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https://biospherix.com/products/c-chamber
Culture chamber for cell culture by BioSpherix. Functionalized by gas controllers for all bioactive gases, e.g. O2, CO2, CO, NO, etc. Made of clear polycarbonate. Magnetic seal door. Temperature is controlled. Combines with ProOx 110, ProCO2, ProOx C21, OxyCycler Series.
Proper citation: BioSpherix: C-Chamber (RRID:SCR_018189) Copy
Free online archive and distribution server for complete but unpublished manuscripts in the medical, clinical, and related health sciences. Preprints are preliminary reports of work that have not been certified by peer review. They should not be relied on to guide clinical practice or health related behavior and should not be reported in news media as established information. Research articles, systematic reviews and meta analyses, clinical research design protocols and data articles may be posted.
Proper citation: medRxiv (RRID:SCR_018222) Copy
http://www.innovision-systems.com/Products/MaxTraq.html
Software package for motion capture analysis by Innovision Systems Inc.
Proper citation: MaxTRAQ (RRID:SCR_018188) Copy
https://www.sonybiotechnology.com/us/instruments/sh800s-cell-sorter/
Benchtop cell sorter that sorts wide range of cell sizes for many applications using microfluidic sorting chips. Integrated with comprehensive fluidics controls and advanced automation for set-up, acquisition, sort and analysis. System software supports sorting into tubes and 96- and 384-well plates. Software generates FCS 3.0 and FCS 3.1 files that can be exported to third party analysis tools. For non-clinical research use only. For applications in which cross-contamination is concern, optional e-beam sterilized consumables can be used to replace sample line and sorting chip. Optional class A2 Level II biosafety cabinet provides protection for personnel and products. Biosafety cabinet meets international standards.Optical design offers up to four collinear excitation lasers (488 nm, 405nm, 561nm and 638nm) and six fluorescence detectors. The six free-form PMTs enable detection of fluorescence signals from any laser based on filter selection.
Proper citation: Sony biotechnology: SH800S Cell Sorter (RRID:SCR_018066) Copy
Software for designing CRISPR/Cas guide RNA with reduced off target sites. Used for rational design of CRISPR/Cas target. Web server for selecting rational CRISPR/Cas targets from input sequence. Server currently incorporates genomic sequences of human, mouse, rat, marmoset, pig, chicken, frog, zebrafish, Ciona, fruit fly, silkworm, Caenorhabditis elegans, Arabidopsis, rice, Sorghum and budding yeast.
Proper citation: CRISPRdirect (RRID:SCR_018186) Copy
http://viewer.shigen.info/medakavw/crisprtool/
Web medaka pattern match tool for short sequence and/or pattern. Used to search database of medaka genome on target and off target sites when editing genome with CRISRP-Cas9.
Proper citation: NBRP Medaka Pattern Match (RRID:SCR_018157) Copy
https://www.mizarimaging.com/wp-content/uploads/2018/11/Tilt-Datasheet-3.pdf
Modular light sheet illumination system designed to image living samples with minimal photobleaching or phototoxicity by Mizar Imaging. Enables high spatial and temporal resolution light sheet imaging to be added to existing or new microscope system.
Proper citation: Mizar Imaging: Tilt High Resolution Light Sheet Imaging System (RRID:SCR_018156) Copy
https://s2genomics.com/singulator-100/
Singulator to automate tissue preparation for single cell and single nucleus analyses. Bench top Singulator System and single use cartridge enable tissue dissociations into singulated cells or nuclei suspensions.
Proper citation: S2 Genomics: Singulator 100 Automated Single Cell Prep Automated System (RRID:SCR_018155) Copy
https://www.yxlon.de/en/products/x-ray-and-ct-inspection-systems/yxlon-ff35-ct
Computed tomography system designed to achieve precise inspection results for wide range of applications by YXLON. Available in single or dual tube configuration, it is perfect for very small to medium sized parts inspection in automotive, electronics, aviation, and material science industries.
Proper citation: YXLON: FF35 CT (RRID:SCR_018208) Copy
http://stmichaelshospitalresearch.ca/wp-content/uploads/2015/09/ZEN-Black-Quick-Guide.pdf
Software used to analyze images obtained from microscope. ZEN Black is software Zeiss uses to run their laser-based instruments.
Proper citation: Black Zen software (RRID:SCR_018163) Copy
Portal enabling web based visualization and analysis of multi omic data describing cell types in developing and adult brain, powered by gEAR and EpiViz. Release 1 on April 2019 includes single cell and bulk tissue RNAseq, ATACseq, and ChIPseq from fetal human prefrontal cortex, as well as from stem cell models of neural induction. Portal will expand to include multiple regions of developing and adult brain and additional analytical tools.
Proper citation: NeMO Analytics (RRID:SCR_018164) Copy
Swinging bucket benchtop centrifuge. Eppendorf 5920 R refrigerated centrifuge.
Proper citation: Eppendorf: 5920R centrifuge (RRID:SCR_018092) Copy
https://github.com/WangHYLab/fcirc
Software Python pipeline for linear and circular RNAs of known fusions exploration. Pipeline for exploring linear transcripts and circRNAs of known fusions based on RNA-Seq data. Known fusion genes are from multiple databases like COSMIC, ChimerDB, TicDB, FARE-CAFE and FusionCancer or user-added gene-pairs.
Proper citation: Fcirc (RRID:SCR_018090) Copy
http://www.prc.boun.edu.tr/appserv/prc/hingeprot/index.html
Web server for predicting rigid protein parts and flexible hinge regions connecting them in native topology of protein chains by employing elastic network (EN) models. Automated prediction of hinges in protein structures.
Proper citation: HingeProt (RRID:SCR_018136) Copy
https://www.beckman.com/liquid-handlers/biomek-i7/b87585
Liquid handling instrument designed to optimize dependability and walk-away time. Biomek i7 Hybrid with enclosure has up to 45 deck positions and includes both Multichannel and Span-8 pipette heads in enclosed work space.
Proper citation: Beckman Coulter: Biomek i7 Hybrid Automated Workstation (RRID:SCR_018094) Copy
Software Python tool as data visualization library based on matplotlib. Provides interface for drawing attractive and informative statistical graphics. Statistical data visualization using matplotlib.
Proper citation: seaborn (RRID:SCR_018132) Copy
https://lifesciencedb.jp/bp3d/
Web application that enables users to build and publish own custom manikins. Used to build three dimensional model of human body using parts registered in BodyParts3D. Server returns image of assembled 3D model as still image, rotating animation, interactive image, etc. Each part can be downloaded as polygon mesh file that can be used with 3D printer.
Proper citation: Anatomography (RRID:SCR_018147) Copy
http://compbio.mit.edu/ChromHMM/
Software tool for chromatin state discovery and characterization. Used for chromatin state discovery and genome annotation of non coding genome using epigenomic information across one or multiple cell types. Combines multiple genome wide epigenomic maps, and uses combinatorial and spatial mark patterns to infer complete annotation for each cell type. Provides automated enrichment analysis of resulting annotations.
Proper citation: ChromHMM (RRID:SCR_018141) Copy
https://github.com/cramerlab/warp
Software tool that automates all preprocessing steps of cryo-EM data acquisition and enables real-time evaluation. Corrects micrographs for global and local motion, estimates local defocus and monitors key parameters for each recorded micrograph or tomographic tilt series in real time. Software includes deep-learning-based models for accurate particle picking and image denoising.
Proper citation: Warp (RRID:SCR_018071) Copy
https://biit.cs.ut.ee/gprofiler/page/r
Software R interface to g:Profiler. Uses publicly available APIs of g:Profiler web tool which ensures that results from all of interfaces are consistent. Used for gene list functional enrichment analysis and namespace conversion. gprofiler2 package supports all the same organisms, namespaces and data sources as the web tool.
Proper citation: gProfiler2 (RRID:SCR_018190) Copy
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