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GSE90864
Mus musculus
34 Downloadable Samples
Affymetrix Mouse Genome 430A 2.0 Array (mouse430a2)
Description
The goal of this study was to identify the transcriptional mechanisms involved in the activation of the immune system by QS-21, a triterpene glycoside purified from the bark of Quillaja saponaria which has adjuvant activity in vivo. Saponins represent a promising class of vaccine adjuvant. Together with the TLR4-ligand MPL, QS-21 is part of the Adjuvant System AS01, a key component of the Malaria and Zoster candidate vaccines that display demonstrated clinical efficacy. However, the mechanism of action of QS-21 in this liposomal formulation is poorly understood. Upon intra-muscular immunisation, we observed that QS-21 rapidly accumulated in CD169+ resident macrophages of the draining lymph node where it elicited a local innate immune response. Depletion of these cells abrogated QS-21-mediated innate cell recruitment to the lymph node, dendritic cell (DC) phenotypic maturation as well as the adjuvant effect on T cell and antibody responses to co-administered antigens. DCs rather than lymph node-resident macrophages were directly involved in T cell priming by QS-21 as revealed by the decrease in antigen-specific T cell response in Batf3/ mice. Further analysis showed that the adjuvant effect of QS-21 depended on the integration of Caspase-1 and MyD88 pathways, at least in part through the local release of HMGB1. Taken together, this work unravels the key role of lymph node sentinel macrophage in controlling the adjuvant effect of a molecule proven to improve vaccine response in humans
Publication Title
Central Role of CD169<sup>+</sup> Lymph Node Resident Macrophages in the Adjuvanticity of the QS-21 Component of AS01.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 24 Downloadable Samples
Illumina HiSeq 2500
Description
Bulk RNA sequencing data from neural progenitor cells under conditions of low or high growth factor and Notch pathway activation Overall design: Cells were treated with high (20 ng/ml EGF and FGF) or low (0.5 ng/ml EGF) recombinant growth factors, with or without Notch pathway inhibitor (DAPT, 10 uM) for 12h.
Publication Title
<i>Cis-</i>activation in the Notch signaling pathway.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 12 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Noval and traditional signaling pathways involved in cervical ripening that were regulated by MPA were identified.
Publication Title
Preventing cervical ripening: the primary mechanism by which progestational agents prevent preterm birth?
Sample Metadata Fields
No sample metadata fields
View Samples- Saccharomyces cerevisiae
- 27 Downloadable Samples
- Illumina HiSeq 2500
Description
We performed RNAseq with Saccharomyces cerevisiae cells under both transient and steady-state conditions to study the regulation of genes by two pulsatile transcription factors, Msn2 and Mig1. The transient data allowed us to identify combinatorial targets while the steady-state data was used to study target expression dependence on the relative pulse timing between the two TFs. Overall design: For transition experiments, 18 samples (3 different strains x 3 dfferent conditions x 2 biological replicates) were analyzed. For steady-state experiments, one strain was analyzed at 9 different glucose concentrations and the other strain was analyzed at one glucose condition.
Publication Title
Combinatorial gene regulation by modulation of relative pulse timing.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 10 Downloadable Samples
- Illumina HiSeq 2500
Description
We develop a theoretical-computational framework for inferring cell state transition dynamics, and apply it to mouse embryonic stem cells states defined by expression levels of Esrrb, Tbx3, and Zscan4. RNA-seq was performed to characterize the larger transcriptional differences between states expressing combinations of these three specific genes, and proceed to explore their dynamic interconversion. Overall design: A double knock-in reporter for Esrrb and Tbx3 with distinct fluorescent proteins was constructed to enable purification of substates defined by their relative expression levels (Esrrb-/Tbx3-; Esrrb+/Tbx3-; Esrrb+/Tbx3+). A second line was constructed using a promoter-fragment reporter to isolate Zscan4+ from Zscan4- cells. Following FACS isolation, the subpopulations were sequenced on an Illumina HiSeq2500. Biological replicates were collected on different days.
Publication Title
Inferring Cell-State Transition Dynamics from Lineage Trees and Endpoint Single-Cell Measurements.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Illumina HiSeq 2500
Description
C2C12 cells expressing constitutively active hN1?ECD were activated by complete DAPT washout for 1h or 6h, or left in 10 uM DAPT Overall design: 2 Samples and 1 Control
Publication Title
Dynamic Ligand Discrimination in the Notch Signaling Pathway.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 22 Downloadable Samples
- Illumina HiSeq 2500
Description
These data consist of an expression survey of three receptor cell lines and the parental cell types was performed to determine expression of BMP related genes. Overall design: Sequence libraries for three cell types were constructed using NEBNext Ultra RNA-seq (NEB #E7530) and sequenced on Illumnia HiSeq2500.
Publication Title
Combinatorial Signal Perception in the BMP Pathway.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 119 Downloadable Samples
- Illumina HiSeq 2500, Illumina HiSeq 2000
Description
We report the application of single-cell and bulk RNA sequencing technology to examine the noncoding transcriptome of cells undergoing reprogramming to the pluripotent state. Overall design: Examination of noncoding RNAs in reprogrammming cells. We examined iPS cells grown in standard ES cell culture conditions, as well as iPS cells grown in "2i" conditions (small molecule inhibition of Mek and Gsk3). We also compared our iPS samples to male and female ES cells (mES, fES).
Publication Title
Single-cell transcriptome analysis reveals dynamic changes in lncRNA expression during reprogramming.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 90 Downloadable Samples
- Illumina HiSeq 2000
Description
During T cell development, multipotent progenitors relinquish competence for other fates and commit to the T cell lineage by turning on Bcl11b, which encodes a transcription factor. To clarify lineage commitment mechanisms, we followed developing T cells at the single-cell level using Bcl11b knock-in fluorescent reporter mice. Notch signaling and Notch activated transcription factors collaborate to activate Bcl11b expression irrespectively of Notch-dependent proliferation. These inputs work via three distinct, asynchronous mechanisms: an early locus ‘poising’ function dependent on TCF-1 and GATA-3, a stochastic-permissivity function dependent on Notch signaling, and a separate amplitude-control function dependent on Runx1, a factor already present in multipotent progenitors. Despite their necessity for Bcl11b activation, these inputs act in a stage specific manner, providing a multitiered mechanism for developmental gene regulation. Overall design: Two sets of samples were generated from DN T-cell sub-populations derived from culture of bone marrow progenitors from mice containing a knock-in Bcl11b-YFP reporter
Publication Title
Asynchronous combinatorial action of four regulatory factors activates Bcl11b for T cell commitment.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 46 Downloadable Samples
- Sentrix Human-6 Expression BeadChip
Description
Special AT-rich binding protein 1 (SATB1) is a global chromatin organizer and a transcription factor induced by interleukin-4 (IL-4) during the early T helper 2 (Th2) cell differentiation. In this study, we investigated the role of SATB1 in T helper cell differentiation by performing gene expression profiling of human differentiating Th cells in which expression of SATB1 was downregulated by RNA interference (RNAi). Our results indicate that SATB1 is involved in the regulation of more than three hundred genes in primary human CD4+ T cells, including several IL-12 and/or IL-4 regulated factors, suggesting a role in the development or function of Th subtypes.
Publication Title
SATB1 dictates expression of multiple genes including IL-5 involved in human T helper cell differentiation.
Sample Metadata Fields
No sample metadata fields
View Samples