The Biospecimen Research Database

Welcome to the Biospecimen Research Database (BRD)!

Article Curations on COVID-19 and SARS-CoV-2

SOPs on COVID-19 and SARS-CoV-2

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 biospecimens@mail.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).

Featured Paper

Small RNA-sequencing for Analysis of Circulating miRNAs: Benchmark Study.

Author(s): Androvic P, Benesova S, Rohlova E, Kubista M, Valihrach L

Publication: J Mol Diagn, 2022, Vol. , Page

PubMed

1 study(s)

This study assessed the potential bias introduced by small RNA sequencing library preparation methods by comparing the next generation sequencing results of the miRXplore universal reference with pooled plasma using 8 different library preparation methods. K₂EDTA blood was collected from three healthy volunteers and plasma was separated by centrifugation at 1500 g for 15 min followed by 3000 g for 15 min, within 30 min of collection. Plasma was stored at -80°C until RNA extraction. RNA was extracted from pooled plasma aliquots using the miRNeasy Serum/Plasma Advanced Kit and evaluated using a real-time PCR panel. Sequencing libraries were prepared in duplicate from RNA extracted from plasma pools and the miRXplore Universal Reference using Norgen, Lexogen, QIAseq (with and without deduplication), NEXTflex, RealSeq, SMARTer, and EdgeSeq. Library yield was quantified by Qubit and fragment size was analyzed by an Agilent Fragment analyzer. Pooled libraries generated with each protocol were separated on a 5% TBE-PAGE on a Mini-PROTEAN tetra cell and fragments of 140-160 nt were cut out and purified with SPRIselect reagent. All libraries were sequenced on a NextSeq 500 high-output machine. EdgeSeq libraries were sequenced on a TATAA Biocenter machine. To verify sequencing results, 35 selected miRNAs were quantified in plasma by real-time PCR..