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https://www.marshallscientific.com/The-MJ-Research-PTC-100-Thermal-Cycler-p/mj-100.htm
Thermocycler that operates with 96 well and 60 well microplates. Has temperature configurations from 0 C to 105 C and pressure and height adjustment via thumbwheel. Comes with 14 pre-programmed protocols.
Proper citation: Marshall Scientific: MJ Research PTC-100 PCR Thermocycler (RRID:SCR_018602) Copy
https://www.labx.com/product/waters-2695
High performance liquid chromatographic system with quaternary, low pressure mixing pump and inline vacuum degassing. It has wavelengths of 190 to 800 nm and flow rates from 50 uL per min to 5 mL per min with 2.1 mm ID columns and larger. Autosampler has maximum capacity of 120 vials (12x32, 2 mL) with programmable temperature control from 4 to 40C. Heated column compartment provides temperatures from 5 degrees above ambient to 65C.
Proper citation: Waters: 2695 HPLC System (RRID:SCR_018649) Copy
Software toolkit for unambiguously describing molecular structure of DNA, RNA, and proteins, including non-canonical monomeric forms, crosslinks, nicks, and circular topologies. Aims to help epigenomics, transcriptomics, proteomics, systems biology, and synthetic biology researchers share and integrate information about DNA modification, post-transcriptional modification, post-translational modification, expanded genetic codes, and synthetic parts.
Proper citation: BpForms (RRID:SCR_018653) Copy
Software toolkit for creating reusable datasets that are both human and machine readable, combining spreadsheets with schemas including classes, their attributes, type of each attribute, and possible relationships between instances of classes.Consists of format for describing schemas for spreadsheets, numerous data types for science, syntax for indicating class and attribute represented by each table and column in workbook, and software for using schemas to rigorously validate, merge, split, compare, and revision datasets. Used for supplementary materials of journal article, as well as for emerging domains which need to quickly build new formats for new types of data and associated software with minimal effort.
Proper citation: ObjTables (RRID:SCR_018652) Copy
https://CRAN.R-project.org/package=trend
Software package includes tests for trends and change points detection. Used in analysis of environmental data.
Proper citation: trend (RRID:SCR_018658) Copy
Cell viability counter. Touchscreen fluorescent automated cell counter for primary samples by Nexcelom Bioscience.
Proper citation: McKinley: Cellometer Auto 2000 Cell Viability Counter (RRID:SCR_018656) Copy
https://hartleys.github.io/QoRTs/
Software package for quality control and data processing of RNA-Seq experiments. Software portable multifunction toolkit for assisting in analysis, quality control, and data management of RNA-Seq and DNA-Seq datasets. Used for detection and identification of errors, biases, and artifacts produced by high throughput sequencing technology. Can be used in operating system that supports Java and R.
Proper citation: QoRTs (RRID:SCR_018665) Copy
http://smithlabresearch.org/software/preseq/
Software package for predicting library complexity and genome coverage in high throughput sequencing. Aimed at predicting yield of distinct reads from genomic library from initial sequencing experiment. Predicting molecular complexity of sequencing libraries.
Proper citation: Preseq (RRID:SCR_018664) Copy
https://mass-spec.stanford.edu/instruments
HFX offers scanning rate to improve proteomic depth for discovery applications. Integrates well with targeted applications such as parallel reaction monitoring. Mass Spectrometer to identify and quantify proteins, peptides, lipids, glycans and small molecules accurately.
Proper citation: Thermo Fisher: QE-HFX mass spectrometer (RRID:SCR_018703) Copy
https://mass-spec.stanford.edu/instruments
System includes Thermo Orbitrap Fusion Tribrid mass spectrometer and Waters M-Class Acquity nanoUPLC. This platform features sequential acquisition capabilities and multiple fragmentation types, enabling complex, in depth proteomic experiments.
Proper citation: Thermo Fisher: Orbitrap Fusion nanoLC/MS system (RRID:SCR_018702) Copy
https://mass-spec.stanford.edu/instruments
LTQ XL ion trap mass spectrometer with Agilent 1100 HPLC system for metabolite identification, stability testing, degradation products, and high abundance quantitation.
Proper citation: Thermo Fisher: LTQ XL LC/MS system (RRID:SCR_018701) Copy
https://github.com/wangdingkang/DiscreteMorse
Discrete Morse based pipeline for neuron tracing on tracer injection and single neuron data sets. Automatically generates set of trees summarization of given neuron imaging data. Used to extract tree skeletons of individual neurons from volumetric brain image data, and to summarize collections of neurons labelled by tracer injections.
Proper citation: Discrete Morse (RRID:SCR_018662) Copy
https://bioconductor.org/packages/minet/
Open source software R package for inferring large transcriptional networks using mutual information. Implements algorithms for inferring networks such as gene networks from microarray data.
Proper citation: minet (RRID:SCR_018661) Copy
Web service for querying or retrieving gene annotation data.
Proper citation: MyGene.info (RRID:SCR_018660) Copy
https://www.mpbio.com/fastprep-24-5g-instrument
Sample disruption instrument that can homogenize, grind, or lyse biological samples. Samples are added to individual lysing matrix tubes and shaken in tridimensional motion.
Proper citation: MP Biochemicals: FastPrep24 Sample Preparation (RRID:SCR_018599) Copy
http://labx.com/product/stratagene-stratalinker-1800
UV crosslinker designed to crosslink DNA or RNA to nylon, nitrocellulose, or nylon reinforced nitrocellulose membranes in 25 to 50 seconds. It is equipped with internal photodetector to compensate for aging ultraviolet bulbs.
Proper citation: Stratagene: 1800 UV Crosslinker (RRID:SCR_018631) Copy
https://www.labx.com/product/sciex-4000-qtrap-
Hybrid triple quadrupole linear ion trap mass spectrometer for drug discovery and development, metabolite identification, contaminant testing, proteomic applications, post translationally modified proteins discovery, protein identification, and biomarker validation.
Proper citation: SCIEX: 4000 QTRAP Mass Spectrometer (RRID:SCR_018630) Copy
https://www.tainstruments.com/3200-system/
Mechanical testing apparatus with 225 N or 450 N maximum force and range of static to 300 Hz frequency response. Tests include torsion testing, creep under dynamic loading, special environment hot cold chambers, biomedical research, and engineered materials test applications..
Proper citation: TA Instruments: Electroforce 3200 Mechanical Testing Apparatus (RRID:SCR_018637) Copy
https://diagnostics.roche.com/global/en/products/instruments/discovery-xt-research-platform.html
Immunohistochemistry processor that can be used for immunohistochemistry and in situ hybridization slide preparation and processing.
Proper citation: Roche: Ventana Discovery XT Immunohistochemistry Processor (RRID:SCR_018643) Copy
Laser capture microdissection system that includes infrared lasers. It can be used for laser capture microdissection LCM, ultraviolet UV laser cutting, sanger sequencing, next generation sequencing, and quantitative PCR.
Proper citation: Thermo Fisher: Arcturus Cellect Laser Capture Microdissection System (RRID:SCR_018641) Copy
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