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http://www.broad.mit.edu/mpr/lung

Data set of a molecular taxonomy of lung carcinoma, the leading cause of cancer death in the United States and worldwide. Using oligonucleotide microarrays, researchers analyzed mRNA expression levels corresponding to 12,600 transcript sequences in 186 lung tumor samples, including 139 adenocarcinomas resected from the lung. Hierarchical and probabilistic clustering of expression data defined distinct sub-classes of lung adenocarcinoma. Among these were tumors with high relative expression of neuroendocrine genes and of type II pneumocyte genes, respectively. Retrospective analysis revealed a less favorable outcome for the adenocarcinomas with neuroendocrine gene expression. The diagnostic potential of expression profiling is emphasized by its ability to discriminate primary lung adenocarcinomas from metastases of extra-pulmonary origin. These results suggest that integration of expression profile data with clinical parameters could aid in diagnosis of lung cancer patients.

Proper citation: Classification of Human Lung Carcinomas by mRNA Expression Profiling Reveals Distinct Adenocarcinoma Sub-classes (RRID:SCR_003010) Copy   

•   Source: SciCrunch Registry

http://www.census.gov/did/www/nlms/

A database based on a random sample of the noninstitutionalized population of the United States, developed for the purpose of studying the effects of demographic and socio-economic characteristics on differentials in mortality rates. It consists of data from 26 U.S. Current Population Surveys (CPS) cohorts, annual Social and Economic Supplements, and the 1980 Census cohort, combined with death certificate information to identify mortality status and cause of death covering the time interval, 1979 to 1998. The Current Population Surveys are March Supplements selected from the time period from March 1973 to March 1998. The NLMS routinely links geographical and demographic information from Census Bureau surveys and censuses to the NLMS database, and other available sources upon request. The Census Bureau and CMS have approved the linkage protocol and data acquisition is currently underway. The plan for the NLMS is to link information on mortality to the NLMS every two years from 1998 through 2006 with research on the resulting database to continue, at least, through 2009. The NLMS will continue to incorporate data from the yearly Annual Social and Economic Supplement into the study as the data become available. Based on the expected size of the Annual Social and Economic Supplements to be conducted, the expected number of deaths to be added to the NLMS through the updating process will increase the mortality content of the study to nearly 500,000 cases out of a total number of approximately 3.3 million records. This effort would also include expanding the NLMS population base by incorporating new March Supplement Current Population Survey data into the study as they become available. Linkages to the SEER and CMS datasets are also available. Data Availability: Due to the confidential nature of the data used in the NLMS, the public use dataset consists of a reduced number of CPS cohorts with a fixed follow-up period of five years. NIA does not make the data available directly. Research access to the entire NLMS database can be obtained through the NIA program contact listed. Interested investigators should email the NIA contact and send in a one page prospectus of the proposed project. NIA will approve projects based on their relevance to NIA/BSR''s areas of emphasis. Approved projects are then assigned to NLMS statisticians at the Census Bureau who work directly with the researcher to interface with the database. A modified version of the public use data files is available also through the Census restricted Data Centers. However, since the database is quite complex, many investigators have found that the most efficient way to access it is through the Census programmers. * Dates of Study: 1973-2009 * Study Features: Longitudinal * Sample Size: ~3.3 Million Link: *ICPSR: http://www.icpsr.umich.edu/icpsrweb/ICPSR/studies/00134

Proper citation: National Longitudinal Mortality Study (RRID:SCR_008946) Copy   

•   Source: SciCrunch Registry

http://www.med.upenn.edu/genetics/dnaseq/index.shtml

Core facility that provides the following services: Large sequencing project support, Sanger sequencing service, High throughput DNA sequencing, Ion Torrent Personal Genome Machine sequencing, Template preparation and purification, Roche 454 sequencing, Sequence analysis and database search support, Construction of targeting vector for gene targeting, Genotyping and Fragment Analysis service, Molecular biology services, Mouse genotyping, and Ion Personal Genome Machine sequencing data analysis. The DNA Sequencing Facility provides long read, automated Sanger sequencing; microsatellite-based genotyping and fragment analysis; plasmid and BAC DNA preparation and purification; and related molecular biological services including PCR, cloning, sub-cloning, site-directed mutagenesis, and preparation of targeting vectors for gene targeting in mice. Core also provides services and support for analysis and interpretation of sequence data as well as the design of approaches to complex sequencing projects. For the last four years the facility has been providing Roche 454 sequencing service that includes library preparation, emulsion PCR and pyrosequencing for both genomic DNA and amplicons.

Proper citation: University of Pennsylvania Genomics Analysis Core (RRID:SCR_011061) Copy   

•   Source: SciCrunch Registry

https://lsom.uthscsa.edu/dcsa/research/cores-facilities/optical-imaging/

Service resource which makes imaging technology available to investigators on UTHSCSA campus and neighboring scientific community. Core Optical Imaging Facility offers access to technology for imaging of living cells, tissues, and animals, consultation, education and assistance regarding theory and application of optical imaging techniques, technical advice on specimen preparation techniques and probe selection.

Proper citation: Texas University Health Science Center at San Antonio Long School of Medicine Department of Cell Systems and Anatomy Optical Imaging Core Facility (RRID:SCR_012171) Copy   

•   Source: SciCrunch Registry

https://www.moffitt.org/research-science/shared-resources/tissue/

Biorepository resource with mission of proper collection, handling, processing and storage of irreplaceable biological specimens to support spectrum of related basic science, translational and clinical research. Provides expertise in nucleic acid extractions, quantification, aliquoting and quality assurance; liquid specimen centrifugation, processing and aliquoting; histological tissue processing, immunohistochemistry and tissue microarray microtomy; pathologist consultation services. Tissue Core operations are divided into four distinct pillars of service that work collaboratively to ensure specimen quality is maintained from procurement to preservation.

Proper citation: Moffitt Cancer Center Tissue Core Facility (RRID:SCR_012364) Copy   

•   Source: SciCrunch Registry

https://cibersort.stanford.edu/

Software tool to provide an estimation of the abundances of member cell types in a mixed cell population, using gene expression data. Used for characterizing cell composition of complex tissues from their gene expression profiles, large scale analysis of RNA mixtures for cellular biomarkers and therapeutic targets.

Proper citation: CIBERSORT (RRID:SCR_016955) Copy   

•   Source: SciCrunch Registry

https://sourceforge.net/projects/saint-apms/files/

Software tool for upgraded implementation of probabilistic scoring of affinity purification mass spectrometry data. Used for filtering high confidence interaction data from affinity purification mass spectrometry experiments. Used for assigning confidence scores to protein-protein interactions based on quantitative proteomics data in AP-MS experiments.

Proper citation: SAINTexpress (RRID:SCR_018562) Copy   

•   Source: SciCrunch Registry

https://cellrank.readthedocs.io/en/stable/

Software package for directed single cell fate mapping in diverse scenarios, including regeneration, reprogramming and disease. Automatically detects initial, intermediate and terminal populations, predicts fate potentials and visualizes continuous gene expression trends along individual lineages. Applied to lineage traced cellular reprogramming data, predicted fate probabilities correctly recover reprogramming outcomes.

Proper citation: CellRank (RRID:SCR_022827) Copy   

•   Source: SciCrunch Registry

https://mcmicro.org

Software tool as scalable, modular image processing pipeline for multiplexed tissue imaging. Transforms multi channel whole slide images into single cell data.

Proper citation: MCMICRO (RRID:SCR_022832) Copy   

•   Source: SciCrunch Registry

https://github.com/JonathanIrish/MEMv3

Software tool to calculate enrichment scores. Generates human and machine readable labels that quantify features enriched in sample. Used to identify multiple populations of cells and to compare each population to all of other remaining cells from original sample.

Proper citation: Marker Enrichment Modeling (RRID:SCR_022495) Copy   

•   Source: SciCrunch Registry

https://github.com/raphael-group/chisel

Software tool to infer allele and haplotype specific copy numbers in individual cells from low coverage single cell DNA sequencing data. Integrates weak allelic signals across individual cells, powering strength of single cell sequencing technologies to overcome weakness. Includes global clustering of RDRs and BAFs, and rigorous model selection procedure for inferring genome ploidy that improves both inference of allele specific and total copy numbers.

Proper citation: CHISEL (RRID:SCR_023220) Copy   

•   Source: SciCrunch Registry

https://github.com/mhammell-laboratory/TEtranscripts

Software package for including transposable elements in differential enrichment analysis of sequencing datasets. Used for including transposable elements in differential expression analysis of RNA-seq datasets. RNAseq TE quantification tool.

Proper citation: TEtranscripts (RRID:SCR_023208) Copy   

•   Source: SciCrunch Registry

http://www.chernobyltissuebank.com/

The CTB (Chernobyl Tissue Bank) is an international cooperation that collects, stores and disseminates biological samples from tumors and normal tissues from patients for whom the aetiology of their disease is known - exposure to radioiodine in childhood following the accident at the Chernobyl power plant. The main objective of this project is to provide a research resource for both ongoing and future studies of the health consequences of the Chernobyl accident. It seeks to maximize the amount of information obtained from small pieces of tumor by providing multiple aliquots of RNA and DNA extracted from well documented pathological specimens to a number of researchers world-wide and to conserve this valuable material for future generations of scientists. It exists to promote collaborative, rather than competitive, research on a limited biological resource. Tissue is collected to an approved standard operating procedure (SOP) and is snap frozen; the presence or absence of tumor is verified by frozen section. A representative paraffin block is also obtained for each case. Where appropriate, we also collect fresh and paraffin-embedded tissue from loco-regional metastases. Currently we do not issue tissue but provide extracted nucleic acid, paraffin sections and sections from tissue microarrays from this material. The project is coordinated from Imperial College, London and works with Institutes in the Russian Federation (the Medical Radiological Research Centre in Obninsk) and Ukraine (the Institute of Endocrinology and Metabolism in Kiev) to support local scientists and clinicians to manage and run a tissue bank for those patients who have developed thyroid tumors following exposure to radiation from the Chernobyl accident. Belarus was also initially included in the project, but is currently suspended for political reasons.

Proper citation: Chernobyl Tissue Bank (RRID:SCR_010662) Copy   

•   Source: SciCrunch Registry

https://reprint-apms.org/?q=chooseworkflow

Database of Mass Spectrometry contaminants and pipeline for Affinity Purification coupled with Mass Spectrometry analysis. Contaminant repository for affinity purification mass spectrometry data. Database of standardized negative controls. Used to identify protein-protein interactions.

Proper citation: CRAPome (RRID:SCR_025008) Copy   

•   Source: SciCrunch Registry

https://redu.ucsd.edu/

Software framework to find and re-analyze public Mass Spectrometry data. Used to find uniformly formatted public MS/MS data in the Global Natural Product Social Molecular Networking Platform (GNPS) via formatted metadata. New or previously collected data can be added provided they adhere to the ReDU metadata standards (the implemented drag-and-drop validator is applicable to any scientific data) and data are available in GNPS/MassIVE.

Proper citation: ReDU (RRID:SCR_025105) Copy   

•   Source: SciCrunch Registry

https://ibeximagingcommunity.github.io/ibex_imaging_knowledge_base/

Open, global repository as central resource for reagents, protocols, panels, publications, software, and datasets. In addition to IBEX, we support standard, single cycle multiplexed imaging (Multiplexed 2D imaging), volume imaging of cleared tissues with clearing enhanced 3D (Ce3D), highly multiplexed 3D imaging (Ce3D-IBEX), and extension of the IBEX dye inactivation protocol to the Leica Cell DIVE (Cell DIVE-IBEX). Committed to sharing knowledge related to multiplexed imaging. Antibody validation community knowledgebase.

Proper citation: IBEX Knowledge Base (RRID:SCR_025296) Copy   

•   Source: SciCrunch Registry

https://github.com/GregorySchwartz/too-many-cells

Software suite of tools, algorithms, and visualizations focusing on relationships between cell clades. This includes new ways of clustering, plotting, choosing differential expression comparisons. Identifies and visualizes relationships of single-cell clades.

Proper citation: TooManyCells (RRID:SCR_025328) Copy   

•   Source: SciCrunch Registry

https://github.com/willtownes/glmpca

Software R package for dimension reduction of non-normally distributed data. Generalized PCA for non-normally distributed data.

Proper citation: glmpca (RRID:SCR_025517) 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