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 ncibbrb@nih.gov. 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 collecting blood in PAXgene versus Tempus tubes and extracting RNA with the tube-specific protocol or a modified protocol on RNA yield and quality, and gene expression profile. For the first experiment, venous blood from four healthy females was drawn directly in PAXgene and Tempus tubes, inverted 10 times, and stored at -80˚C. For experiment 2, frozen blood from six healthy females in PAXgene tubes was obtained from the Norwegian Women and Cancer Cohort (NOWAC) and frozen blood from seven healthy females in Tempus tubes was obtained from Health Survey of North-Trøndelag. Experiment 3 included 41 specimens in PAXgene tubes from NOWAC and 20 specimens in Tempus tubes from HUNT3. Blood was thawed at room temperature for 16 h and then specimens for Experiments 1 and 2 were split for RNA extraction using the tube-specific protocol (PAXgene Blood RNA Tube protocol or the Tempus Spin RNA Isolation Kit) and the modified protocol. RNA from Experiment 3 was extracted using only the modified protocol which included PBS dilution, centrifugation, resuspension of the pellet in PAXgene kit buffer, proteinase K digestion in PAXgene buffer 2 for 10 min at 55˚C, filtration through a PAXgene spin column, addition of ethanol, filtration through a mirVana filter, filter washing and DNAse treatment, and elution in heated nuclease-free water. RNA yield and purity were determined spectrophotometrically. Integrity was determined by bioanalyzer. miRNA levels were assayed using TaqMan real-time PCR assays for miR-16, miR-181, and miR-423. Gene expression was determined by hybridizing Illumina TotalPrep RNA Amplification Kit amplified RNA to IlluminaHumanHT-12 v4 Expression BeadChips.
| Technology Platform | Analyte | Spectrophotometry | RNA | Bioanalyzer | RNA | DNA microarray | RNA | Real-time qRT-PCR | RNA |
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Don't miss BBRB's presentation on comparisons among SOPs from the BRD's SOP Library during this Wednesday's (5/23/18) morning session at the ISBER 2018 Annual Meeting.
Later, stop by and visit the ISBER Tool Bench at 3:30 pm (Wednesday, 5/23/18) to learn more about the BRD and how it may be of use to you.
Stop by and visit BBRB's poster (Abstract #4763) on the BRD and the Biospecimen Evidence-Based Practices document series at the AACR Annual Meeting 2018 on 4/17.
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