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https://www.openicpsr.org/openicpsr/covid19

Repository for data examining social, behavioral, public health, and economic impact of novel coronavirus global pandemic. Free self publishing option for any researcher who wants to share data related to COVID-19. Deposits should include all data, annotated program code, command files, and documentation necessary to understand data collection and/or replicate research findings.

Proper citation: COVID-19 Data Repository (RRID:SCR_019105) Copy   

•   Source: SciCrunch Registry
  

https://brads.nichd.nih.gov/Home/

Access to data from the Division of Intramural Population Health Research (DIPHR) of the Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD) from completed studies, including biospecimens and ancillary data.

Proper citation: Biospecimen Repository Access and Data Sharing (RRID:SCR_017383) Copy   

•   Source: SciCrunch Registry
  

https://portal.gdc.cancer.gov/

A unified data repository of the National Cancer Institute (NCI)'s Genomic Data Commons (GDC) that enables data sharing across cancer genomic studies in support of precision medicine. The GDC supports several cancer genome programs at the NCI Center for Cancer Genomics (CCG), including The Cancer Genome Atlas (TCGA), Therapeutically Applicable Research to Generate Effective Treatments (TARGET), and the Cancer Genome Characterization Initiative (CGCI). The GDC Data Portal provides a platform for efficiently querying and downloading high quality and complete data. The GDC also provides a GDC Data Transfer Tool and a GDC API for programmatic access.

Proper citation: Genomic Data Commons Data Portal (GDC Data Portal) (RRID:SCR_014514) Copy   

•   Source: SciCrunch Registry
  

http://ccr.coriell.org/Sections/Collections/HuREF/?SsId=78

The Human Reference Genetic Material Repository makes available DNA from a single individual, J. Craig Venter, whose genome has been sequenced and assembled. The DNA samples are prepared from a lymphoblastoid cell line established at Coriell Cell Repositories from a sample of peripheral blood. The DNA samples are available in 50 microgram aliquots. The lymphoblastoid cell line is not available for distribution. The human DNA sample provided is that of J. Craig Venter whose DNA from white blood cells and sperm was sequenced using Sanger chemistry (ABI Capillary Electrophoresis Platforms 3700 and 3730xl), assembled using the Celera Assembler and was published in PLoS Biology . J. Craig Venter, born on 14 October 1946, is a Caucasian male of self-reported European-American ancestry. The data available on this sample, whose genome assembly is referred to as HuRef, includes: * Whole Genome Shotgun Sequencing data * Sequence trace set deposited by JCVI in the NCBI trace archive * Human Genome Browser displaying sequence assembly, DNA variants and gene annotations Additional data sets from this study include: * Full set of Sanger reads used for genome assembly * SNP and insertion/deletion variant on the human genome sequence coordinates (NCBI version 36) * Affymetrix 500K GeneChip data * Illumina HumanHap650Y Genotyping BeadChip data Given the amount of data publicly available the genomic content of this sample, HuRef will be useful as a reference for many genetic studies.

Proper citation: Human Reference Genetic Material Repository (RRID:SCR_004693) Copy   

•   Source: SciCrunch Registry
  

https://grigoriefflab.umassmed.edu/paper_rejection_repository

Repository of rejections of papers - letters and comments - that were ultimately accepted by a journal to educate others. Your rejection letters and comments are welcome. Some journals have begun including reviewers' comments with accepted papers to make the views of experts available to the reader. However, often the paper has been submitted to several journals and rejected before it is finally accepted. The rejection letters and comments are equally useful in helping to judge what kind of papers might be acceptable to a journal, and what kind of comments lead to rejections. Rather than hiding these low points in the trajectory of a scientific paper, this forum offers a place to publish these letters and comments to educate others.

Proper citation: Paper Rejection Repository (RRID:SCR_002643) Copy   

•   Source: SciCrunch Registry
  

http://ccr.coriell.org/Sections/Collections/NIGMS/?SsId=8

Highly characterized cell lines and high quality DNA for cell and genetic research representing a variety of disease states, chromosomal abnormalities, apparently healthy individuals and many distinct human populations. The NIGMS Repository contains more than 10,600 cell lines, primarily fibroblasts and transformed lymphoblasts, and over 5,500 DNA samples. The NIGMS Repository has a major emphasis on heritable diseases and chromosomally aberrant cell lines. In addition, it contains a large collection dedicated to understanding human variation that includes samples from populations around the world, the CEPH collection, the Polymorphism Discovery Resource, and many apparently healthy controls. Human induced pluripotent stem cell lines, many of which were derived from NIGMS Repository fibroblasts, have recently become available through the NIGMS Repository. Sample donation facilitates all areas of research by making available well-characterized materials to any qualified researcher who might have otherwise been unable to invest the time and resources to collect needed samples independently. Donations to the Repository have created a resource of unparalleled scope. Samples from the collection have been used in more than 5,500 publications and are distributed to scientists in more than 50 countries. This resource is continuously expanding to support new directions in human genetics.

Proper citation: NIGMS Human Genetic Cell Repository (RRID:SCR_004517) Copy   

•   Source: SciCrunch Registry
  

http://ccr.coriell.org/Sections/Collections/USIDNET/?SsId=15

The USIDNET DNA and Cell Repository has been established as part of an NIH-funded program - the US Immunodeficiency Network - to provide a resource of DNA and functional lymphoid cells obtained from patients with various primary immunodeficiency diseases. These uncommon disorders include patients with defects in T cell, B cell and/or granulocyte function as well as patients with abnormalities in antibodies / immunoglobulins, complement and other host defense mechanisms. All samples in this Repository have been de-identified to protect the privacy of the individual donors. The USIDNET also operates a Patient Data Registry in addition to this Repository and certain clinical data relating to a specific sample may be available through the Registry for some of the patient samples in the Repository collection. Materials in the collection are being made available at modest cost to qualified investigators in academic and commercial organizations in an effort to stimulate research to increase understanding of these orphan diseases and to promote development of new treatments. Requestors are required to complete a Statement of Research Intent briefly describing their proposed use of materials obtained from the Repository and must sign an Assurance agreeing to conditions established by USIDNET for distribution of samples from its collection. Requestors wishing to obtain additional clinical data specific to individual samples in the Repository collection must make a separate application for that information to the Registry (see www.usidnet.org) Physicians or Patients wishing to submit cell samples for the Repository collection should first contact Coriell to arrange for the Repository to send them the correct sample collection tubes as well as prepaid mailers for returning the collected sample(s) to Coriell. Separate collection and shipping procedures may be involved depending on how many samples are to be shipped at one time and whether the shipment will involve freshly obtained blood or already established cell lines.

Proper citation: USIDNET DNA and Cell Repository (RRID:SCR_004661) Copy   

•   Source: SciCrunch Registry
  

http://biorxiv.org/content/early/2013/11/27/000455

A subset of the CARMEN repository, a curated set of data and code of multielectrode array recordings of spontaneous activity in developing mouse and ferret retina. The data have been annotated with minimal metadata and converted into HDF5 (Hierarchical data format, version 5) including the essential features of the recordings, such as developmental age, and genotype. All code and tools used in the analyses are also fully available for reuse, giving the ability to regenerate each figure and table and know exactly how the results were calculated, adding confidence in the research output and allowing others to easily build upon previous work. The addition of published data to the repository is encouraged.

Proper citation: Retinal wave repository (RRID:SCR_010462) Copy   

•   Source: SciCrunch Registry
  

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   

•   Source: SciCrunch Registry
  

http://cre.jax.org/index.html

Repository of Cre Driver lines and related information resources. Their services include analysis of Cre line excision function in both target and non-target tissues using Cre reporter lines and presenting the annotated data in the expression data portion of this website, http://cre.jax.org/data.html.

Proper citation: JAX Cre Repository (RRID:SCR_005566) Copy   

•   Source: SciCrunch Registry
  

http://pathology.duke.edu/biospecimen-repository-processing-core

The Duke Institute for Genome Sciences & Policy (IGSP), in partnership with the Duke University School of Medicine Research Foundation and Department of Pathology (SOMRF), has established the Duke IGSP Biospecimen Repository as a centralized and accessible biological resource for Duke Investigators and research programs. The Repository is a standardized, regulatory-compliant and privacy protected repository for fluid and tissue biospecimens, and enables Duke investigators to reduce costs, and eliminate redundancies and significant risks associated with alternative biobanking practices, while facilitating integration of clinical trials and translational research programs with molecular profiling technologies. In order to ensure sample and data integrity and comparability, the Biorepository is developing, evaluating, and implementing evidence-based biobanking ''best practices''. Centralization of activities to a dedicated and expert staff and facility allows small and large research programs to reduce costs through elimination of redundancies and achieving efficiencies and economies of scale. The Duke-IGSP Biorepository is committed to ensuring appropriate consent, approved use, and protection of privacy through compliance with HIPAA regulations and IRB guidelines. The Duke-IGSP Biospecimen Repository will facilitate the integration of clinical research programs with molecular profiling technologies, enabling large-scale ''omic'' research programs that will inform and drive the development of new generations of targeted diagnostics, therapies, and preventions, which in turn will transform clinical outcomes.

Proper citation: Duke Biospecimen Repository (RRID:SCR_004306) Copy   

•   Source: SciCrunch Registry
  

http://www.cellml.org/models

Repository of biological models created using CellML, a free, open-source, eXtensible markup language based standard for defining mathematical models of cellular function. Models may be browsed by category, which include: Calcium Dynamics, Cardiovascular Circulation, Cell Cycle, Cell Migration, Circadian Rhythms, Electrophysiology, Endocrine, Excitation-Contraction Coupling, Gene Regulation, Hepatology, Immunology, Ion Transport, Mechanical Constitutive Laws, Metabolism, Myofilament Mechanics, Neurobiology, pH Regulation, PKPD, Signal Transduction, Synthetic Biology. The community can contribute their models to this resource.

Proper citation: CellML Model Repository (RRID:SCR_008113) Copy   

•   Source: SciCrunch Registry
  

http://www.acceleratedcure.org/impact/repository/nmo

Special collection of Neuromyelitis Optica (NMO) biological samples and data to foster scientific collaboration for NMO Spectrum Disease that will lead to the prevention, clinical treatment programs and a potential cure for Neuromyelitis Optica (NMO) Spectrum Disease. In this initiative, people with NMO can enroll into the repository at ACP''s collection sites located in leading neurology clinics across the US. Participants provide blood samples and information, which will in turn be used by qualified scientists whose research will contribute to the diagnosis, prevention, treatment, and/or cure of NMO. NMO subjects are primarily enrolled through the efforts of a study nurse employed by UTSW. Accelerated Cure Project (ACP), University of Texas Southwestern (UTSW), and Guthy-Jackson will work together to invite people with NMO to participate in the repository. Participants can enroll by visiting one of the ACP repository sites or by accepting an enrollment visit from the UTSW nurse.

Proper citation: Guthy-Jackson Repository for Neuromyelitis Optica (RRID:SCR_004183) Copy   

•   Source: SciCrunch Registry
  

http://www.remedyinformatics.com/

Software to harmonize the data that you have in different Excel files, databases, repositories, biospecimen applications, etc. and maps it to one common registry. Remedy Informatics' platform aggregates data from multiple sources, harmonizes the data via Ontology, and provides data visualization and pattern recognition and querying tools.

Proper citation: Registry Builder Data Harmonization and Aggregation Tool (RRID:SCR_006559) Copy   

•   Source: SciCrunch Registry
  

http://ccr.coriell.org/Sections/Collections/NHGRI/?SsId=11

DNA samples and cell lines from fifteen populations, including the samples used for the International HapMap Project, the HapMap 3 Project and the 1000 Genomes Project (except for the CEPH samples). All of the samples were contributed with consent to broad data release and to their use in many future studies, including for extensive genotyping and sequencing, gene expression and proteomics studies, and all other types of genetic variation research. NHGRI led the contribution of the NIH to the International HapMap Project, which developed a haplotype map of the human genome. This haplotype map, called the HapMap is a publicly available tool that allows researchers to find genes and genetic variations that affect health and disease. The samples from four populations used to develop the HapMap were initially housed in the Human Genetic Cell Repository of the National Institute of General Medical Sciences (NIGMS). Except for the Utah CEPH samples that were in the NIGMS Repository before the initiation of the HapMap Project and remain there, the NHGRI Repository now houses all of the HapMap samples. The NHGRI repository also houses the extended set of HapMap samples, which includes additional samples from the HapMap populations and samples from seven additional populations. All of the samples were collected with extensive community engagement, including discussions with members of the donor communities about the ethical and social implications of human genetic variation research. These samples were studied as part of the HapMap 3 Project. The NHGRI repository also houses the samples for the International 1000 Genomes Project. This Project is lightly sequencing genome-wide 2500 samples from 27 populations. This project aims to provide a detailed map of human genetic variation, including common and rare SNPs and structural variants. This map will allow more precise localization of genomic regions that contribute to health and disease. The 1000 Genomes Project includes many of the samples from the HapMap and extended set of HapMap samples, as well as samples being collected from additional populations. Currently, samples from five additional populations are available; the others will become available during 2011 and 2012. No identifying or phenotypic information is available for the samples. Donors gave broad consent for use of the samples, including for genotyping, sequencing, and cellular phenotype studies. Samples collected from other populations for the study of human genetic variation may be added to the collection in the future. The NHGRI Repository distributes high quality lymphoblastoid cell lines and DNA from the samples to researchers. DNA is provided in plates or panels of 70 to 100 samples or as individual samples. Cell cultures and DNA samples are distributed only to qualified professional persons who are associated with recognized research, medical, educational, or industrial organizations engaged in health-related research or health delivery.

Proper citation: NHGRI Sample Repository for Human Genetic Research (RRID:SCR_004528) Copy   

•   Source: SciCrunch Registry
  

http://www.seattle.eric.research.va.gov/VETR/biospecimen_repository.asp

The Vietnam Era Twin (VET) Registry maintains a repository of biological specimens obtained from Registry members. The VET Registry Biospecimen Repository includes DNA, plasma, and serum samples obtained from selected VET Registry members. As the VET Registry is a national resource for studies investigating genetic and non-genetic influences on health and disease in middle age men, this enhances the value of the information collected from VET Registry members to the research community. The VET Registry has developed a general system of protocols for the collection and storage of biological specimens that assures confidentiality for all participants. The biological specimens currently in use are stored at the R&D Core Laboratory at the VA Puget Sound Health Care System (VAPSHCS) in Seattle, WA. The R&D Core Laboratory performs DNA extraction procedures and separates out DNA, plasma, and serum for testing and storage. It is important to note that Core Laboratory staff has absolutely no phenotypic (non-genetic) information about VET Registry members, as the lab is completely blinded to the identity, disease characteristics, and any other research data collected from VET Registry members. The Massachusetts Veterans Epidemiology Research and Information Center (MAVERIC) Core Laboratory is located at the VA Boston Health Care System in Boston, MA, and serves as the long-term storage site for the VET Registry Biospecimen Repository. Before a VET Registry member decides whether to participate in the Biospecimen Repository, the procedures, confidentiality safeguards, and potential risks are explained in great detail. To be able to accommodate the wishes of members, a so-called layered consent process is used which allows members to choose from several options with regard to how their biological specimen will be used in current or future research studies. Such options may include: 1) not having their samples used for any testing beyond the immediate goals of the study; 2) allowing for future testing of their samples restricted to the study for which they provided the sample; or 3) allowing unrestricted future research use of their samples. Members are informed that any future use of their samples would have to be approved by the VET Registry, in addition to an independent ethics committee that protects the rights and welfare of research subjects, this board is more commonly known as an Institutional Review Board or IRB. Confidentiality safeguards include assigning code numbers, as opposed to name or other personal information, on all biological specimens. Zygosity Testing The accuracy of DNA testing makes it the best method for determining zygosity, identical (monozygotic) versus fraternal (non-identical or dizygotic), in VET Registry twin members. The use of DNA for zygosity testing is only performed when both members of a twin pair agree to the testing. Other Genetic Testing for specific genes will not necessarily involve providing the participants with test results.

Proper citation: Vietnam Era Twin Registry Biospecimen Repository (RRID:SCR_008808) Copy   

•   Source: SciCrunch Registry
  

http://aws.amazon.com/datasets

A multidisciplinary repository of public data sets such as the Human Genome and US Census data that can be seamlessly integrated into AWS cloud-based applications. AWS is hosting the public data sets at no charge for the community. Anyone can access these data sets from their Amazon Elastic Compute Cloud (Amazon EC2) instances and start computing on the data within minutes. Users can also leverage the entire AWS ecosystem and easily collaborate with other AWS users. If you have a public domain or non-proprietary data set that you think is useful and interesting to the AWS community, please submit a request and the AWS team will review your submission and get back to you. Typically the data sets in the repository are between 1 GB to 1 TB in size (based on the Amazon EBS volume limit), but they can work with you to host larger data sets as well. You must have the right to make the data freely available.

Proper citation: Amazon Web Services Public Data Sets (RRID:SCR_006318) Copy   

•   Source: SciCrunch Registry
  

http://isps.yale.edu/research/data

Data archive to assist in the sharing of research grade information pertaining to the social and economic sciences. The majority of digital content currently consists of social science research data from experiments, program files with the code for analyzing the data, requisite documentation to use and understand the data, and associated files. Access to the ISPS Data Archive is provided at no cost and is granted for scholarship and research purposes only. When possible, Data is linked to Projects and Publications, via the ISPS KnowledgeBase. ISPS operates in accordance with the prevailing standards and practices of the digital preservation community including the Open Archival Information System (OAIS) Reference Model (ISO 14721:2003) and the Data Documentation Initiative (DDI) standard. Accordingly, ISPS supports digital life-cycle management, interoperability, and preferred methods of preservation. The ISPS Data Archive is intended for use by social science researchers, policy-makers, and practitioners who are conducting or analyzing field (and other) experiments in various social science disciplines. Currently, Replication Files originate with ISPS-affiliated scholars.

Proper citation: ISPS Data Archive (RRID:SCR_003127) Copy   

•   Source: SciCrunch Registry
  

http://ccr.coriell.org/Sections/Collections/COHORT/?SsId=44

A repository of information related to Huntington's disease and its causes, progression, treatments, and possible cures. It stores and accepts data and specimens to accelerate research on Huntington's disease and provides scientists with prospectively collected clinical data and biological specimens. The COHORT sample includes individuals which manifest Huntington's disease (HD), unaffected individuals known to carry the HD gene or who are at risk of carrying the HD gene, and family members who have no risk for HD (control subjects). Clinical data includes demographics, clinical features, family history, and genetic characteristics. Biological specimens include blood with a potential of collecting urine or other samples in the future. The COHORT biological specimen repository will provide research specimens for current and future scientific research aimed at developing useful biomarkers of HD.

Proper citation: COHORT Repository (RRID:SCR_004539) Copy   

•   Source: SciCrunch Registry
  

https://pypi.org/project/pmlb/

Python wrapper for Penn Machine Learning Benchmark data repository. Large, curated repository of benchmark datasets for evaluating supervised machine learning algorithms. Part of PyPI https://pypi.org/

Proper citation: Penn machine learning benchmark repository (RRID:SCR_017138) Copy   

•   Source: SciCrunch Registry