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https://github.com/rbundschuh/CLEAR

Software workflow that identifies reliably quantifiable transcripts in limiting-cell RNA-seq (lcRNA-seq) data for differentially expressed genes (DEG) analysis. Coverage-based Limiting-cell Experiment Analysis for RNA-seq.

Proper citation: CLEAR (RRID:SCR_027171) Copy   

•   Source: SciCrunch Registry

https://bioconductor.org/packages/RAIDS/

Software R package to enable genetic ancestry inference from various cancer sequence sources (RNA, Exome, and Whole-Genome sequences). This package also implements simulation algorithm that generates synthetic cancer-derived data. Used for accurate and robust inference of genetic ancestry from cancer-derived molecular data across genomic platforms

Proper citation: RAIDS (Robust Ancestry Inference using Data Synthesis) (RRID:SCR_027265) Copy   

•   Source: SciCrunch Registry

http://igm.ucsd.edu/genomics/

Provides services including sequencing library preparation and sequencing on Illumina MiSeq and NovaSeq 6000 platforms. Supports single cell sequencing on 10X Genomics Chromium Controller. Provides Illumina Infinium Beadchips, which includes variety of whole genome genotyping arrays as well as Infinium MethylationEPIC BeadChip.

Proper citation: University of California at San Diego Institute for Genomic Medicine Genomics Center Core Facilitiy (RRID:SCR_022740) Copy   

•   Source: SciCrunch Registry

https://health.ucdavis.edu/cancer/research/sharedresources/im.html

Clinical Laboratory Improvement Amendments certified laboratory established to provide scientific support to investigators conducting clinical studies in humans, preclinical studies in animals and/or studies in veterinary medicine. Conducts immunology based assays needed to monitor patients in clinical immunotherapy trials. Offers molecular and cellular assays for investigators in different fields, including custom assays designes.

Proper citation: University of California Davis Health Immune Modeling, Analysis and Diagnostics Shared Resource Core Facility (RRID:SCR_023587) Copy   

•   Source: SciCrunch Registry

https://health.ucdavis.edu/cancer/research/sharedresources/ger.html

Provides expertise and comprehensive services to accomplish virtually every application of next generation sequencing based genomics research, including gene expression profiling, mutation/variant analyses, copy number analysis, epigenomics, metagenomics, single cell sequencing and spatial transcriptomics services. GSR also specializes in development of custom protocols and extensive data analysis and integrative bioinformatics support. The shared resource provides wide range of additional services for translational and clinical genomics research.

Proper citation: University of California Davis Health Genomics Shared Resource Core Facility (RRID:SCR_023586) Copy   

•   Source: SciCrunch Registry

https://health.ucdavis.edu/cancer/research/sharedresources/specimen.html

Provides specimens with annotated data for clinical and basic science research purposes.Biorepository functions as centralized tissue bank to provide researchers access to cancer- and non-cancer-related specimens including fresh or frozen tissue, paraffin blocks,sections and fluids, procured and stored using international standards of best practices and protocols compliant with Office for Human Research Protection. Specimens can be obtained prospectively as part of clinical trials or accessed through UC Davis Health Clinical Laboratories, where over 5.5 million blood specimens are processed annually.

Proper citation: University of California Davis Health Biorepository Shared Resource Core Facility (RRID:SCR_023583) Copy   

•   Source: SciCrunch Registry

https://health.ucdavis.edu/cancer/research/sharedresources/animalimaging.html

Provides access to in vivo imaging technologies including molecular imaging, optical imaging, quantitative physiologic and anatomic imaging, and whole body PET/CT scanning in humans and animals. Provides targeted imaging probes and tracers as well as expertise in planning, executing and analyzing in vivo imaging studies. Supports imaging studies in small animals, large animals and humans.This resource is located in three adjacent buildings in the Health Sciences district of the Davis campus:Center for Molecular and Genomic Imaging (CMGI), Genome and Biomedical Sciences Facility (small-animal imaging);Nuclear Magnetic Resonance (NMR) Facility, Tupper Hall (small-animal MRI);Center for Imaging Sciences (CIS), Veterinary School (large-animal imaging).

Proper citation: University of California Davis Health In Vivo Translational Imaging Shared Resource Core Facility (RRID:SCR_023589) Copy   

•   Source: SciCrunch Registry

https://www.mskcc.org/research/ski/core-facilities/monoclonal-antibody-core-facility

ABCF can provide MAbs from established hybridomas for RESEARCH PURPOSES ONLY, can assist in generating MAbs, offers a weekly mycoplasmal contamination screening service for tissue culture samples, distributes cell lines developed at Memorial Sloan Kettering Cancer Center and Rockefeller University.

Proper citation: Memorial Sloan Kettering Cancer Center Antibody and Bioresource Core Facility (RRID:SCR_017691) Copy   

•   Source: SciCrunch Registry

http://mass-spec.stanford.edu

Core mass spec and proteomic services include open access lab for trained users with GC/MS, LC/MS, high resolution LC/MS, and MALDI-TOF instruments, help with intact protein analysis, targeted quantitation, drug discovery support, pathway analysis, protein interactions, FFPE tissue analysis, both labeled and label-free proteomics, and more. Please contact SUMS to discuss these and other custom projects including new application development.

Proper citation: Stanford University Vincent Coates Foundation Mass Spectrometry Laboratory Core Facility (RRID:SCR_017801) Copy   

•   Source: SciCrunch Registry

http://rhlccflow.facilities.northwestern.edu

Provides 6 cell sorters and 5 benchtop analyzers. Helps investigators to define their projects in the early stages of development to make optimal and efficient use of flow cytometry. Educates ALL users (faculty and staff) in the science and technology of flow cytometry.

Proper citation: Northwestern University Cancer Center Flow Cytometry Core Facility (RRID:SCR_017766) Copy   

•   Source: SciCrunch Registry

http://cancer.northwestern.edu/research/shared-resources/pathology-core-facility.html

Centralized, comprehensive, core laboratory providing histology, immunohistochemistry, molecular analysis and extraction and microscopic evaluation services for human tissue-based studies. Serves integral marker studies that require biomarker-based treatment arm assignment. Performs procurement of fresh biospecimens for clinical trials and biobanking.

Proper citation: Northwestern University School of Medicine Lurie Cancer Center Pathology Core Facility (RRID:SCR_017769) Copy   

•   Source: SciCrunch Registry

http://www.med.unc.edu/csb/sbi

Core provides consultations and collaborations on research studies requiring computational structural biology methods. Analyses available are to study of static structures, molecular dynamics studies for analyzing contribution of dynamic and collective motions to macromolecular functionality. Trains researchers in computational structural biology techniques, or works in collaborative manner with researchers.Provides access to software tools for protein and DNA sequence analysis, protein fold determination, homology modeling, active site identification, and analysis of effects of various mutations on structure and function of protein, along with additional computational analyses.

Proper citation: North Carolina University at Chapel Hill R.L. Juliano Structural Bioinformatics Core Facility (RRID:SCR_017836) Copy   

•   Source: SciCrunch Registry

https://www.med.unc.edu/csb/nmr/

Core to support academic and industrial users. Spectrometer time is available to trained users for an hourly fee. Lab manager trains new users, consults to determine whether NMR will be useful in their research, and helps design experimental plan to obtain information they need. Manager also operates spectrometer for users whose experiments do not justify time and expense of individual training.

Proper citation: North Carolina University at Chapel Hill School of Medicine Biomolecular NMR Laboratory Core Facility (RRID:SCR_017841) Copy   

•   Source: SciCrunch Registry

http://www.med.unc.edu/csb/pep

Core specializes in production of pure, functional proteins for structural, biophysical, and biochemical studies. Facility offers three categories of service:Protein Expression,Protein Purification,Scientific Consultation, Mentoring, and Training; Offers Isotope labeled proteins for NMR;High production scales for immunizations, drug discovery, structural biology;Endotoxin-free protein production;Stable cell line generation;Expert baculovirus expression;Custom packages to efficiently suit your needs.

Proper citation: North Carolina University at Chapel Hill School of Medicine Protein Expression and Purification Core Facility (RRID:SCR_017843) Copy   

•   Source: SciCrunch Registry

http://www.ucdmc.ucdavis.edu/cancer/research/sharedresources/flowcytometry.html

Core provides access to expertise and instrumentation for analytical flow cytometry, cell sorting and laser scanning cytometry.Cell sorting and analytical cytometers are located at three sites in Davis and Sacramento for research use on recharge basis. Provides cell sorters for assisted sorting on appointment basis and provides training to investigators in acquiring data on analytic cytometers.Can advise on experiment design for flow cytometry, provides training to enable independent use of analytical cytometers, and familiarize investigators with popular data analysis software tools such as BD Diva and CellQuest, FlowJo, ModFit and iBrowser.

Proper citation: University of California Davis Flow Cytometry Shared Resource Laboratory Core Facility (RRID:SCR_017826) Copy   

•   Source: SciCrunch Registry

https://med.virginia.edu/flow-cytometry-facility/

Services include unassisted and assisted sample acquisition, cell sorting, mass cytometry (CyTOF), Luminex cytokine assays, antibody conjugation and data analysis.

Proper citation: University of Virginia School of Medicine Flow Cytometry Core Facility (RRID:SCR_017829) Copy   

•   Source: SciCrunch Registry

https://med.nyu.edu/research/scientific-cores-shared-resources/proteomics-laboratory

Core offers specialized expertise for analysis of proteins and peptides using mass spectrometry. Develops new methods and customized approaches for proteomic analysis and suggests experimental strategies and sample preparation prior to mass spectrometry analysis. Services include:comprehensive protein identification ,analysis of affinity purified complexes,characterizing protein post-translational modifications,de novo sequencing,label and label-free quantitation ,multiplexed quantitation global phosphorylation and ubiquitin analysis,analysis of laser-capture microdissected formalin-fixed paraffin-embedded tissue,secretome analysis,crosslinking analysis,disulfide mapping.

Proper citation: New York University School of Medicine Langone Health Proteomics Laboratory Core Facility (RRID:SCR_017926) Copy   

•   Source: SciCrunch Registry

https://isairr.bsd.uchicago.edu/

Core offers imaging modalities, techniques, and services for in vivo imaging of small animals and ex vivo imaging of tissue/organ specimens. iSAIRR sub-cores feature magnetic resonance imaging and spectroscopy (MRIS); optical imaging (bioluminescence and fluorescence); positron emission tomography, single photon emission computed tomography, and computed tomography (PET/SPECT/CT).Services include Assistance with experimental design,Assisted and/or independent image acquisition,Veterinary support for all imaging modalities,Assistance with data processing and interpretation.

Proper citation: Chicago University Integrated Small Animal Imaging Research Resource Core Facility (RRID:SCR_017923) Copy   

•   Source: SciCrunch Registry

https://med.nyu.edu/research/scientific-cores-shared-resources/microscopy-laboratory

Core offers comprehensive light and electron microscopy technologies. Our scientists use light microscopes and electron microscopes at resolutions ranging from centimeters to angstroms, providing clear and detailed images.We assist at every stage of your experiment, offering research-design consultation and instrument training, as well as guidance in study execution, analysis, and presentation for publication.

Proper citation: New York University School of Medicine Langone Health Microscopy Laboratory Core Facility (RRID:SCR_017934) Copy   

•   Source: SciCrunch Registry

https://github.com/katerinakazantseva/strainy

Software tool for phasing and assembly of bacterial strains from long-read sequencing data (either Oxford Nanopore or PacBio). Given reference (or collapsed de novo assembly) and set of aligned reads as input, tool produces multi-allelic phasing, individual strain haplotypes and strain-specific variant calls. Used for phasing and assembly of strain haplotypes from long-read metagenome sequencing.

Proper citation: Strainy (RRID:SCR_026430) Copy   

•   Source: SciCrunch Registry