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GSE11539
Mus musculus
4 Downloadable Samples
Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
We generated gene expression profiles of 5 time points in murine lung development (E11.5, E13.5, E14.5, E16.5 and P5). The goal of this study was to establish a reference data set for exploration of large-scale similarities between transcriptomes in development and cancer.
Publication Title
Analysis of gene expression in a developmental context emphasizes distinct biological leitmotifs in human cancers.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 8 Downloadable Samples
Illumina HiSeq 2500
Description
In the developing brain, heightened plasticity during the critical period enables the proper formation of neural circuits. Here we identify the “navigator” neurons, a group of perinatally born olfactory sensory neurons, as playing an essential role in establishing the olfactory map during the critical period. The navigator axons project circuitously in the olfactory bulb and traverse multiple glomeruli before terminating in perspective glomeruli. These neurons undergo a phase of exuberant axon growth and exhibit a shortened lifespan. Single cell transcriptome analyses reveal distinct molecular signatures for the navigators. Extending their lifespan prolongs the period of exuberant growth and perturbs axon convergence. Conversely, genetic ablation experiment indicates that, despite postnatal neurogenesis, only the navigators are endowed with the ability to establish a convergent map. The presence and the proper removal of the navigator neurons are both required to establish tight axon convergence into the glomeruli. Overall design: 10X scRNA-seq was preformed on 4 samples of 4 ages of the olfactory epethelium of CD-1 mice. These ages were postanatal days 0, 3, 7, 21.
Publication Title
A Population of Navigator Neurons Is Essential for Olfactory Map Formation during the Critical Period.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 127 Downloadable Samples
- Illumina HiSeq 2000
Description
We investigated the expression profiles in the CD4+, CD8, and CD14+ peripheral blood cells (PBLs) of the stage IV melanoma patients and the healthy donors. Overall design: Examination of long noncoding RNA in the CD4+, CD8, and CD14+ peripheral blood cells (PBLs) of the stage IV melanoma patients and the healthy donors.
Publication Title
Integrative Genome-Wide Analysis of Long Noncoding RNAs in Diverse Immune Cell Types of Melanoma Patients.
Sample Metadata Fields
Specimen part, Subject
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
- 12 Downloadable Samples
- Illumina HiSeq 2500
Description
This experiment analyzes the set of RNAs copurifying with the protein TNIP2 (amino acids 196-346) Overall design: HEK293 cells were transfected with constructs expressing either Halo tag (controls) or Halo-TNIP2 196-346. Total RNA was purified from an aliquot of the whole cell extract (Input samples). Halo-tagged proteins were purified from the remainder of the whole cell extract, and RNA subsequently purified from the Halo purified samples (Pulldown samples).
Publication Title
TNIP2 is a Hub Protein in the NF-κB Network with Both Protein and RNA Mediated Interactions.
Sample Metadata Fields
Cell line, Subject
View Samples- Mus musculus
- 6 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Mice that are mutant for both Fgfr1 and Fgfr2 specifically in the developing retina develop coloboma. To analyze the transcripts that are affected by defective FGF signaling, we micro-dissected the optic fissure region from the control and FGFR condtional mutant mice and did microarray analysis.
Publication Title
Defective FGF signaling causes coloboma formation and disrupts retinal neurogenesis.
Sample Metadata Fields
Specimen part
View Samples- Saccharomyces cerevisiae
- 18 Downloadable Samples
- Illumina HiSeq 2500
Description
The Saccharomyces cerevisiae R2TP protein complex consists of Rvb1, Rvb2, Pih1 and Tah1. The R2TP complex has been implicated in various cellular processes such as assembly of snoRNP complex, RNA polymerase II complex, apoptosis and PIKK signaling. The involvement of R2TP in assembling various complexes seems to be in part due to Pih1 and Tah1, which serve as adapter/recruiter proteins. Here, we have performed high resolution RNA-seq. analyses to identify differential expression levels between wild type and PIH1 and TAH1 deletion strains of Saccharomyces cerevisiae that can help in unraveling other functions of Pih1 and Tah1. Both wild type and deletion strains contained TAP (tandem affinity purification) tag at the C-terminal end of either RVB1 or RVB2. Overall design: 3 biological replicates were performed for each strains
Publication Title
Proteomic and Genomic Analyses of the Rvb1 and Rvb2 Interaction Network upon Deletion of R2TP Complex Components.
Sample Metadata Fields
Cell line, Subject
View Samples- Saccharomyces cerevisiae
- 35 Downloadable Samples
- Affymetrix Yeast Genome 2.0 Array (yeast2)
Description
The cohesin protein complex is well known for playing a role in chromosome segregation. However, it has additional less understood roles in transcription, DNA repair, and chromosome condensation. Mutants in two yeast orthologues (Eco1 and Scc2) of human cohesinopathy disease alleles were examined by transcriptional profiling in response to perturbation of the transcriptional program by amino acid starvation.
Publication Title
Cohesin proteins promote ribosomal RNA production and protein translation in yeast and human cells.
Sample Metadata Fields
Time
View Samples- Homo sapiens
- 12 Downloadable Samples
- Illumina HiSeq 3000
Description
Keratinocytes isolated from one healthy donor were stimulated in triplicate for 24h with IL-36a, IL-36ß or IL-36? Overall design: Gene expression profile of IL-36 stimulated keratinocytes
Publication Title
An analysis of IL-36 signature genes and individuals with <i>IL1RL2</i> knockout mutations validates IL-36 as a psoriasis therapeutic target.
Sample Metadata Fields
Specimen part, Subject
View Samples- Mus musculus
- 8 Downloadable Samples
- Illumina HiSeq 2500
Description
Macrophages polarize to divergent functional phenotypes depending on their microenvironment in a highly coordinated process of metabolic and transcriptional rewiring that is still poorly understood. We developed an Integrated Metabolomics and Gene Expression (IMAGE) profiling and analysis pipeline and applied it to extensively characterize global metabolic programs of macrophage polarization. IMAGE analysis identified 7 major (novel and known) regulatory modules responsible for metabolic rewiring during polarization, which we validated through extensive carbon and nitrogen labeling experiments. M1-specific modules included: inflammatory variant of the aspartate-arginosuccinate shunt; TCA cycle break at Idh expression accompanied by citrate accumulation and production of itaconate and fatty acid synthesis. In M2 macrophages we discovered significant role of glutamine in polarization, providing nitrogen for UDP-GlcNAc synthesis. Consistently, glutamine deprivation results in significant M2-specific defect in polarization. Our data provide, for the first time, a global view of the integrated transcriptional and metabolic changes that result in M1 and M2 polarization. Overall design: Bone-marrow derived macrophages were generated from C57BL/6 mice were plated at ~100k cells per well in 96-well plate and stimulated with either Il4 or combination of LPS&IFNg or left unstimulated for 24 h mRNA was derived from lysates using Invitrogen oligo-dT beads
Publication Title
Cell-intrinsic lysosomal lipolysis is essential for alternative activation of macrophages.
Sample Metadata Fields
No sample metadata fields
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