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SRP055200
Mus musculus
9 Downloadable Samples
Illumina HiSeq 2500
Description
We examined global gene expression patterns of mouse embryonic stem cells overexpressing EGFP, Nanog wild-type, or Nanog L122A mutants in normal, "-LIF" or "+RA" culture conditions by RNA-seq experiments. In “+RA” culture conditions, the expression patterns of the RA-responsive genes were slightly different in WT transfectants and more different in L122A transfectants compared with EGFP transfectants. These results suggested that L122A transfectants showed partial resistant activity against RA-induced differentiation, which was not found in WT mNANOG transfectants. Overall design: Examination of 3 different transfectants from mouse embryonic stem cell, RF8 line, in 3 different culture conditions.
Publication Title
Structure-based discovery of NANOG variant with enhanced properties to promote self-renewal and reprogramming of pluripotent stem cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 38 Downloadable Samples
- Illumina HiSeq 2500
Description
Numerous microRNAs and their target mRNAs are co-expressed across diverse cell types. However, it is unknown whether they are regulated in a cellular context-independent or -dependent manner. Here, we explored transcriptome-wide targeting and gene regulation by miR-155, whose activation-induced expression plays important roles in innate and adaptive immunity. Through mapping of miR-155 targets using differential Argonaute iCLIP, mRNA quantification with RNA-Seq, and 3'UTR usage analysis using polyadenylation (polyA)-Seq in activated miR-155-sufficient and deficient macrophages, dendritic cells, T and B lymphocytes, we identified numerous targets differentially bound by miR-155. While alternative cleavage and polyadenylation (ApA) contributed to differential miR-155 binding to some transcripts, in a majority of cases identical 3'UTR isoforms were differentially regulated across cell types, suggesting ApA-independent and cellular context-dependent miR-155-mediated gene regulation reminiscent of sequence-specific transcription factors. Our study provides comprehensive maps of miR-155 regulatory RNA networks and offers a valuable resource for dissecting context-dependent and -independent miRNA-mediated gene regulation in key cell types of the adaptive and innate immune systems. Overall design: Primary dendritic cells, B cells, CD4 T cells, and macrophages from C57BL/6J wild type and miR-155 KO mice were cultured in RPMI medium with 10% FBS. Prior to harvesting primary dendritic cells, mice were subcutaneously injected with one million B16 melanoma cells expressing Flt3 ligand for about two weeks. After purification of splenic CD11c+ dendritic cells by CD11c microbeads (Miltenyi Biotec), dendritic cells were activated in a medium containing 100 ng/ml LPS (SIGMA) and 20 ng/ml GMSCF (Tonbo). Splenic primary B cells were purified by negative selection using Dynabeads Mouse CD43 (Invitrogen), and activated in a medium containing 25 ug/ml LPS and 6.5 ng/ml mIL4 (PeproTech). CD4 T cells from lymph node and spleen were purified with Dynabeads FlowComp Kit (Invitrogen). CD4+CD25-CD44- T cells were then activated with Dynabeads Mouse T-Activator CD3/CD28 (Invitrogen). Intraperitoneal macrophages, induced by thioglycollate injection, were harvested and activated with 100 ng/ml LPS.
Publication Title
The effect of cellular context on miR-155-mediated gene regulation in four major immune cell types.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Mus musculus
- 24 Downloadable Samples
- Illumina HiSeq 2500
Description
Numerous microRNAs and their target mRNAs are co-expressed across diverse cell types. However, it is unknown whether they are regulated in a cellular context-independent or -dependent manner. Here, we explored transcriptome-wide targeting and gene regulation by miR-155, whose activation-induced expression plays important roles in innate and adaptive immunity. Through mapping of miR-155 targets using differential Argonaute iCLIP, mRNA quantification with RNA-Seq, and 3'UTR usage analysis using polyadenylation (polyA)-Seq in activated miR-155-sufficient and deficient macrophages, dendritic cells, T and B lymphocytes, we identified numerous targets differentially bound by miR-155. While alternative cleavage and polyadenylation (ApA) contributed to differential miR-155 binding to some transcripts, in a majority of cases identical 3'UTR isoforms were differentially regulated across cell types, suggesting ApA-independent and cellular context-dependent miR-155-mediated gene regulation reminiscent of sequence-specific transcription factors. Our study provides comprehensive maps of miR-155 regulatory RNA networks and offers a valuable resource for dissecting context-dependent and -independent miRNA-mediated gene regulation in key cell types of the adaptive and innate immune systems. Overall design: Primary dendritic cells, B cells, CD4 T cells, and macrophages from C57BL/6J wild type and miR-155 KO mice were cultured in RPMI medium with 10% FBS. Prior to harvesting primary dendritic cells, mice were subcutaneously injected with one million B16 melanoma cells expressing Flt3 ligand for about two weeks. After purification of splenic CD11c+ dendritic cells by CD11c microbeads (Miltenyi Biotec), dendritic cells were activated in a medium containing 100 ng/ml LPS (SIGMA) and 20 ng/ml GMSCF (Tonbo). Splenic primary B cells were purified by negative selection using Dynabeads Mouse CD43 (Invitrogen), and activated in a medium containing 25 ug/ml LPS and 6.5 ng/ml mIL4 (PeproTech). CD4 T cells from lymph node and spleen were purified with Dynabeads FlowComp Kit (Invitrogen). CD4+CD25-CD44- T cells were then activated with Dynabeads Mouse T-Activator CD3/CD28 (Invitrogen). Intraperitoneal macrophages, induced by thioglycollate injection, were harvested and activated with 100 ng/ml LPS. Each condition has 3 sequencing replicates.
Publication Title
The effect of cellular context on miR-155-mediated gene regulation in four major immune cell types.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Mus musculus
- 88 Downloadable Samples
- Illumina HiSeq 2500
Description
Regulatory T (Treg) cells, expressing abundant amounts of the IL-2 receptor (IL-2R), are reliant on IL-2 produced by activated T cells. This feature implied a key role for a simple network based on IL-2 consumption by Treg cells in their suppressor function. However, congenital deficiency in IL-2R results in reduced expression of the Treg lineage specification factor Foxp3, confounding experimental efforts to understand the role of IL-2R expression and signaling in Treg suppressor function. Using genetic gain and loss of function approaches, we demonstrate that IL-2 capture is dispensable for control of CD4+ T cells, but is important for limiting CD8+ T cell activation, and that IL-2R dependent STAT5 transcription factor activation plays an essential role in Treg suppressor function separable from T cell receptor signaling. Overall design: Gene expression profiles in Treg cells with or without an expression of an active form of STAT5 were compared by RNA sequencing. Male 8-wk-old Foxp3Cre-ERT2Rosa26Stat5bCA (STAT5b-CA) and Foxp3Cre-ERT2 (control) mice, nine mice for each experimental group, received a single dose (4 mg) of tamoxifen by oral gavage 4 months before isolation. Splenic CD4+Foxp3(YFP/GFP)+GITRhiCD25hi Treg and CD4+Foxp3(YFP/GFP)-CD62LhiCD44lo T naive cells were double sorted using a BD FACSAria II cell sorter. The T cell subsets isolated from three individual mice in the same experimental group (genotype) was pooled into one biological replicate; three biological replicates were generated. A total of 12 samples, i.e., two genotypes, two cell cypes, and three replicates, was subjected to RNA-seq analysis. Samples were sequenced on the Illumina HiSeq 2500 to an average depth of 27.5 million 50-bp read pairs per sample.
Publication Title
Transcription factor Foxp1 regulates Foxp3 chromatin binding and coordinates regulatory T cell function.
Sample Metadata Fields
Sex, Specimen part, Subject
View Samples- Homo sapiens
- 30 Downloadable Samples
- Illumina HiSeq 2500
Description
Transcriptomic Analysis of Wild Type and FOXA2-/- ES-derived Pancreatic Progenitors Overall design: Examination of triplicates per genotypes for each differentiation stage
Publication Title
FOXA2 Is Required for Enhancer Priming during Pancreatic Differentiation.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 24 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Microarrays were used to analyze differential gene expression and to help determine the efficacy of Iressa (gefitinib), a tyrosine kinase inhibitor, on endometrial cancer cells.
Publication Title
EGFR isoforms and gene regulation in human endometrial cancer cells.
Sample Metadata Fields
Specimen part, Cell line
View Samples- Homo sapiens
- 4 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
Microarrays were used to determine the efficacy of bevacizumab (a monoclonal antibody against the vascular endothelial growth factor and its receptors.) on endometrial cancer cells.
Publication Title
Effects of bevacizumab in mouse model of endometrial cancer: Defining the molecular basis for resistance.
Sample Metadata Fields
Specimen part
View Samples- Saccharomyces cerevisiae
- 24 Downloadable Samples
- Affymetrix Yeast Genome S98 Array (ygs98)
Description
Deciphering gene regulatory mechanisms through the analysis of high-throughput expression data is a challenging computational problem. Previous computational studies have used large expression datasets in order to resolve fine patterns of coexpression, producing clusters or modules of potentially coregulated genes. These methods typically examine promoter sequence information, such as DNA motifs or transcription factor occupancy data, in a separate step after clustering. We needed an alternative and more integrative approach to study the oxygen regulatory network in Saccharomyces cerevisiae using a small dataset of perturbation experiments. Mechanisms of oxygen sensing and regulation underlie many physiological and pathological processes, and only a handful of oxygen regulators have been identified in previous studies. We used a new machine learning algorithm called MEDUSA to uncover detailed information about the oxygen regulatory network using genome-wide expression changes in response to perturbations in the levels of oxygen, heme, Hap1, and Co2+. MEDUSA integrates mRNA expression, promoter sequence, and ChIP-chip occupancy data to learn a model that accurately predicts the differential expression of target genes in held-out data. We used a novel margin-based score to extract significant condition-specific regulators and assemble a global map of the oxygen sensing and regulatory network. This network includes both known oxygen and heme regulators, such as Hap1, Mga2, Hap4, and Upc2, as well as many new candidate regulators. MEDUSA also identified many DNA motifs that are consistent with previous experimentally identified transcription factor binding sites. Because MEDUSA's regulatory program associates regulators to target genes through their promoter sequences, we directly tested the predicted regulators for OLE1, a gene specifically induced under hypoxia, by experimental analysis of the activity of its promoter. In each case, deletion of the candidate regulator resulted in the predicted effect on promoter activity, confirming that several novel regulators identified by MEDUSA are indeed involved in oxygen regulation. MEDUSA can reveal important information from a small dataset and generate testable hypotheses for further experimental analysis.
Publication Title
A predictive model of the oxygen and heme regulatory network in yeast.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 16 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
This SuperSeries is composed of the SubSeries listed below.
Publication Title
Ets transcription factor GABP controls T cell homeostasis and immunity.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 16 Downloadable Samples
- Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
Ets family transcription factor GA-binding protein (GABP) regulates gene expression in CD4 and CD8 T cells.
Publication Title
Ets transcription factor GABP controls T cell homeostasis and immunity.
Sample Metadata Fields
Specimen part
View Samples