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 firstname.lastname@example.org. 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).
This study investigated the effects of long-term storage of tissue specimens in VPLN on RNA yield, RNA purity, RIN, and DNA integrity. Tumor and normal adjacent tissue specimens (bladder, breast, central nervous system, colon, endocrine, esophagus, stomach, head and neck, lung, ovary, rectum, kidney, soft tissue sarcoma, and uterus) from 87 cases were collected between 2005 and 2014 by five collection centers and immediately transported from the operating room to the pathology department. Specimens were snap-frozen by an unspecified method within 30 minutes of resection in 2 mL cryovials and stored in vapor-phase liquid nitrogen (VPLN). As part of an external quality assessment, specimens were shipped on dry ice to the processing site and RNA was extracted within one year of collection from ~100 mg of tissue using a standard chloroform-based method (prior to 2010) or using the RNeasy Mini Kit and Qiacube automatic extractor (2010 and later). RNA was extracted from additional specimens of the same tumors after storage in VPLN for up to 11 years. These specimens were incubated overnight at an unspecified temperature in three volumes of RNALater-Ice, diced, transferred to 2.5 mL of QIAzol Lysis Reagent, and homogenized using a tissue disruptor before RNA extraction using the RNeasy Mini Kit or the miRNeasy Mini Kit. RNA yield and purity were measured with a spectrophotometer and RINs determined by bioanalyzer. DNA was extracted from ~50mg of tissue from a subset of samples (n=20) using the DNeasy Blood and Tissue Kit. DNA integrity was assessed by DNA integrity number (DIN) using a TapeStation.
|Technology Platform||Analyte||Automated electrophoresis/Bioanalyzer||RNA||Automated electrophoresis/Bioanalyzer||DNA||Spectrophotometry||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...