Curator Dashboard

Core provides access to technology, experience, and expertise in molecular biology methods.Offers expertise in bioinformatics needed to acquire, analyze, and visualize data generated from high throughput technologies used in genomics research. Services include Illumina sequencing,Bioinformatics and statistical analysis,PacBio sequencing,Oxford Nanpore sequencing,High-throughput DNA and RNA library preparation,Double-barcoded amplicon sequencing. GBRC also participates in many of the bioinformatic analyses from the projects including De novo genome and transcriptome assembly, RNAseq differential expression analysis, SNP calling, RAD sequence analysis, Dual-barcoded amplicon community analysis, Phylogenetic analysis, CRISPR transformant profiling,Speed congenics, Novel agriculture virus detection and assembly.

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• SciCrunch
• 1 year ago - submitted by Edyta Vieth

Core provides training and equipment. Instruments include Pacific Biosciences VEGA benchtop long-read system, Oxford Nanopore Technologies minION and an Illumina MiSeq Next Generation Sequencing instrumentation, ABI Capillary Electrophoresis Genetic Analyzer (3130xl); an Eppendorf epMotion 5073m NGS liquid handling workstation; Promega MaxwellRSC Nucleic Acid extraction robot; real-time qPCR instruments (Rotor-Gene Q with HRM, Bio-Rad CFX Connect, QuantStudio 7 Flex [384/96 well interchangeable blocks]), and Bio-Rad ddPCR QX200 system, laser Attune NxT Flow Cytometer for analysis, laser BD FACS Melody Flow Cytometer for sorting, UV NanoDrop spectro photometers (ND1000, ND2200), and NanoDrop (ND3300) Fluorospectrophotometer; Promega Quantus, Agilent Bioanalyzer 2100; Covaris M220 Ultrasonic Nucleic Acid Shearer, a Sage BluePippin, seven 96 well gradient capable PCR thermal cyclers, two thermally controlled table top centrifuges capable of accepting 96-well plates used for DNA template preparation; two Eppendorf ThermoMixer C mixing units (384 well PCR to 50 mL tube format), two benchtop micro-centrifuges, Molecular Devices SpectraMax iD5 microplate reader, KTA-FPLC with UV detector and fractions collector, UV-1600PC UV-VIS Spectrophotometer with Sipper module, AlphaInnotechHP Gel Imaging System, Bio-Rad ChemiDoc MP Imaging System, Bio-Rad Dodeca-Cell Criterion PAGE system, several Bio-Rad Mini-Protean Gel Apparatus, Bio-Rad IEF Focusing Cells; numerous power-packs for gel electrophoresis, DNA gel boxes, pipettors, multi-channel pipettors. Provides computers (Linux & Win10), including four Ubuntu O/S based workstations for genome assembly and related bioinformatics analyses. CBFG maintains paid licenses for CLC Genomics Workbench, CLC Main Workbench, BioBam OmicsBox, SnapGene, FlowJo 10, SoftMax 7.1, Biogazelle qBasePLUS, and CANOCO.

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• SciCrunch
• 1 year ago - submitted by Edyta Vieth

Core provides services in human skin tissue procurement, isolation, and culture of human and murine skin-derived primary cells, 3D organotypic skin cultures, tissue processing, and basic histologic stains. The Core trains researchers in the development and use of these various techniques.

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• SciCrunch
• 1 year ago - submitted by Edyta Vieth

Integrated genomics/bioinformatics facility located at MIT. Provides Illumina HiSeq2000, NextSeq500 and MiSeq sequencing instruments as well as PacBio Sequel and Oxford Minion. Provides services in preparing Illumina libraries for high-throughput sequencing samples using several different methods, supports technologies including Agilent BioAnalyzer, AATI Fragment Analyzer, AATI FemtoPulse, Roche LC480 qPCR machines, automated liquid handling through Tecan Evo150s, TTP Labtech Mosquito HV. Supports 10X Chromium and single cell work using NamoCell single cell dispenser and custom oligo synthesis using Dr.Oligo 192. Supports informatics and bioIT tools. Core administers ~2PB of data storage on several platforms, including 600TB Isilon server. Hosts 400 processor Dell cluster and Dell Quad Core 2950 application server for Illumina sequencing and bioinformatic applications. All application servers and storage servers are interconnected by 1gigabyte private networks or by fiber optic lines and are administered by IT staff that are part of the BioMicro Center. Servers are configurable to provide secure data storage for clinical data if required.

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• SciCrunch
• 1 year ago - submitted by Edyta Vieth

Core develops solutions to meet your needs in electrophysiology data. Provides electrophysiology services to the neuroscience scientific community. Core has standard recording equipment such as patch clamp techniques or electroencephalographic (EEG) recordings.

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• RRID
• 1 year ago - submitted by Carine Dalle

Software fast and flexible alignment trimming tool that keeps phylogenetically informative sites and removes others. Multiple sequence alignment-trimming algorithm for accurate phylogenomic inference.

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• RRID
• 1 year ago - by Anonymous

Software tool as virus-focused assembler that does both assembly and polishing into unified workflow. Viral genome assembler enables detection of subtle genomic variations that can significantly impact viral function and pathogenicity.

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• RRID
• 1 year ago - submitted by Zhi Song

Software minimal tool for segmentation of irradiated tumor spheroids using optimized U-Net.

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• RRID
• 1 year ago - submitted by Steffen Lange

Software fast and flexible QC and signal summarization tool for long read sequencing data.

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• RRID
• 1 year ago - by Anonymous

Software tool designed to identify anomalous nodes in weighted graphs. By estimating expected edge weights and analyzing deviations, WGAND scores nodes to detect anomalies.

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• RRID
• 1 year ago - submitted by Michael Fire

Weighted Graph Anomalous Node Detection, WGAND, is a machine learning algorithm designed to identify anomalous nodes in weighted graphs. By estimating expected edge weights and analyzing deviations, WGAND scores nodes to detect anomalies.

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• RRID
• 1 year ago - submitted by Michael Fire

Core facility offers fluorescence, confocal, super resolution, multi-photon, laser capture and atomic force microscopy. Provides central preparatory laboratory and high-end computer workstations for data analysis and image processing. Technical support ranges from investigator training on instrumentation, allowing independent use, to complete processing of samples and final imaging by facility staff. The facility is GRP accredited, undergoes annual compliance checks and provides extensive standard operating procedures for all instrumentation.

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• RRID
• 1 year ago - by Anonymous

Academic core facility provides analytical and phenotypical measures to the scientific community. Provides services related to metabolic disorders (diabetes and obesity), cancer, aging neurological disorders, etc. Provides letters of support for grant proposals and research applications.

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• RRID
• 1 year ago - by Anonymous

Software comprehensive genome annotation pipeline with precision control through semi-supervised random forest gene model filter.

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• RRID
• 1 year ago - submitted by Johnathan Lomas

Core is component of the GEM Program collaborative research effort focused on accelerating discovery and innovation using patient tissue-derived organoids. GEM Core staff generate and maintain living biobank of tissue-derived organoids with matched original tissue and blood specimens and provide access to specialized training, protocols, and reagents.

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• SciCrunch
• 1 year ago - submitted by Edyta Vieth

Software graphical user interface to help to set up which bonds will treated as rotatable in the ligand and to analyze dockings. Used for automated docking with selective receptor flexibility. Designed to predict how small molecules, such as substrates or drug candidates, bind to receptor of known 3D structure.

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• RRID
• 1 year ago - submitted by Weihao Tang

Software tool for rapid and standardized annotation of bacterial genomes via alignment free sequence identification. Implemented in Python 3 and runs on MacOS and Linux systems.

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• RRID
• 1 year ago - by Anonymous

Small size uScopeMXII-20 digital microscope comes with 20x/0.4NA 160mm conjugate objective. This model is suited to applications where very high depth of field is required. The uScopeMXII-20 has wider depth of field than higher power models of the uScopeMXII. So, tissue samples and smears can be thicker with more of the image in focus. This unit is able to produce very high-quality digital microscope while browsing or scanning an area of interest.

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• RRID
• 1 year ago - by Anonymous

Real-time polymerase chain reaction (PCR) system used for quantitative PCR (qPCR) to measure and analyze nucleic acids in biological samples. Applications include gene expression analysis, pathogen detection, and DNA methylation analysis.

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• RRID
• 1 year ago - by Anonymous

Core Facility provides essential medicinal and organic chemistry support for drug discovery. The core specializes in the lead optimization of an initial lead compound to improve biological activity and drug-like properties, and to elucidate structure activity relationships. Other services include the design and synthesis of fluorescent and isotopic probes, compound scale up (1 – 5 grams), and custom synthesis.

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• RRID
• 1 year ago - submitted by Joe Burlison