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GSE81145
Homo sapiens
2 Downloadable Samples
Affymetrix Human Gene 2.0 ST Array (hugene20st)
Description
To identify the role of the SH3PXD2A-HTRA1 fusion on gene expression in Schwann cells
Publication Title
The genomic landscape of schwannoma.
Sample Metadata Fields
Specimen part
View Samples- Homo sapiens
- 35 Downloadable Samples
- Affymetrix Human Gene 1.1 ST Array (hugene11st)
Description
Purpose: Myxopapillary ependymoma (MPE) is a distinct histological variant of ependymoma arising commonly in the spinal cord. Despite an overall favorable prognosis, distant metastases, subarachnoid dissemination, and late recurrences have been reported. Currently the only effective treatment for MPE is gross-total resection. We characterized the genomic and transcriptional landscape of spinal ependymomas in an effort to delineate the genetic basis of this disease and identify new leads for therapy.
Publication Title
Spinal Myxopapillary Ependymomas Demonstrate a Warburg Phenotype.
Sample Metadata Fields
Sex, Specimen part, Disease stage
View Samples- Homo sapiens
- 10 Downloadable Samples
Illumina Genome Analyzer II
Description
Specific mutations in the XPD subunit of transcription factor IIH result in combined xeroderma pigmentosum (XP)/Cockayne syndrome (CS), a severe DNA repair disorder characterized at the cellular level by a transcriptional arrest following UV irradiation. This transcriptional arrest has always been thought to be the result of faulty transcription-coupled repair. In the present study, we investigate the transcriptional dysregulation that follows UV irradiation in XP-D/CS compared with “pure” XP-D cells or WT cells. We also study how this process is affected by the inhibition of the histone deacetylase Sirt1.
Publication Title
Sirt1 suppresses RNA synthesis after UV irradiation in combined xeroderma pigmentosum group D/Cockayne syndrome (XP-D/CS) cells.
Sample Metadata Fields
No sample metadata fields
View Samples- Mus musculus
- 179 Downloadable Samples
- NextSeq 500
Description
Lung development and function arises from the interactions between diverse cell types and lineages. Using single cell RNA-seq we characterize the cellular composition of the lung during development and identify vast dynamics in both the composition of cells and their molecular characteristics. Analyzing 818 ligand-receptor interaction pairs within and between cell lineages, we identify broadly interacting cells, including AT2, ILC and basophils. Using IL33-receptor knockout mice and in vitro experiments, we show that basophils establish a lung-specific function imprinted by IL-33 and GM-CSF, characterized by unique signaling of cytokines and growth factors important for stromal, epithelial and myeloid cell fates. Antibody depletion strategies, diphtheria toxin–mediated selective depletion of basophils, and co-culture studies, show that lung resident basophils are important regulators of alveolar macrophage development and function. Together, our study demonstrates how whole tissue cell interaction analysis on the single cell level can broaden our understanding of cellular networks in health and disease. Overall design: Transcriptional profiling of single cells from the different timepoints of lung development, generated from deep sequencing of tens of thousands of cells, sequenced in several batches on illumina Nextseq500 metadata.txt: Meta data file associating each single cell with its amplification batch and index sorting readouts
Publication Title
Lung Single-Cell Signaling Interaction Map Reveals Basophil Role in Macrophage Imprinting.
Sample Metadata Fields
Specimen part, Cell line, Treatment, Subject
View Samples- Homo sapiens
- 22 Downloadable Samples
- NextSeq 500
Description
Alterations in gene expression following fatty acid synthase inhibtion were evaluated in androgen sensitive LNCaP cells and castration resistant 22Rv1 and LNCaP-95 cells. Cell were exposed to 2 concentrations (0.1 and 0.5 uM) of FASN inhibitor IPI-9119 or DMSO for 6 days. Overall design: Differential gene expression anlaysis in 3 prostate cancer cell lines treated with FASN inhibitor IPI-9119
Publication Title
Inhibition of de novo lipogenesis targets androgen receptor signaling in castration-resistant prostate cancer.
Sample Metadata Fields
Specimen part, Cell line, Subject
View Samples- Homo sapiens
- 135 Downloadable Samples
- NextSeq 500
Description
Multiple myeloma (MM), a plasma cell (PC) malignancy, is the second most common blood cancer. Despite extensive research, disease heterogeneity within and between patients is poorly characterized, hampering efforts for early diagnosis and improved treatments. Here, we apply single cell RNA-seq to study the heterogeneity of 40 individuals along the MM progression spectrum. We define malignant PC at single cell resolution, demonstrating high inter-patient variability that can be explained by expression of known MM drivers and additional putative factors. Within newly diagnosed patients, we identify extensive sub-clonal structures for 10/29 patients. In asymptomatic patients with early disease and in minimal residual disease post-treatment, we detect tumor PC for a subset of the patients, with the same drivers of active myeloma. Single cell analysis of rare circulating tumor cells (CTC) allows detection of malignant PC, which reflect the BM disease. Our work establishes scRNA-seq for dissecting blood malignancies and devising detailed molecular characterization of tumor cells in symptomatic and asymptomatic patients. Overall design: The study includes 29 newly diagnosed patients with plasma cell neoplasms and 11 control donors, for which bone marrow plasma cells were single cell sorted by FACS, and their mRNA sequenced. For 11 patients, targeted genomic DNA panel analysis for myeloma was performed.
Publication Title
Single cell dissection of plasma cell heterogeneity in symptomatic and asymptomatic myeloma.
Sample Metadata Fields
Specimen part, Treatment, Subject
View Samples