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http://www.swanrepository.com/

The SWAN Repository is the biologic specimen bank of the Study of Women''s Health Across the Nation (SWAN). SWAN is a National Institutes of Health funded, multi-site, longitudinal study of the natural history of the midlife including the menopausal transition. The overall goal of SWAN is to describe the chronology of the biological and psychosocial characteristics that occur during midlife and the menopausal transition. In addition, SWAN is describing the effect of the transition and its associated characteristics on subsequent health and risk factors for age related chronic diseases. SWAN was designed to collect and analyze information on demographics, health and social characteristics, reproductive history, pre-existing illness, physical activity, and health practices of mid-life women in multi-ethnic, community-based samples; elucidate factors that differentiate symptomatic from asymptomatic women during the menopausal transition; identify and utilize appropriate markers of the aging of the ovarian-hypothalamo-pituitary axis and relate these markers to alterations in menstrual cycle characteristics as women approach and traverse the menopause; and explain factors that differentiate women most susceptible to long-term pathophysiological consequences of ovarian hormone deficiency from those who are protected. The biological specimen bank can also be linked by identification number (not by participant name) to data collected in the Core SWAN protocol. The specimen bank can also be linked with data from the Daily Hormone Study as well as menstrual calendars. Types of data include: epidemiological data, psychosocial data, physical measures, as well as data from assays (endocrine and cardiovascular information). SWAN has seven clinical study sites located in six states, two in California, and one each in Chicago, Boston, Detroit area, northern New Jersey and Pittsburgh. The SWAN cohort was recruited in 1996/7 and consists of 3302 African American, Caucasian, Chinese American, Hispanic and Japanese American women. Cohort members complete an annual clinic visit. The Core Repository includes over 1.8 million samples from the first 11 years of specimen collection. This includes samples from annual visits and samples from the Daily Hormone Sub-study (DHS). During an Annual visit, participants provide materials for up to 24-28 aliquots to be incorporated into the Repository. During a DHS visit, a participant provides 6 serum samples and between ~30-50 urine samples depending upon the length of her menstrual cycle. DHS participants (887) provide urine samples collected throughout one menstrual cycle each year. A typical DHS collection consists of a blood draw plus collection of 10 ml of urine daily throughout the month-long menstrual cycle, up to 50 days. DHS Repository samples consist of 6 serum samples and 30 5 ml urine samples. Specimen collection occurs from the time of menstrual bleed to the subsequent menstrual bleed or up to 50 days, whichever come first. The current DHS collection consists of more than 200,000 specimens stored in 5 ml vials. The SWAN DNA Repository currently contains extracted diluted DNA from 1538 SWAN participants. B-lymphocytes were transformed with Epstein Barr virus, and the resulting transformed b-cells aliquoted. Information about using these transformed cells for genomic or proteomic studies is available. DNA has been extracted from one aliquot (per woman) of the immortalized cells using the Puregene system. There was an average DNA yield of 217.0 mg/mL and a A260/A280 average ratio of 1.86. This DNA, in turn, has been aliquoted into 20ng/1 ml units for release by the DNA Repository. Samples are free of personal identifiers and collected under consents that allow a broad range of activities related to women''s health. All of these samples are available to researchers who wish to study the midlife and menopausal transition. Scientists who use these specimens can also request data collected during a participant''s annual visit including medical and health history, psychosocial measures, biological measures and anthropometry.

Proper citation: Study of Womens Health Across the Nation (SWAN) Repository (RRID:SCR_008810) Copy   

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http://www.mouse-genome.bcm.tmc.edu/ENU/MutagenesisProj.asp

THIS RESOURCE IS NO LONGER IN SERVICE. For updated mutant information, please visit MMRRC or The Jackson Laboratory. Produces, characterizes, and distributes mutant mouse strains with defects in embryonic and postembryonic development. The goal of the ENU Mutagenesis project III is to determine the function of genes on mouse Chromosome 11 by saturating the chromosome with recessive mutations. The distal 40 cM of mouse Chr 11 exhibits linkage conservation with human Chromosome 17. We are using the chemical N-ethyl-N-nitrosourea (ENU) to saturate wild type chromosomes with point mutations. By determining the function of genes on a mouse chromosome, we can extrapolate to predict function on a human chromosome. We expect many of the new mutants to represent models of human diseases such as birth defects, patterning defects, growth and endocrine defects, neurological anomalies, and blood defects. Because many of the mutations we expect to isolate may be lethal or detrimental to the mice, we are using a unique approach to isolate mutations. This approach uses a balancer chromosome that is homozygous lethal and carries a dominant coat color marker to suppress recombination over a reasonable interval.

Proper citation: Mouse Mutagenesis Center for Developmental Defects (RRID:SCR_007321) Copy   

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http://www.grc.nia.nih.gov/

A research program of the NIA which focuses on neuroscience, aging biology, and translational gerontology. The central focus of the program's research is understanding age-related changes in physiology and the ability to adapt to environmental stress, and using that understanding to develop insight about the pathophysiology of age-related diseases. The IRP webpage provides access to other NIH resources such as the Biological Biochemical Image Database, the Bioinformatics Portal, and the Baltimore Longitudinal Study of Aging., THIS RESOURCE IS NO LONGER IN SERVICE. Documented on September 16,2025.

Proper citation: Intramural Research Program (RRID:SCR_012734) Copy   

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http://mrtools.mgh.harvard.edu/index.php/TBR

A tool for functional connectivity analysis of fcMRI data that maps functional data from individual sessions onto a priori spatial components from group level parcellations.

Proper citation: Template Based Rotation (RRID:SCR_012157) Copy   

•   Source: SciCrunch Registry

http://cbl.uh.edu/ORION/

Project to develop tools that explore single neuron function via sophisticated image analysis. ORION software bridges advanced optical imaging and compartmental modeling of neuronal function by rapidly, accurately, and robustly generating, from structural image data, a cylindrical morphology model suitable for simulating neuronal function.

Proper citation: ORION (RRID:SCR_010621) Copy   

•   Source: SciCrunch Registry

https://www.archrproject.com/

Software R package for processing and analyzing single-cell ATAC-seq data. Used for integrative single cell chromatin accessibility analysis.Provides intuitive, user focused interface for complex single cell analysis, including doublet removal, single cell clustering and cell type identification, unified peak set generation, cellular trajectory identification, DNA element-to-gene linkage, transcription factor footprinting, mRNA expression level prediction from chromatin accessibility and multi-omic integration with single-cell RNA sequencing.

Proper citation: ArchR (RRID:SCR_020982) Copy   

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https://alzped.nia.nih.gov

Publicly available, searchable, data resource that aims to increase transparency, reproducibility and translatability of preclinical efficacy studies of candidate therapeutics for Alzheimer’s disease. Knowledge platform for dissemination of data and analysis to scientists, from academic centers, industry, disease focused foundations. Provides quick access and visibility to integrated preclinical efficacy data from published and unpublished studies.

Proper citation: Alzheimer Disease Preclinical Efficacy Database (RRID:SCR_021230) Copy   

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http://hms-dbmi.github.io/scde/index.html

Software package that implements a set of statistical methods for analyzing single-cell RNA-seq data, including differential expression analysis (Kharchenko et al.) and pathway and geneset overdispersion analysis (Fan et al.)

Proper citation: SCDE (RRID:SCR_015952) Copy   

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https://www.rdocumentation.org/packages/DGCA/versions/1.0.2

Software R package to perform differential gene correlation analysis. Performs differential correlation analysis on input matrices, with multiple conditions specified by design matrix.

Proper citation: Differential Gene Correlation Analysis (RRID:SCR_020964) Copy   

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https://github.com/denisecailab/minian

Software miniscope analysis pipeline that requires low memory and computational demand so it can be run without specialized hardware. Offers interactive visualization that allows users to see how parameters in each step of pipeline affect output.

Proper citation: Minian (RRID:SCR_022601) Copy   

•   Source: SciCrunch Registry

https://github.com/nskvir/RepEnrich

Software tool to profile enrichment of next generation sequencing reads at transposable elements. Method to estimate repetitive element enrichment using high throughput sequencing data. Used to study genome wide transcriptional regulation of repetitive elements.RepEnrich2 is updated method to estimate repetitive element enrichment using high-throughput sequencing data.

Proper citation: RepEnrich (RRID:SCR_021733) Copy   

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https://github.com/evarol/HYDRA

Software tool as novel non-linear learning algorithm for simultaneous binary classification and subtype identification. Can handle imaging and non-imaging data and can find applications in exploratory analyses other than clustering of brain images.Software performs clustering of heterogenous disease patterns within patient group.

Proper citation: Heterogeneity through Discriminative Analysis (RRID:SCR_021958) Copy   

•   Source: SciCrunch Registry

https://imputationserver.sph.umich.edu/

Web server to implement whole genotype imputation workflow for efficient parallelization of computationally intensive tasks. Service for imputation that facilitates access to new reference panels and greatly improves user experience and productivity. Used to find haplotype segments and reference panel of sequenced genomes, assign genotypes at untyped markers, improve genome coverage, facilitate comparison and combination of studies that use different marker panels, increase power to detect genetic association, and guide fine mapping.

Proper citation: Michigan Imputation Server (RRID:SCR_017579) Copy   

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https://imputationserver.sph.umich.edu/index.html#!pages/home

Web based service for imputation that facilitates access to new reference panels and improves user experience and productivity. Server implements whole genotype imputation workflow using MapReduce programming model for efficient parallelization of computationally intensive tasks. Genotype imputation service using Minimac4.

Proper citation: Michigan Imputation Server (RRID:SCR_023554) Copy   

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https://masst.gnps2.org/microbemasst/

Web taxonomically informed mass spectrometry search tool, tackles limited microbial metabolite annotation in untargeted metabolomics experiments. Leveraging database of over 60,000 microbial monocultures, users can search known and unknown MS/MS spectra and link them to their respective microbial producers via MS/MS fragmentation patterns.

Proper citation: microbeMASST (RRID:SCR_024713) Copy   

•   Source: SciCrunch Registry

http://www.nitrc.org/projects/frats/

Software for the analysis of multiple diffusion properties along fiber bundle as functions in an infinite dimensional space and their association with a set of covariates of interest, such as age, diagnostic status and gender, in real applications. The resulting analysis pipeline can be used for understanding normal brain development, the neural bases of neuropsychiatric disorders, and the joint effects of environmental and genetic factors on white matter fiber bundles.

Proper citation: Functional Regression Analysis of DTI Tract Statistics (RRID:SCR_002293) Copy   

•   Source: SciCrunch Registry

http://www.nia.nih.gov/research/dab/aged-rodent-tissue-bank-handbook

A repository of tissue collected from the NIA Aged Rodent Colonies under contractual arrangement with BioReliance. The NIA colonies are barrier maintained and Specific Pathogen Free. Tissues are fresh frozen and stored at -80 degrees Celsius. Tissue from the NIA Aged Rodent Tissue Bank is available to investigators at academic and nonprofit research institutions who are engaged in funded research on aging. The project name and source of funding must accompany all orders. It may not be possible to ship tissue to foreign countries that have restrictions on the import of animal tissues or products. Please Note: Incomplete order forms will be returned. We can only offer following week delivery for those orders for which completed order forms are received by the deadline of Tuesday noon, Eastern time. Starting April 1, 2012, a copy (.pdf) of the purchase order must be emailed along with the order form.

Proper citation: Aged Rodent Tissue Bank (RRID:SCR_010607) Copy   

•   Source: SciCrunch Registry

http://www.uky.edu/coa/adc/investigators-research-resources

An organization which includes a tissue bank, a database, study design consultation, clinical resources, and a community registry database. The UK-ADC shares data with the NIA national database (NACC), as well as with independent, qualified investigators both within and outside the UK-ADC. This resource's associated tissue bank is comprised of anonymized brain tissue, blood, and cerebrospinal fluid samples from patients in the clinic, as well as frozen post-mortem brain tissue samples. This organization also shares research resources with the National Alzheimer's Coordinating Center (NACC), NACC collaborative initiatives, the Alzheimer's Disease Neuroimaging Initiative (ADNI), other Alzheimer Disease Centers (ADCs), and any qualified investigators from either the University of Kentucky or the general scientific community.

Proper citation: University of Kentucky's Alzheimer's Disease Center (RRID:SCR_008766) Copy   

•   Source: SciCrunch Registry

http://www.adcs.org/

An initiative for Alzheimer's disease clinical studies that works to facilitate the discovery, development and testing of new drugs, and is a part of the Alzheimer's Disease Prevention Initiative. This resource has an emphasis on expanding the range of its patients, mainly by enhancing the recruitment of minority groups. There is a further emphasis placed on testing agents that cannot be patented, as well as developing novel compounds that had been developed by individuals, academic institutions and drug discovery units. This resource also helps in the development of Alzheimer's disease centers to carry out studies, as well as establish administrative, data, operations and medical cores in San Diego. This organization is specifically involved in studies demonstrating the lack of benefit associated, previously used treatments such as: the use of estrogen, non-steroidal anti-inflammatory drugs, B vitamins and a statin drug. The Alzheimer's Disease Cooperative Study also develops assessment instruments to be used in clinical trials. The most frequently used of these tools include: the Alzheimer's Disease Assessment Scale-Cognitive sub-scale (ADAS-cog), Activities of Daily Living (ADL), and the Clinical Global Impression of Change Scale (CGIC). There is also an associated tissue bank at UCSD that includes materials from the clinical trials including: human tissue, blood, plasma, DNA, urine and cerebrospinal fluid.

Proper citation: Alzheimer's Disease Cooperative Study (RRID:SCR_008254) Copy   

•   Source: SciCrunch Registry

http://brainmap.wisc.edu/monkey.html

NO LONGER AVAILABLE. Documented on September 17, 2019. A set of multi-subject atlas templates to facilitate functional and structural imaging studies of the rhesus macaque. These atlases enable alignment of individual scans to improve localization and statistical power of the results, and allow comparison of results between studies and institutions. This population-average MRI-based atlas collection can be used with common brain mapping packages such as SPM or FSL.

Proper citation: Rhesus Macaque Atlases for Functional and Structural Imaging Studies (RRID:SCR_008650) Copy   

•   Source: SciCrunch Registry