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 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 firstname.lastname@example.org. 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).
The purpose of this study was to determine the effects of preservation method (PAXgene fixation, snap-frozen, or formalin fixation) on the extractability and analysis of phosphoproteins by Western blot, ELISA, and 2-dimentional SDS-PAGE. A total of 24 tissue specimens were used in this study including ovarian, breast, and prostate cancer specimens, a leiomyosarcoma, and non-malignant stomach, esophagus, colon, duodenum, uterus, ovary, prostate, bladder, breast, liver, spleen, gall bladder, pancreas, skin, muscle, tongue, salivary gland, lung, thyroid, and cystadenoma specimens. Each tissue was divided into equal parts and either snap-frozen in liquid nitrogen, fixed by PAXgene Tissue Fix, or fixed in formalin. PFPE specimens were transferred to PAXgene Stabilizer reagent and were then processed identically to FFPE specimens. Protein extraction was performed using the Qproteome FFPE Tissue Kit for all specimens, with modifications to the suggested protocol for PFPE and snap-frozen specimens, and different extraction buffers used for each ELISA kit.
|Technology Platform||Analyte||ELISA||Protein||Western blot||Protein||1D/2D gels||Protein||Colorimetric assay||Protein|
The purpose of this study was to determine the impacts of fixation time, stabilization time, storage temperature, and storage duration on protein yield and quality for PAXgene-fixed tissue specimens. A total of 18 malignant and non-malignant tissue specimens were used in this study including pancreas, colon, liver, stomach, spleen, muscle, kidney, duodenum, and breast specimens. Protein extraction was performed using the Qproteome FFPE Tissue Kit with modifications to the suggested protocol.
|Technology Platform||Analyte||Colorimetric assay||Protein||Western blot||Protein|
Look for a link to the BRD on the bottom of the PubMed abstract page, under "LinkOut-more resources".
The review appears in Cancer Research's OnlineFirst section, and both summarizes the challenges associated with molecular analysis of FFPE biospecimens as well as highlights analytical techniques and parameters that result in strong concordance with a fresh or frozen cohort.More...