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Database containing RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of cerebral cortex. Collection of RNA-Seq transcriptome and splicing data from glia, neurons, and vascular cells of mouse cerebral cortex. RNA-Seq of cell types isolated from mouse and human brain.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Born of the desire to systematize analyses from The Cancer Genome Atlas pilot and scale their execution to the dozens of remaining diseases to be studied, GDAC Firehose now sits atop terabytes of analysis-ready TCGA data and reliably executes thousands of pipelines per month.

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• RRID
• 1 year ago - by Anonymous

The Loma Linda University Cancer Center Biospecimen Laboratory provides specimens for researchers as they search for the causes of cancer, and look for new means of prevention and treatment. The specimens include tissues, blood products (blood cell, plasma and serum) and bone marrow cells. Researchers interested in gaining access to the Biospecimen Laboratory''s samples should email Dr. Saied Mirshahidi, requesting access. The number and types of samples we have available for research can be viewed, http://www.llu.edu/catissuesummary/. Use the Biospecimen Laboratory Tissue Request Form to request specimens for research studies.

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• SciCrunch
• 16 years ago - by Anonymous

Web based gene set analysis toolkit designed for functional genomic, proteomic, and large-scale genetic studies from which large number of gene lists (e.g. differentially expressed gene sets, co-expressed gene sets etc) are continuously generated. WebGestalt incorporates information from different public resources and provides a way for biologists to make sense out of gene lists. This version of WebGestalt supports eight organisms, including human, mouse, rat, worm, fly, yeast, dog, and zebrafish.

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• SciCrunch
• 17 years ago - by Anonymous

Core to advance understanding of mechanism of vascular dysfunction in chronic disease, identify how vascular dysfunction contributes to exercise intolerance, evaluate how exercise training improves vascular dysfunction and exercise intolerance using innovative clinical trial designs.

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• SciCrunch
• 1 year ago - submitted by Edyta Vieth

This database contains anonymized information describing the tumor, treatment and follow-up as well as tumor sample availability and molecular biology analyses for mesenchymal tumors except GIST and bone tumors. The query tool allows users to ask questions about the overall content of the database in order to evaluate the feasibility of specific collaborative studies. We hope this database will become an important tool for increasing our knowledge on these rare tumors and for developing joint research programs. The tool can be used as a local center database thanks to its rules for access to patient data and material. Conticabase currently contains the following data from 31 out of the 48 registered centers (Last modification on 28/03/2012): * 11518 Patients * 11562 Tumors * 13897 Samples (13636 Paraffin and 5773 Frozen) Use of conticabase data At anytime, a data manager can export data of patients from his (her) Centre or group according to his (her) level of rights. To obtain data from another Centre, a partner should ask the coordinator of the corresponding Centre for these data. To use data for a cooperative study, a member should write a short text describing the project and send it to partners of interest. Each partner may decide whether to participate or not and therefore, whether to send or not the corresponding data to the project leader. In the event that the data from the conticabase result in a publication, acknowledgement is required. Use of tumour material entered in the ConticaBank To obtain material from another Centre for a cooperative study, a partner should write a short text describing the project and send it to the partners of interest. Each partner may decide whether to participate or not and, therefore, whether to send or not the corresponding material to the project leader. In the event that the material used result in a publication, acknowledgement is required.

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• SciCrunch
• 16 years ago - by Anonymous

Strategy guide for HED Annotation. Framework for systematically describing laboratory and real world events.HED tags are comma separated path strings. Organized in forest of groups with roots Event, Item, Sensory presentation, Attribute, Action, Participant, Experiment context, and Paradigm. Used for preparing brain imaging data for automated analysis and meta analysis. Applied to brain imaging EEG, MEG, fNIRS, multimodal mobile brain or body imaging, ECG, EMG, GSR, or behavioral data. Part of Brain Imaging Data Structure standard for brain imaging.

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• RRID-Legacy
• 7 years ago - submitted by Anita Bandrowski

Core provides services in analyzing genetic variation, performing genome-wide association studies, conducting non-human genotyping. Offers flexible platforms from low to high throughput, tailored to research needs. Specializes in Illumina Genotyping Arrays and TaqMan Allelic Discrimination Assays, with fully automated processing using Tecan EVOs and BioMek liquid handlers and Genologics LIMS for reliable data tracking.Applications include: GWAS – Identify genetic variants linked to traits and diseases; PRS Analysis – Assess genetic risk for complex diseases; Pharmacogenomics – Study genetic factors in drug response; Population Genetics – Explore ancestry and genetic diversity; CNV Analysis – Detect large-scale genomic variations; Methylation Analysis.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

A virtual database currently indexing authoritative information on disease and treatment options from NINDS Disorder List and PubMed Health.

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• SciCrunch
• 14 years ago - by Anonymous

Software toolbox for quantitative MRI in neuroscience and clinical research. Open source and flexible tool for qMRI data handling and processing. Allows estimation of high quality multi parameter qMRI maps followed by spatial registration in common space for statistical analysis.

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• SciCrunch
• 7 years ago - by Anonymous

Facility provides diverse range of equipment, expertise and training in field of biochemistry, molecular, structural and cellular biology. Facility consists of several research laboratories and support areas.

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• RRID
• 1 year ago - by Anonymous

Database of research protocols in a variety of life science fields, it contains protocols contributed by worldwide researchers as well as links to web protocols hosted by worldwide research labs, biotech companies, personal web sites. The data is stored in a MySql relational database. Protocol Online also hosts discipline specific discussion forums (BioForum), and provides a free PubMed search and alerting service (PubAlert).

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• SciCrunch
• 16 years ago - by Anonymous

Core provides analytical and preparative flow cytometers, to facilitate range of experiments in biology of both normal and cancer cells. Experimental analyses, including:Complex, 19 fluorescence parameter immuno-phenotyping;DNA content, ploidy and cell cycle analysis; 17 fluorescence parameter cell sorting and single-cell flow cloning; High speed (10,000 � 30,000+ cells per second) and efficiency (95%+ purity) cell sorting;Assessment of apoptosis;Molecular cytogenetics;Cell function studies;Micro-biological applications;Multiplexed and micro-particle-based analysis;Mass cytometry analysis and imaging;Fluidigm Helios plasma mass cytometer. Cells are labeled with antibodies conjugated to heavy metal markers, vaporized in plasma and detected with time-of-flight mass spectrometry;Fluidigm Hyperion solid tissue imager provides simultaneous imaging of labeled solid tissue sections, for mass cytometry analysis. FCSR has bank of metal reagent kits (for custom antibody conjugation), available for purchase at favorable rates compared to those available commercially. The bank has 35 unique labeling metals, for users to create custom reagents and panels. Please contact FCSR for further information and pricing. Robotic automated cell transfer A.L.S. CellCelector automated cell transfer robot. For automated transfer of single cells and colonies from culture plates, without pre-treatment. Integral bio-safety cabinet for BSL-2 cultures.

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• SciCrunch
• 7 years ago - submitted by Edyta Vieth

Core Facility for flow cytometry at the Ludwig-Maximilian-University Hospital Munich. Provides access and services for flow cytometry and cell sorters.

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• RRID
• 1 year ago - by Anonymous

Tennessee Donor Services (TDS) is a nonprofit, independent organization authorized by the Federal Government to accept anatomical gifts for transplantation and research. Its mission is to support families in our communities who have sustained the loss of a loved one by providing an opportunity for organ, eye and tissue donation and by facilitating the recovery and transplantation of these gifts to help others in need. In our area (TN & VA), over 4,600 people now wait for an organ transplant, (heart, liver, lungs, kidneys, intestine or pancreas). Annually, our service area has approximately 300 people who donate one or more organs upon death and over 900 who donate corneas and/or tissues annually. The need for transplants far exceeds the number of donations in the area covered by TDS, and across the nation. Currently, in the United States, more than 108,000 people wait for an organ transplant. One third of them will die waiting for a transplant. TDS'' designated service area includes 84 counties in Tennessee, 10 counties in Virginia, 3 counties in Georgia and 1 county in Kentucky.

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• SciCrunch
• 16 years ago - by Anonymous

Database that annotates SNPs with known and predicted regulatory elements in intergenic regions of H. sapiens genome. Known and predicted regulatory DNA elements include regions of DNAase hypersensitivity, binding sites of transcription factors, and promoter regions that have been biochemically characterized to regulation transcription. Source of these data include public datasets from GEO, ENCODE project, and published literature.

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• RRID-Legacy
• 7 years ago - by Anonymous

Bioimaging Platform provides access to and support for wide variety of advanced microscopy and flow cytometry instruments, enabling researchers to perform studies from the tissue level and down to sub-cellular scales. Provides access to analytical imaging technologies. As such, the platform comprises of advanced microscopy systems for high resolution studies of fixed and live samples as well as for low-phototoxicity imaging of whole organs and organisms.Bioimaging platform includes seven advanced microscopy systems, two flow cytometers and several high-performance analysis workstations.

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• RRID
• 1 year ago - submitted by Paul Antony

A set of tools designed to cluster large numbers (>1 million) of pre-aligned nucleotide sequences. It performs the clustering of sequences using the Hierarchical Clustering Algorithm (HCA). There are currently three different cluster metrics implemented: single-linkage, complete-linkage, and average-linkage. In addition, there are currently four sequence distance functions implemented, these are: identity (gap-gap counting as match), nogap (gap-gap being ignored), nogap-single (like nogap, but consecutive gap-nogap''s count as a single mismatch), tamura (distance is calculated with the knowledge that transitions are more likely than transversions). One advantage that HCA has over other algorithms is that instead of producing only the clustering at a given threshold, it produces the set of merges occuring at each threshold. With this approach, the clusters can afterwards very quickly be reported for every arbitrary threshold with little extra computation. This approach also allows the plotting of the variation of number of clusters with clustering threshold without requiring the clustering to be run for each threshold independently. Another feature of the way HPC-CLUST is implemented is that the single-, complete-, and average-linkage clusterings can be computed in a single run with little overhead.

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• SciCrunch
• 13 years ago - by Anonymous

Software tool to enable flexible online visualization of action potential alignment to external events. Performs spike detection based on raw Open Ephys data exported via ZeroMQ. Requires triggers from Open Ephys for histogram display as spikes are detected around them.

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• RRID-Legacy
• 7 years ago - submitted by Sergio Martinez-Bellver

Software R package for copy number prediction with correction for GC and mappability bias for HTS data.

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• RRID
• 1 year ago - submitted by Wei Lv