The BioSpecimen Processing Lab (BSPL) provides a suite of biospecimen services to support clinical, translational, and basic life sciences research:
Biospecimen Acquisiton
Our team is specially trained in obtaining tissue and fluids in coordination with clinical procedures. We work with the clinical teams to develop procedures that permit research specimen collection while not impacting clinical sample evaluation.
Biopsy Collection - To ensure study requirements are communicated and high qualtity tissue is procured, a Research Associate attends biopsy procedures to receive tissue samples directly from the clinician and promptly preserve samples per study requirements.
Surgical Collection - Our team of Pathologists' Assistants are trained to perform complex tissue dissection in accordance with pathology departmental guidelines while prioritizing patient diagnostic safety. Specimens are retreived from surgical suites, rapidly dissected and fresh, frozen and fixed tissue procured per study requirements.
Available preparation methods:
Fresh tissue in media
Snap frozen, frozen in OCT, viable cryopreservation
Frozen tissue sectioning
Formalin-fixed tissue processed into FFPE blocks
Slide sectioning and staining
Biofluid Processing
Samples can be processed via one of our validated standard operating procedures, or according to specialized methods or sponsor requirements.
Separation of whole blood into serum, plasma, buffy coat
PBMC isolation and preservation
Centrifugation, aliquoting and shipping of biofluids (urine, CSF, saliva, etc.)
Biospecimen Custodianship (Long-Term Storage)
Our Mt. Zion BSPL provides secure, round-the-clock monitored biospecimen storage and inventory mangement via a regulatory-complient online database.
Storage of blood, body fluids and tissue
Ambient, 4°C, -20°C -80°C, and liquid nitrogen sample storage
Controlled access, freezer alarms, back-up power and redundant temperature monitoring.
24/7 personnel coverage for off-hour freezer issues
Samples acquired and/or processed by the Biobank are 2D barcode labeled.
Inventory management through MBioLIMS, a web-based regulatory compliant database to track samples through collection, processing, storage and distribution.
BSP Lab Guidelines for Liquid Sample Processing:
Hours of operation (all campuses):
Please see below for hours of specific labs.
Last samples must be received by 4:00pm.
Samples with same-day shipments must be received by 1:30pm to meet outbound shipping cutoffs.
Samples with complex processing, such as PBMCs, whole blood stimulations, must be received by 2:30pm.
If same-day shipment samples are received past the cut-off time, samples will be shipped the next business day. Ambient samples are generally more time sensitive and require same-day shipment.
If your protocol has samples that will be collected past the same-day processing cut off time, please consult with your PI and/or sponsor for next steps. We can store samples overnight at ambient and refrigerated (4C) temperatures for processing the next day, but only with PI and/or sponsor approval.
Management
Aras Mattis, MD PhD - Director (aras.mattis@ucsf.edu)
Ron Honrada - Associate Director (ronald.honrada@ucsf.edu)
After-hours sample processing or Custom processing
Routine centrifugation of biofluids that occur after processing cut-offs or after business hours Monday through Friday. Must be coordinated at least two weeks in advance.
Inquire
After-hours surgical collection
Collection of surgical tissue after 5:30pm. Subject to BSP PA availability.
Inquire
Aliquoting Only
Transfer of unprocessed blood or body fluids into up to 10 storage tubes. No other processing.
Routine centrifugation of bio-fluids with aliquoting of supernate and cell pellet isolation (up to 10 aliquots). Additional processing steps or aliquoting in over 10 cryovials will be charged as an "Additional spin, wash, or preparation".
Inquire
Biopsy - Collection
A biobank technician attends biopsy procedure and coordinates with research staff and clinical staff to collect specified type and quantiy of material required for study. Tissue is collected and preserved in the procedure room to ensure viability. Does not include cost of supplies (Tissue Prep Kit) if not provided by the study team.
Inquire
Biopsy - Processing only
Overnight fixation and transfer of biopsy tissue to ethanol. Does not include acquisition of tissue. Tissue must be dropped off by study team to one of our processing lab locations.
Inquire
Blood Processing
Centrifugation of blood collection tubes to isolate serum, plasma or buffy coat. Pooled blood tubes are treated as a single specimen; each additional tube type or special processing step is subject to additional fee.
Inquire
Body Fluid Processing
Centrifuge, wash and pellet up to 1 L fluid. Isolate pellet and process to frozen or FFPE block.
Inquire
LN2 Long Term Inventory Management and Administration, Freezer storage
Long term sample storage and inventory managment services at the Mt Zion freezer farm billed per box. All samples are logged into online inventory managment to track storage location, current inventory and sample distribution. Vapor phase LN2 tank termperatures are monitored and recorded 24/7.
Rates are per storage unit per month:
2-3" standard freezer Box = 1 unit
4-5" tall freezer Box = 2 units
Inquire
PBMC Isolation (Up to 40mL)
Isolation of PBMC by one of the Biobank Laboratory standard protocols (up to 40mL of blood). Draw volumes beyond 40mL will be charged as two PBMC charges.
SepMate Isolation Method (Ficoll)
CPT Tube Processing
Inquire
RNA or DNA Extraction - Blood, Saliva, Tissue
The Biobank & Processing Core extracts DNA from formalin-fixed paraffin embedded (FFPE) tissue, frozen tissue blood and body fluids. Our protocols utilize commercially available kits and methods have been further optimized in house. DNA & RNA quantitation via Nanodrop. Sample preparation, specialty kits, small runs and custom methods are subject to additional fees.
Frozen Tissue: Genotyping and other DNA analyses using PCR or next-generation sequencing (NGS) require a suitable amount of high-quality genomic DNA as starting material. The most common bottleneck to obtaining high-quality DNA is tissue lysis. Fibrous or other hard-to-lyse tissues require lengthy and tedious protocols that often result in low yields of low-quality DNA. The QIAamp Fast DNA Tissue Kit overcomes this bottleneck by providing innovative disruption tubes that significantly improve yield and shorten the overall time to result.
Blood & Body Fluids: Fresh and frozen whole blood with common anticoagulants, such as citrate, EDTA, and heparin, may be processed. The QIAamp DNA Blood Mini Kit processes sample sizes of up to 200 µl. The typical yield from 200 µl healthy whole blood is 4–12 µg, with an elution volume of 50–200 µl. QIAamp DNA Blood technology yields genomic, mitochondrial, or viral DNA from blood and related body fluids ready to use in PCR and blotting procedures.
Fresh and frozen whole blood or buffy coat
Plasma or serum
Bone marrow
Lymphocytes
Platelets
Body fluids
Formalin Fixed Paraffin Embedded Tissue*: Artificial C>T mutations caused by cytosine deamination are critical in next-generation sequencing (NGS). These artifacts are caused by formalin fixation and aging, and result in sequencing errors. The GeneRead FFPE purification procedure also includes enzymatic removal of these artifacts, while ensuring high yields and purity, making it especially suitable for NGS applications.
PAXgene Blood DNA*: Purification of up to 500 µg genomic DNA from fresh or frozen whole blood collected. Used in conjunction with PAXgene DNA blood collection tubes.
PAXgene Blood RNA*: Purification of intracellular RNA from whole blood for applications in molecular diagnostic testing, such as real-time RT-PCR analysis of specific transcripts. Used in conjunction with PAXGene RNA blood collection tubes.
* Subject to specialty kit surcharge
Inquire
Send out only
Accessioning and preparation of sample for shipment or long-term storage. No other processing.
Inquire
Short Term Sample storage, freezer or refrigerator
Short term sample storage and inventory managment services in the processing laboratories billed per sample. All samples are logged into online inventory managment to track storage location, current inventory and sample distribution. Freezers undergo annual preventative maintenance and termperatures are monitored and recorded 24/7.
Inquire
Simple Surgical Collection
A BSP PA coordinates with the operating room team and surgical pathology department to collect simple specimens from surgical procedures that require no gross manipulation by the PA. The PA's are trained to determine fragments of tissue that are in excess of what is needed for pathology so that clinical evaluation of the specimens are not impacted. Tissue will be prepared for storage or downstream assays according to requestors specifications or via the Biobank protocols.
Inquire
Tissue Prep Kit
Add-on charge for surgical tissue and biopsy collections when BSP must provide tubes, media, OCT molds, etc.
Inquire
Urine Processing
Centrifugation of urine with aliquoting of supernate and cell pellet isolation. Up to 100mL and 10 aliquots.
Centrifugation of blood collection tubes to isolate serum, plasma or buffy coat. Pooled blood tubes are treated as a single specimen; each additional tube type or special processing step is subject to additional fee.
Inquire
Urine Processing
Centrifugation of urine with aliquoting of supernate and cell pellet isolation. Up to 100mL and 10 aliquots.
Inquire
Body Fluid Processing
Centrifuge, wash and pellet up to 1 L fluid. Isolate pellet and process to frozen or FFPE block.
Routine centrifugation of bio-fluids with aliquoting of supernate and cell pellet isolation (up to 10 aliquots). Additional processing steps or aliquoting in over 10 cryovials will be charged as an "Additional spin, wash, or preparation".
Inquire
PBMC Isolation (Up to 40mL)
Isolation of PBMC by one of the Biobank Laboratory standard protocols (up to 40mL of blood). Draw volumes beyond 40mL will be charged as two PBMC charges.
SepMate Isolation Method (Ficoll)
CPT Tube Processing
Inquire
Aliquoting Only
Transfer of unprocessed blood or body fluids into up to 10 storage tubes. No other processing.
Inquire
Send out only
Accessioning and preparation of sample for shipment or long-term storage. No other processing.
Inquire
After-hours sample processing or Custom processing
Routine centrifugation of biofluids that occur after processing cut-offs or after business hours Monday through Friday. Must be coordinated at least two weeks in advance.
Overnight fixation and transfer of biopsy tissue to ethanol. Does not include acquisition of tissue. Tissue must be dropped off by study team to one of our processing lab locations.
Inquire
Biopsy - Collection
A biobank technician attends biopsy procedure and coordinates with research staff and clinical staff to collect specified type and quantiy of material required for study. Tissue is collected and preserved in the procedure room to ensure viability. Does not include cost of supplies (Tissue Prep Kit) if not provided by the study team.
LN2 Long Term Inventory Management and Administration, Freezer storage
Long term sample storage and inventory managment services at the Mt Zion freezer farm billed per box. All samples are logged into online inventory managment to track storage location, current inventory and sample distribution. Vapor phase LN2 tank termperatures are monitored and recorded 24/7.
Rates are per storage unit per month:
2-3" standard freezer Box = 1 unit
4-5" tall freezer Box = 2 units
Inquire
Short Term Sample storage, freezer or refrigerator
Short term sample storage and inventory managment services in the processing laboratories billed per sample. All samples are logged into online inventory managment to track storage location, current inventory and sample distribution. Freezers undergo annual preventative maintenance and termperatures are monitored and recorded 24/7.
The Biobank & Processing Core extracts DNA from formalin-fixed paraffin embedded (FFPE) tissue, frozen tissue blood and body fluids. Our protocols utilize commercially available kits and methods have been further optimized in house. DNA & RNA quantitation via Nanodrop. Sample preparation, specialty kits, small runs and custom methods are subject to additional fees.
Frozen Tissue: Genotyping and other DNA analyses using PCR or next-generation sequencing (NGS) require a suitable amount of high-quality genomic DNA as starting material. The most common bottleneck to obtaining high-quality DNA is tissue lysis. Fibrous or other hard-to-lyse tissues require lengthy and tedious protocols that often result in low yields of low-quality DNA. The QIAamp Fast DNA Tissue Kit overcomes this bottleneck by providing innovative disruption tubes that significantly improve yield and shorten the overall time to result.
Blood & Body Fluids: Fresh and frozen whole blood with common anticoagulants, such as citrate, EDTA, and heparin, may be processed. The QIAamp DNA Blood Mini Kit processes sample sizes of up to 200 µl. The typical yield from 200 µl healthy whole blood is 4–12 µg, with an elution volume of 50–200 µl. QIAamp DNA Blood technology yields genomic, mitochondrial, or viral DNA from blood and related body fluids ready to use in PCR and blotting procedures.
Fresh and frozen whole blood or buffy coat
Plasma or serum
Bone marrow
Lymphocytes
Platelets
Body fluids
Formalin Fixed Paraffin Embedded Tissue*: Artificial C>T mutations caused by cytosine deamination are critical in next-generation sequencing (NGS). These artifacts are caused by formalin fixation and aging, and result in sequencing errors. The GeneRead FFPE purification procedure also includes enzymatic removal of these artifacts, while ensuring high yields and purity, making it especially suitable for NGS applications.
PAXgene Blood DNA*: Purification of up to 500 µg genomic DNA from fresh or frozen whole blood collected. Used in conjunction with PAXgene DNA blood collection tubes.
PAXgene Blood RNA*: Purification of intracellular RNA from whole blood for applications in molecular diagnostic testing, such as real-time RT-PCR analysis of specific transcripts. Used in conjunction with PAXGene RNA blood collection tubes.
A BSP PA coordinates with the operating room team and surgical pathology department to collect simple specimens from surgical procedures that require no gross manipulation by the PA. The PA's are trained to determine fragments of tissue that are in excess of what is needed for pathology so that clinical evaluation of the specimens are not impacted. Tissue will be prepared for storage or downstream assays according to requestors specifications or via the Biobank protocols.
Inquire
After-hours surgical collection
Collection of surgical tissue after 5:30pm. Subject to BSP PA availability.
Inquire
Tissue Prep Kit
Add-on charge for surgical tissue and biopsy collections when BSP must provide tubes, media, OCT molds, etc.
