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SRP147921
Mus musculus
127 Downloadable Samples
Illumina HiSeq 2500, Illumina HiSeq 4000, MinION
Description
The goal of this study was to isolate individual cochlear hair cells and supporting cells from wild type animals in order to characterize the transcriptome of functionally mature auditory hair cells in the mammalian cochlea. Overall design: Single-cell RNA sequencing is a powerful tool by which to characterize the transcriptional profile of low-abundance cell types, however its application to the inner ear has been hampered by the bony labyrinth, tissue sparsity and difficulties in dissociating the ultra-rare cells of the membranous cochlea. Herein, we present a method to isolate individual inner hair cells (IHCs), outer hair cells (OHCs) and Deiters' cells (DCs) from the murine cochlea at any post-natal time point. We isolated of 132 single cells from OHC, IHC, and DC cell types at postnatal day 15 (p15) and performed RNA-Sequencing of these cells using smartseq2 and Illumina HiSeq. An additional 12 single OHCs from the same timepoint were isolated and sequenced using smartseq2 and the Nanopore MinION 1D reads. We leverage single-cell RNA sequencing to analyze these three cell types and generate a multidimensional overview of their transcriptomes. The data provide new insights into OHC motility and the architecture of gene products implicated in hereditary hearing loss. This refined view of transcription in the organ of Corti will enhance to our understanding of the biology of hearing and deafness.
Publication Title
Insights into the Biology of Hearing and Deafness Revealed by Single-Cell RNA Sequencing.
Sample Metadata Fields
Specimen part, Subject
View Samples- Homo sapiens
- 7 Downloadable Samples
Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
We assessed the apoptotic and antiproliferative effects of resveratrol, pycnogenol and its metabolites on HT1080 human fibrosarcoma cells in vitro. Viability, apoptosis and necrosis were quantified by FACS analysis (Propidiumiodide/AnnexinV staining). Gene expression was analysed by RNA-Microarray. Cell proliferation was analysed by BrdU ELISA assay.
Publication Title
Resveratrol induces apoptosis and alters gene expression in human fibrosarcoma cells.
Sample Metadata Fields
Cell line, Treatment
View Samples- Homo sapiens
- 27 Downloadable Samples
- Affymetrix Human Genome U133 Plus 2.0 Array (hgu133plus2)
Description
The CD19 positive antibody secreting cells (ASC) in both bone marrow (BM) have the capacity to provide immune memory in addition to cells traditionally considered long-lived, the CD19-negative BM ASC. We performed flow cytometry (FCM) immunophenotyping, fluorescence-activated cell sorting (FACS) for cell subset isolation, ELISpot assays detecting the isotype of antibody secretion as well as antibodies against vaccine derived antigens, and comparative gene expression analyses of CD19- ASC, CD19+ ASC, CD20- B cells, and CD20+ B cells from BM. The findings may aid in the understanding of the differential cell subsets created through vaccination and lead to improved vaccine strategies and production. FACS sorted tissue B cells and antibody secreting cell subset gene expression.
Publication Title
CD19-positive antibody-secreting cells provide immune memory.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
Investigation whether hypoxic stabilization of HIF-1alpha quantitatively or qualitatively modifies the gene expression pattern induced by poly I:C, a TLR ligand that does not induce normoxic HIF-1alpha stabilization on its own (non-HIF-1alpha-stabilizing TLR ligand).
Publication Title
Toll-like receptor activation and hypoxia use distinct signaling pathways to stabilize hypoxia-inducible factor 1α (HIF1A) and result in differential HIF1A-dependent gene expression.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 48 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The transcription factor STAT1 is essential for interferon- (IFN) mediated protective immunity in humans and mice. Two splice isoforms of STAT1, STAT1 and STAT1, differ with regard to a C-terminal transactivation domain, which is absent in STAT1. Dimers of STAT1 are therefore considered transcriptionally inactive and potential competitive inhibitors of STAT1. Contrasting this view, generation and analysis of mice deficient for either STAT1 or STAT1 demonstrated transcriptional activity of the STAT1 isoform and its enhancement of innate immunity. Gene expression profiling in primary cells revealed overlapping, but also non-redundant and gene-specific activities of STAT1 and STAT1 in response to IFN. Consistently, both isoforms mediated protective, IFN-dependent immunity against the bacterium Listeria monocytogenes, although with remarkably different efficiency. In contrast, STAT1 and STAT1 were largely redundant for transcriptional responses to IFN/ and for IFN/-dependent antiviral activity. Collectively, our data shed new light on how STAT1 isoforms contribute to antimicrobial immunity.
Publication Title
STAT1β is not dominant negative and is capable of contributing to gamma interferon-dependent innate immunity.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 6 Downloadable Samples
- Illumina HumanHT-12 V4.0 expression beadchip
Description
The prognosis of advanced stage neuroblastoma patients remains poor and, despite intensive therapy, the 5-year survival rate remains less than 50%. We previously identified histone deacetylase (HDAC) 8 as an indicator of poor clinical outcome and a selective drug target for differentiation therapy in vitro and in vivo. Here we performed kinome-wide RNAi screening to identify genes that are synthetically lethal with HDAC8 inhibitors. These experiments identified the neuroblastoma predisposition gene ALK as a candidate gene. Accordingly, the combination of the ALK/MET inhibitor crizotinib and selective HDAC8 inhibitors (3-6M PCI-34051 or 10M 20a) efficiently killed neuroblastoma cell lines carrying wildtype ALK (SK-N-BE(2)-C, IMR5/75), amplified ALK (NB-1), and those carrying the activating ALK F1174L mutation (Kelly), and, in cells carrying the activating R1275Q mutation (LAN-5), combination treatment decreased viable cell count. The effective dose of crizotinib in neuroblastoma cell lines ranged from 0.05M (ALK-amplified) to 0.8M (wildtype ALK). The combinatorial inhibition of ALK and HDAC8 also decreased tumor growth in an in vivo zebrafish xenograft model. Bioinformatic analyses revealed that the mRNA expression level of HDAC8 was significantly correlated with that of ALK in two independent patient cohorts, the Academic Medical Center cohort (n=88) and the German Neuroblastoma Trial cohort (n=649), and co-expression of both target genes identified patients with very poor outcome. Mechanistically, HDAC8 and ALK converge at the level of receptor tyrosine kinase (RTK) signaling and their downstream survival pathways, such as ERK signaling. Combination treatment of HDAC8 inhibitor with crizotinib efficiently blocked the activation of growth receptor survival signaling and shifted the cell cycle arrest and differentiation phenotype toward effective cell death of neuroblastoma cell lines, including sensitization of resistant models, but not of normal cells. These findings reveal combined targeting of ALK and HDAC8 as a novel strategy for the treatment of neuroblastoma.
Publication Title
A kinome-wide RNAi screen identifies ALK as a target to sensitize neuroblastoma cells for HDAC8-inhibitor treatment.
Sample Metadata Fields
Specimen part
View Samples- Mus musculus
- 30 Downloadable Samples
- Affymetrix Mouse Genome 430 2.0 Array (mouse4302)
Description
Autoantibodies that arise in autoimmunity can be present years to decades prior to the onset of disease manifestations. This suggests that the initial autoimmune trigger involves a peripheral lymphoid component, which then drives disease pathology in local tissues later in life. To explore the impact of early peripheral immune dysregulation on the progression of Sjgrens Syndrome, we blocked the CD40-CD40L pathway in young female NOD.H-2h4 mice at 4 weeks of age with a single injection of anti-CD40L antibody, and collected total salivary gland at the age of week 8, 16 and 24. RNA was extracted and submitted to transcriptome profiling using Affymetrix microarray.
Publication Title
Autoimmune manifestations in aged mice arise from early-life immune dysregulation.
Sample Metadata Fields
Treatment
View Samples- Homo sapiens
- 48 Downloadable Samples
- Illumina HiSeq 2000
Description
CD11c+ B cells (IgD+ and IgD-) are pathogenic B cells expanded in autoimmune disease. The purpose of this study is to identify the pathways unique to IgD+ CD11c B cells and IgD- CD11c B cells. Overall design: B cell subsets were isolated from peripheral blood and RNA sequencing was performed with Hiseq 2000 platform
Publication Title
IL-21 drives expansion and plasma cell differentiation of autoreactive CD11c<sup>hi</sup>T-bet<sup>+</sup> B cells in SLE.
Sample Metadata Fields
Specimen part, Disease, Subject
View Samples- Homo sapiens
- 6 Downloadable Samples
- Affymetrix Human Gene 1.0 ST Array (hugene10st)
Description
The classical sacrococcygeal chordoma tumor presents with a typical morphology of lobulated myxoid tumor tissue with cords, strands and nests of tumor cells consisting of small non-vacuolated cells, intermediate cells with a wide range of vacuolization and large heavily vacuolated (physaliferous) cells. Because of its rare incidence, lack of suited model systems and technical limitations analysis was only performed on bulk tumor mass neglecting its heterogeneous composition. We aimed at elucidating the differences between small non-vacuolated and large physaliferous cells on the genomic and transcriptomic level. Secondly, we intended to clarify whether the observed cell types are derived from genetically distinct clones or rather represent different phenotypes. Using the chordoma cell line MUG-Chor1 we monitored morphological changes via time lapse experiments. We isolated pure fractions of each phenotype by means of laser microdissection or micromanipulation allowing phenotype-specific analysis. Pools of 100 cells each were genetically profiled after whole genome amplification by array comparative genomic hybridization. For expression analysis 20 cells each were subjected to whole transcriptom amplification, forwarded to RNA microarray analysis and qRT-PCR. Time lapse analysis unveiled small non-vacuolated cells to develop into large physaliferous cells via intermediate cells containing an increasing amount of vacuoles. Furthermore, we showed small and large physaliferous cells to proliferate at the same rate but intermediate cells to be the most proliferating cell phenotype. Small non-vacuolated and large physaliferous cells showed identical copy number variations. Despite their obvious morphological disparities we detected only modest changes in over all gene expression. However, verification of candidate genes yielded significant up-regulation of ALG11 (700-fold), PPP2CB (18.6-fold), and UCHL3 (18.7-fold) in large physaliferous cells.
Publication Title
Resolving tumor heterogeneity: genes involved in chordoma cell development identified by low-template analysis of morphologically distinct cells.
Sample Metadata Fields
Cell line
View Samples- Mus musculus
- 4 Downloadable Samples
- Affymetrix Mouse Gene 1.0 ST Array (mogene10st)
Description
The relevance of DNA-dependent poly-ADP ribose production for neuronal differentiation of adult stem- and progenitor cells from the SVZ was studied. To identify genes whose up- or downregulation during neuronal differentiation requires the activity of poly-ADP-Ribosylase (PARP) 1 or 2, SVZ-derived adult neurosphere cultures were differentiated in the presence or absence of Olaparib.
Publication Title
MEIS homeodomain proteins facilitate PARP1/ARTD1-mediated eviction of histone H1.
Sample Metadata Fields
Treatment
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