Welcome to the newest version of the Biospecimen Research Database (BRD), which accommodates Standard Operating Procedures (SOP). We encourage your contributions to our new SOP library!
The BRD is a free and publicly accessible database that contains peer-reviewed primary and review articles as well as SOPs in the field of human Biospecimen Science. Each literature curation has been created by a Ph.D.-level scientist to capture the following: (1) relevant parameters that include the biospecimen investigated (type and location, patient diagnosis), preservation method, analyte(s) of interest and technology platform(s) used for analysis; (2) the pre-analytical factors investigated, including those relating to pre-acquisition, acquisition, preservation, processing, storage, and analysis; and (3) an original summary of relevant results. Browse literature curations or submit specific queries using the Advanced Search page with keyword search for specific biomakers or genes, PubMed ID, or pre-analytical factor values (anticoagulant, fixative, reagent, etc).
SOPs are organized in a hierarchy system consisting of two tiers: (1) SOPs, established protocols; and (2) Biospecimen Evidence-based Practices (BEBP), procedural guidelines developed using literature evidence. SOP-tiered documents are a product of the Source organization specified. SOPs shared by external organizations are done so only with their consent, and have not been vetted by BBRB. SOP documents are searchable by keyword, or by curated fields (source organization, tier, applicable biospecimens, and topic) on the Search SOPs page. Related SOP documents are assembled in Compendiums, which are viewable on the SOP Compendiums page. You can also create your own Compendium and download SOPs together rather than individually.
We encourage you to submit SOPs from your lab or institution for inclusion in the BRD by clicking on the Submit an SOP tab or at email@example.com. Individuals and organizations that suggest articles for inclusion in the BRD will receive acknowledgement on the paper's curation page. Articles may be submitted by clicking on the Suggest a New Paper tab or via the email above. Feedback is also welcome.
The BRD is an initiative of the NCI Biorepositories and Biospecimen Research Branch (BBRB).
The purpose of this study was to assess the impact of cold ischemia time on miRNA and mRNA expression profiles of breast tumor specimens. Ten primary breast tumor specimens were macrodissected by a pathologist to ensure the primary tumor was represented in all aliquots. Specimens were then placed in a cryotube and left at room temperature for 0.5, 1, 3, or 6 h. A core needle biopsy representing a cold ischemia time of 0 h was obtained immediately after surgical resection from five patients and served as a control. All specimens were then snap-frozen in liquid nitrogen. RNA was extracted using the Trizol method and RNA concentration and quality were determined by Nanodrop spectrophotometry and a bioanalyzer, respectively. Expression profiles of mRNA and miRNA were assessed using the Agilent Technologies 4 x 44 K Whole Human Genome Microarray and the Human miRNA Microarray Kit V2, respectively. Feature Extraction files containing mRNA and miRNA microarray data were processed and normalized using R (v2.10.1) and Bioconductor, respectively, and all data was log2 transformed.
|Technology Platform||Analyte||DNA microarray||RNA||Spectrophotometry||RNA||Automated electrophoresis/Bioanalyzer||RNA|
The top 5 most downloaded SOPs in the BRD in 2018 were supplied by:
GAPPS Repository: https://brd.nci.nih.gov/brd/sop/show/890
A new article from NCI's BPV Program is now available that reports deleterious effects of formalin-fixation and delays to fixation on RNA and miRNA-Seq profiles.
View the PubMed Abstract at https://www.ncbi.nlm.nih.gov/pubmed/31061401More...