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).
This study investigated the effects of formalin-fixation and DTF on RNA and miRNA profiles as determined by next-generation sequencing. As part of the National Cancer Institute’s Biospecimen Pre-analytical Variables (BPV) program, 30 tumor specimens including 10 renal clear cell carcinomas (kidney), 10 serous ovarian carcinomas (ovary), and 10 colon adenocarcinomas (colon) were collected at four medical centers. Each specimen was divided into six samples. One specimen was snap-frozen in liquid nitrogen vapor within 1 h of resection. The remaining samples were stored in a humidified chamber at room temperature for 1, 2, 3, or 12 h; fixed in 10% neutral buffered formalin (NBF) for 12 hours; and then paraffin-embedded. FFPE blocks were stored for 3 to 18 months before sectioning. RNA was extracted from three 10 µm sections using the QIAsymphony kits. Sequencing libraries were constructed using the Illumina TruSeq Stranded Total RNA Sample Kit and the Illumina's TruSeq Small RNA Sample Preparation Kit and sequenced on a HiSeq 2500.
|Technology Platform||Analyte||Next generation sequencing||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...