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 preservation method and fixation time on RNA yield, integrity, and transcript stability as well as tissue morphology and immunohistochemical analysis of colorectal tumor tissue. Specimens from 10 colorectal cancer patients undergoing colectomy from October 2012 to January 2013 were divided into eight smaller pieces: one was placed in RNAlater and frozen at -80°C for 48–72 h; one was fixed in PAXgene Tissue FIX Solution for 2–4 h, transferred to PAXgene Tissue STABILIZER and stored at -20°C for 48 h followed by dehydration by ethanol, chloroform treatment, and then embedded in paraffin; and six pieces were fixed in non-buffered 20% formalin or 10% or 20% neutral-buffered formalin (NBF) for 6 or 48 h. RNA was extracted from RNAlater specimens using the RNeasy Mini Kit, from PAXgene specimens using the PAXgene Tissue RNA Kit and from formalin specimens using the RNeasy FFPE Kit. Total RNA yield was determined by spectrophotometer, and RNA integrity number (RIN) was determined by bioanalyzer. Real-time RT-PCR of GAPDH, GPX1, VDAC2, ABL1, and EGR1 short (95 bp, 133 bp, 115 bp, 130 bp, and 114 bp; respectively) and long amplicons (430 bp, 345 bp 580 bp, 467 bp, and 355 bp, respectively) was performed to evaluate transcript stability and degradation. PAXgene and formalin specimens (3 µm sections) were H&E-stained for morphology assessment or IHC-stained for Ki-67, CEA, and EGFR.
|Technology Platform||Analyte||H-and-E microscopy||Morphology||Bioanalyzer||RNA||Immunohistochemistry||Protein||Spectrophotometry||RNA||Real-time qRT-PCR||RNA|
The top 5 most downloaded SOPs in the BRD in 2016 were supplied by
GAPPS Repository: https://brd.nci.nih.gov/brd/sop/show/890
UCHC Tissue Repository: https://brd.nci.nih.gov/brd/sop/show/841
New SOPs from the Consortium de Recherche en Oncologie Clinique du Québec (Q-CROC) were added to the BRD. View them at https://brd.nci.nih.gov/brd/sop-compendium/show/601.More...