Welcome to the Biospecimen Research Database (BRD)!
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, storage temperature, thawing method, and sampling location on microbiome and metabolome profiles of fecal specimens. Stool specimens were collected in a prepared sterile enamel tray from three healthy 34-month-old study participants in their home. Specimens were divided equally along the longitudinal axis. To evaluate the effects of storage and thawing conditions, half was homogenized immediately and four aliquots were collected for each preservation/storage method (two 200-mg aliquots for microbiome analysis and two 100-mg aliquots for metabolomics analysis). Aliquots were preserved using seven different methods: snap-freezing in liquid nitrogen for 52 h (control); freezing in a common household freezer (-16°C) for 48 h; freezing in RNALater in a household freezer (-16°C) for 48 h; storage at room temperature for 52 h (48 h plus 4 h) with or without RNALater. To investigate the effects of thawing method, specimens stored in household freezer with or without RNA later for 48 h were thawed at room temperature for 4 h either gradually (on ice) or fast (no ice). To investigate differences between sampling regions, the other half of each stool specimen was separated into three equal sections according to the order of defecation (head, body, and tail) and four aliquots (two 200-mg aliquots for microbiome analysis and two 100-mg aliquots for metabolomics analysis) were collected from the surface, core, and a combination of surface and core. DNA was extracted from all specimens using the Qiagen Stool Minikit according to the manufacturer’s instructions. PCR amplification of the bacterial hypervariable V3 region of the 16S rRNA gene was performed. Sequencing libraries were generated using the Illumina TruSeq DNA PCR-Free Library Preparation Kit and the library was sequenced on an Illumina HiSeq platform. For metabolite analysis, specimens were homogenized by vortexing for 15 sec and centrifuged at 14,000 x g for 15 min. Supernatants were filtered through a 22 µm membrane, dried, reconstituted in deionized water, and then analyzed by ultrahigh performance liquid chromatography coupled to tandem mass spectrometry (UHPLC-MS/MS).
|Technology Platform||Analyte||HPLC-MS||Small molecule||Next generation sequencing||DNA|
Two new compendiums of SOPs related to snap-freezing tissue specimens are now available:
For SOPs that specify dry ice CLICK HERE.
For SOPs that specify liquid nitrogen CLICK HERE.
The NCI BEBP document for snap-freezing tissue can be found at HERE.
CLICK HERE to view the ISBER 2020 electronic poster on the BRD.
View other's electronic posters on the ISBER 2020 main page HERE.