAS1 knockdown by siRNA in endothelial cells
Purpose: By integrating DNA methylation and gene expression of COPD lung tissues, we identified EPAS...
GSE52583: High throughput quantitative whole transcriptome analysis of distal mouse lung epithelial cells from various developmental stages (E14.5, E16.5, E18.5 and adult)
We used microfluidic single cell RNA-seq on 198 individual mouse lung epithelial cells at 4 differen...
GSE57054: A subcutaneous adipose tissue-liver axis in the control of hepatic gluconeogenesis
We performed RNA sequencing analysis of hepatic gene expression a few hours after amlexanox treatmen...
GSE63703: Short and Long RNA sequencing of human mature erythrocytes
We employed high-throughput sequencing of both short (~18-24nt) and long (>200nt) RNAs in human eryt...
GSE57871: RNA-seq analysis of vorinostat-resistant HCT116 cells following gene knockdown of GLI1 or PSMD13 with or without vorinostat treatment
Transcriptome analysis was conducted on vorinostat resistant HCT116 cells (HCT116-VR) upon knockdown...
GSE57078: Lysine-specific demethylase 1 metastasis of androgen-independent PCa cells [RNA-seq]
The aim of this study is to identify the LSD1 target genes in metastatic androgen independent prosta...
GSE60040: Wide-spread disruption of transcription termination in HSV-1 infection: Next-generation sequencing of translational activityd by ribosome profiling
Primary human foreskin fibroblasts (HFF) were infected with wild-type simplex virus 1 (HSV-1) strain...
GSE54549: Role of LDB1 in the transition from chromatin looping to transcription activation
Many questions remain about how close association of genes and distant enhancers occurs and how this...
GSE54588: BAFF engages distinct NFkappaB effectors in maturing and proliferating B cells
Identify genes which are induced in wild type B cells under antigenic stimuli, anti-IgM vs pro-survi...
GSE57866: RNAseq transcriptome data from reprogramming human CD34+ cells to iPS
We reprogrammed human CD34+ cells from cord blood using a lentiviral vector encoding OCT4, SOX2 and ...
GSE57116: 4sUDRB-seq: measuring transcription elongation and initiation genomewide
A new method to measure elongation and intitiation rates SOURCE: Gilad Fuchs (gilad.fuchs@weizmann.a...
GSE120622: Fucosyltransferase 4 promotes cancer metastasis via enhancing EGFR/TGFBR signaling network and is associated with poor prognosis in non-small cell lung cancer
Purpose: Aberrant glycosylation has been known to regulate cancer cell trafficking via promoting int...
GSE54016: The developmental dynamics and disease potential of random monoallelic gene expression
X-chromosome inactivation (XCI) in females and allelic exclusion of olfactory receptor or immunoglob...
GSE60647: From mouse to humans: detecting preventing vaccination targets associated to melanoma cancer stem cells. Gene-level analysis: CT26
The efficacy of cancer treatments have improved constantly in the last decade. However, therapeutic ...
GSE62902: RNA-Seq Versus Oligonucleotide Array Assessment of Dose-Dependent TCDD-elicited Hepatic Gene Expression in Mice [RNA-Seq]
Dose-dependent hepatic gene expression was examined following repeated exposure (every 4 days for 28...
GSE56690: Characterizing the contrasting roles of JMJD3 and UTX histone demethylases in T cell acute lymphoblastic leukemia [UTXKO_RNA-seq]
T-cell acute lymphoblastic leukemia (T-ALL) is an immature hematopoietic malignancy driven mainly by...
GSE57875: RNA-Seq analysis of hnRNPL KO fetal liver cells
fetal liver cells from either hnRNPL wild-type or hnRNPL KO embryos were analysed for differential e...
GSE58363: Differential expression analysis for RNA-seq data between cardiac progenitor and uncommitted cells at day 4.75
We report the differential expression between cardiac progenitor and uncommitted cells at day 4.75 S...
GSE56785: RNA-Seq characterization of human H1-derived NPC differentiation timecourse
High resolution transcriptional profiling of H1-derived human neuronal precursor cells over a timeco...
GSE58323: Evollutionally dynamic L1 regulation in embryonic stem cells
Mobile elements are important evolutionary forces that challenge genomic integrity. Long intersperse...
GSE58619: Genome-wide transcriptome analyses by the RNA-seq method
We performed the whole transcriptome analysis in Zscan4 positive ES cells (Em+) and Zscan4 negative ...
GSE60738: Dynamics of gene silencing during X inactivation using allele-specific RNA-Seq
Background: During early embryonic development, one of the two X chromosomes in mammalian female cel...
GSE53244: m6a peak analysis in normal, FTO deficient and five stages of adipogenesis (D-2/0/2/5/10) in Mouse embryo fibroblast 3T3-L1 pre-adipocytes
Total RNA was extracted using TRI Reagent (Sigma). cDNA was synthesized by RevertAid First Strand cD...
GSE60537: Human resistin alters lung mRNA expression from helminth-infected lungs.
Goal: To examine the effects of human resistin during helminth infection.; Methodology: To examine t...
GSE102856: SENP6 in OCP maintenance
To understand the role of sumoylation/desumoylation pathway in skeletla development and homeostasis,...
GSE63124: Large-scale epigenetic reprogramming is punctuated late during the evolution of pancreatic cancer progression [RNA-Seq]
During pancreatic cancer progression, heterogeneous subclonal populations evolve in the primary tumo...
GSE58017: Gene silencing triggers Polycomb Repressive Complex 2 recruitment to CpG islands genome-wide [RNA-seq_differentiation]
Polycomb group (PcG) proteins are required for normal differentiation and development, and their act...
GSE63646: Expression and Prognostic impact of LncRNAs in Acute Myeloid Leukemia
Long noncoding RNAs (lncRNAs) are transcripts longer than 200 nucleotides located within the interge...
GSE141142: An immune-centric exploration of BRCA1 and BRCA2 germline mutation related breast and ovarian cancers
Background:This study was a hypothesis generating exploration of genomic data collected at diagnosis...
GSE147424: Single-cell transcriptome analysis of human skin identifies novel fibroblast subpopulation and enrichment of immune subsets in atopic dermatitis
Background: Atopic dermatitis (AD) is a prevalent inflammatory skin disease with a complex pathogene...
GSE58966: GATA2 shRNA Expression in Castration Resistant Prostate Cancer Cell Lines
The transcription factor GATA2 regulates chemotherapy resistance in prostate cancer. We report a nov...
GSE63721: A common cell state in Triple Negative Breast Cancers represents a druggable vulnerability
A basal (MDAMB468) and luminal (ZR75-1) cell line were treated with DMSO or PKC412 for 6h SOURCE: Se...
GSE157299: Positional influence on cellular transcriptional identity revealed through spatially segmented single-cell transcriptomics
Single-cell RNA-sequencing (scRNA-seq) is a powerful technique for describing cell states. Unfortuna...
GSE59810: Discovery of biomarkers predictive of GSI response in triple negative breast cancer and adenoid cystic carcinoma
Next generation sequencing was used to identify Notch mutations in a large collection of diverse sol...
GSE57278: A global regulatory mechanism for activating an exon network required for neurogenesis
The vertebrate and neural-specific SR-related protein nSR100/SRRM4 regulates an extensive program of...
GSE134375: Multi-omics profiling reveals key signaling pathways in ovarian cancer controlled by STAT3
Inhibiting STAT3 signaling reduces tumor progression, metastases and chemoresistance, however the pr...
GSE58108: Rlf, a widely-spaced zinc finger protein, is involved in maintaining epigenetic marks at CpG island shores and enhancer elements across the genome
We recently identified a novel protein, Rearranged L-myc fusion (Rlf), that is required for DNA hypo...
GSE58111: Genome-wide analysis of transcriptome and translatome following eIF4A1 knockdown in MCF7 cells [RNA-Seq]
To identify which genes were regulated by mRNA helicase activity, the effect of eIF4A1 knockdown on ...
GSE58972: RNAseq data from in vitro-stimulated (6 hours) murine relafl/flCD19-Cre and CD19-Cre splenic B cells purified by magnetic cell separation (RELA)
RNAseq analysis of CD40 + IgM in vitro-stimulated (6 hours) murine relafl/flCD19-Cre (furtheron desi...
GSE109844 (human): The expression profiles of CD4low(HLA-G+) T cells
The aim of the dataset was to demonstrate that CD4low T cells were murine homolog of CD4lowHLA-G+ T ...
GSE60827: RNA-Seq analysis comparing p53-null versus Np63/;p53-null or Np73/;p53-null thymic lymphoma tumors
We performed an RNA-Seq analysis comparing thymic lymphoma tissues from the p53-null(n=2) and Np63/;...
GSE57959: Comparison of expression data of 2 & 4- months old CRYAAN101D versus CRYAAWT lenses
To understand the global view of dysregulated genes and pathwyas in CRYAAN101D lenses, RNA sequenci...
GSE58423: Musashi proteins are post-transcriptional regulators of the epithelial-luminal cell state
mRNA-seq and ribosome profiling of neural stem cells overexpressing or knocked out for Musashi RNA-b...
GSE56575: Rapid proliferation and differentiation impairs the development of memory CD8+ T cells in early life
Neonates often generate incomplete immunity against intracellular pathogens, although the mechanism ...
GSE58372: Gene profile of aged Wt, miR-155-/-, miR-146a-/- and DKO CD4+ T cells
Differential gene expression profile of CD4+ T cells from 10 months old Wt, miR-155-/-, miR-146a-/- ...
GSE107011: RNA-Seq profiling of 29 immune cell types and peripheral blood mononuclear cells
We performed RNA-Seq transcriptome profiling on 29 immune cell types consituting peripheral blood mo...
GSE57973: Age dependent gene expression changes in human islets
We report the transcriptomic profiling of islet cell subtypes obtained from young and old human dono...
GSE59442: Polycomb Repressor Complex2 and REST-associated histone deacetylases are independent pathways toward a mature neuronal phenotype
These experiments were designed to test the hypothesis that REST and Polycomb Repressor Complex 2 fu...
GSE60178: Human embryonic stem cell, rhesus embryonic stem cell and mouse transchromosomic (hsa11) embryonic stem cell (with and without ectopic ZNF91 expression) RNA-seq
We compared the expression in embryonic stem cells of KRAB ZNF proteins and retrotransposon elements...
GSE58998: The chromatin-modifying enzyme Ezh2 is a CD28-dependent molecule critical for the maintenance of Treg identity
Regulatory T cells (Tregs) are essential for maintaining proper immune homeostasis. Extracellular si...
GSE58801: Genomic deletion by CRISPR/Cas9 reveals a critical role for Evx1as/Evx1 locus in regulating embryonic stem cell differentiation
We report that head to head long noncoding RNAs contribute to transcription and developmental proces...
GSE60603 (human): An alternative pluripotent state confers interspecies chimaeric competency [RNA-Seq]
Here we show that by simple modulation of extrinsic signaling pathways, a new class of pluripotent s...
GSE59009: RNA-seq profiles after SP-2509 Treatment of LNCaP, C42B, and PC3 cells
LSD1 (also known as KDM1A) is a histone demethylase and a key regulator of gene expression in embryo...
GSE125428: RNA-seq experiment on five mouse brain regions--hypothalamus, hippocampus, neocortex, cerebellum, and the amygdala --comparing expression in virgin females to primiparous females three weeks after pup weaning.
RNA-seq experiment on five mouse brain regions-- --comparing expression in virgin females to primipa...
GSE131470: Expression analysis of ethanol treatment on SK-N-BE(2)
To evaluate the impact of ethanol treatment on neuronal cells, we examined the expression of SK-N-BE...
GSE55727 (mouse): Integrative Genomic Analysis Reveals Widespread Enhancer Regulation by p53 in Response to DNA Damage
The tumor suppressor p53 has been studied extensively as a direct transcriptional activator of prote...
GSE60328: Transcriptional profiling of CHB8 human embryonic stem cells with insulin receptor knockdown
While insulin receptor (IR) signaling is involved in the maintenance and proliferation of human embr...
GSE60941: Molecular mechanism behind the hematopoiesis-enhancing effect of SRT3025
We used wild-type 129 mice to understand the mechanism of action behind SRT3025s hematopoiesis-enhan...
GSE62741: Thymic T-cell progenitor development is supported by membrane bound Kit ligand provided by a combined vascular endothelial and epithelial niche.
Gene expression analysis of purified KitL-tomato+ and KitL-tomato- thymic vascular endothelial ce...
GSE70389 (human): Gene expression profiling of human and murine in vitro muscle differentiation
Total RNA sequencing of human and murine myoblasts and myotubes was extracted, depleted of ribosomal...
GSE103864: Identification of global XBP1s target gene expression in human prostate cancer cells
To gain insight into the global XBP1s target gene profile in prostate cancer cells, we performed RNA...
GSE104056: mRNA expression profiles in primary microglia cells treated with R848, IFN-, and R848+ IFN-
Using RNA-seq, we have reported signaling crosstalk between IFN- and R848 at the level of transcript...
GSE58318: Next Generation Sequencing and Quantitative Analysis of Wild Type and p110gamma-/- macrophages
Purpose: The goals of this study were to identify quantitative gene expression differences between m...
GSE62432: Comparative transcriptomic analysis of self-organized, in vitro generated optic tissues
Embryonic stem (ES) cells have a remarkable capacity to self-organize complex, multi-layered optic c...
GSE59233: Impaired DNA damage metabolism promotes autoimmunity in TREX1 deficiency
Constitutive low level DNA damage is linked to innate immune activation. Hierarchical clustering of ...
GSE60450: Transcriptome analysis of luminal and basal cell subpopulations in the lactating versus pregnant mammary gland
To identify genes specifically expressed in lactating mammary glands, the gene expression profiles o...
GSE58557: Conversion of Gastric Epithelia to Endoderm Progenitors by Small Molecules [gene expression]
Forced expression of transcription factors for lineage reprogramming brings hope to cell-based thera...
GSE59855: Gene expression profiling associated with knockdown of LKB1 in human intrahepatic cholangiocarcinoma
The experiment was designed to display differential gene expression profiling in three human intrahe...
GSE60226: CTCF functions as a chromatin insulator in the HoxA cluster during neurogenesis [RNA-Seq]
In this experiment, we sought to analyze how the transcriptome of WT, 5|6, and 5|6:7|9 cells vary du...
GSE59547: RNA-Seq of regenerating DRG neurons
To identify isoform differential expression underlying peripheral nerve regeneration we performed RN...
GSE74961: Transcription Factor RFX2 Is a Key Regulator of Mouse Spermiogenesis
To identify RFX2-dependent genes during spermatogenesis, We chose 24-day-old wild-type and mutant te...