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16 protocols using cryotube vials

1

X-Ray Scaffold Irradiation Protocol

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Dry scaffolds are placed in CryoTube™ vials (Thermo Scientific, UK), and placed in the centre of the X-Ray chamber (0.5 mm Cu filter, 220 kV, 14 mA, Pantak PMC1000). Each scaffold is irradiated at a dose of 417 cGy/min for 18 minutes.
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2

PBMC Isolation and Cryopreservation Protocol

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Whole blood was collected from 8 subjects (SA = 5; HC = 3) into BD Vacutainer® Sodium Heparin Tubes (BD Biosciences, Franklin Lakes, NJ). PBMCs were isolated using Lymphoprep and SepMate™-15(IVD) (STEMCELL Technologies, Vancouver, Canada) according to the manufacturer’s protocol. Isolated PBMCs were aliquoted and stored in cryotube vials (Thermo Scientific, Waltham, MA) with freezing medium (80% FBS, 20% DMSO) at a concentration of 5 × 106 cells/mL. Cells were stored overnight in Nalgene™ Cryo 1 °C Freezing Container (Thermo Fisher, Rochester, NY) at − 80 °C, then transferred into liquid nitrogen for long-term storage. Figure 1 (created with Biorender.com) summarizes the study’s experimental and analytical workflow.
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3

Serum and Brain Collection in Mice

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Mice were euthanized with carbon dioxide and tissue was harvested on the day after the last behavioral test (day 31, after 29 days of arbaclofen treatment). Serum harvesting was performed 1 hour after lights-on and brain harvesting was performed 2 hours after lights-on, on the same day. Following isoflurane anesthesia, retro-orbitral blood (200 microliters) was collected in a Microvette 500 K3E (Sarstedt, Numbrecht, Germany). Serum was transferred to CryoTube Vials (1.8ML, Thermo Fisher, Illkirch, France) for storage at −80 °C. Brains were extracted, rinsed with saline, and bisected sagittally. Half of each brain was placed in a 15 mL conical vial and flash frozen to −80 °C.
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4

Whole Blood Collection and Plasma Isolation

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Human whole blood from healthy volunteers was collected in 4.5 mL cryotubes (Cryo Tube™ Vials; Thermo Scientific, Waltham, MA) containing lepirudin (50 mg/mL), a specific thrombin inhibitor (Refludan; Celgene, Uxbridge, UK), as an anticoagulant. Plasma was isolated by whole blood centrifugation at 3000 x g for 15 minutes, and a normal human plasma pool (NHP) was created by pooling plasma from six donors. All samples were stored at -80°C. To prepare platelet-rich plasma (PRP), whole blood was centrifuged at room temperature, 22°C at 180 x g for 10 minutes. PRP was immediately used in the respective applications.
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5

Isolation and Cryopreservation of PBMCs

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Venous blood samples (10–30 mL) were collected in heparinized tubes (BD Vacutainer LH 170 U.I.). On the same day, blood was processed in a biosafety level 2 laboratory at Gustave Roussy Institute, Villejuif, France, or in IHU Méditerranée Infection, Marseille, France. PBMCs were freshly isolated by the lymphocyte separation medium (Eurobio Scientific) density gradient centrifugation according to the manufacturer's instructions (Leucosep tubes, Greiner; Biocoll, Bio&SELL). PBMCs were then collected, washed once with phosphate-buffered saline solution (PBS), and aliquoted in 1 mL of cryopreservation medium (CryoStor, STEMCELLS Technologies) in cryovials (two cryovials per patient). Cryovials (Cryotube vials, Thermo Fisher Scientific) were conserved for 24 hours at −80°C in a cryo-freezing container (Mr. Frosty, Thermo Fisher Scientific) before storage in liquid nitrogen.
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6

Cryopreservation of Human PBMCs

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Blood samples were collected in heparinized tubes, BD Vacutainer LH 170 U.I., from Dutscher (cat. #367526), diluted in PBS 1× purchased from Eurobio Scientific (cat. #CS3PBS01-01) and transferred in Leucosep–50 mL purchased from Greiner Bio-One (cat. #227290). Blood was centrifuged using MF48-R centrifuge from AWEL Industries (cat. #20023001). PBMCs were collected in a centrifuge tube, 50 mL, TPP from Dutscher (cat. #91050), washed with PBS 1×, resuspended in CryoStor CS10 purchased from STEMCELL Technologies (cat. #5100-0001), and transferred in CryoTube vials from Thermo Fisher Scientific (cat. #377267). Samples were finally conserved for 24 hours at −80°C in a cryo-freezing container (Mr. Frosty, Thermo Fisher Scientific) before storage in liquid nitrogen.
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7

Sickle Cell Disease Plasma Collection

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Patients with sickle cell disease were recruited at Children’s Healthcare of Atlanta, Georgia, USA, under a local IRB-approved study. Ethylenediaminetetraacetic acid (EDTA)-plasma samples were collected at two time points; hospital admission for acute vasoocclusive pain crisis (VOC) and during their baseline outpatient clinic at least four weeks later. Whole blood was collected from healthy donors (n = 20) in 4.5 mL cryotubes (Cryo Tube™ Vials; Thermo Scientific, Waltham, MA) containing thrombin inhibitor, lepirudin (Refludan; Celgene, Uxbridge, UK) at a final concentration of 50 μg/mL. Whole blood was centrifuged at 3000 x g for 15 minutes to collect plasma. A human plasma pool (NHP) was created by pooling plasma from six healthy donors. All plasma samples were stored at -80°C.
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8

Liver Metabolite Profiling by NMR

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Mice in the RT and no-RT groups (n = 6 each) were anesthetized as described above before undergoing portal vein perfusion. Samples were removed bilaterally from the liver parenchyma and stored (100 µg each) at −80 °C in CryoTube™ vials (1.8 mL; Thermo Fisher Scientific, Waltham, MA, USA). Aqueous extracts were resuspended in a buffer (650 µL) containing 0.008% trisodium phosphate, 7.5 mM Na2HPO4, 0.2 mM NaN3, and 92% D2O. After centrifugation at 4 °C for 5 min, sample supernatants (600 µL) were withdrawn in SampleJet NMR tubes (Bruker, Billerica, MA, USA).
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9

HLA Typing of Ugandan Samples

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EDTA buffy coats containing one to three million cells per sample in 1.8 ml CryoTube vials (Thermo Fisher Scientific, Roskilde, Denmark) were shipped from Uganda to USA on dry ice and stored in a −80ºC freezer. DNA was prepared using the QIAamp DNA Blood Midi Kit (Qiagen Sciences Inc, Germantown, MD, USA) following manufacture’s protocols. HLA typing was performed using Roche 454/Fluidigm HLA Typing Kits following the Roche protocols [15 (link)]. Briefly locus-specific primers were used to amplify 14 polymorphic exons of HLA-A, B, C, DPB1, DQA1, DQB1 and DRB genes with Fluidigm Access Array (Fluidigm Singapore PTE Ltd, Singapore). The 14 Fluidigm PCR amplicons were pooled and subjected to sequencing on a 454 FLX Genome Sequencer (454 Life Sciences Corporation, Branford, CT, USA). HLA alleles and genotypes were called using the Conexio ATF 454 HLA typing software (Conexio Genomics Inc, Perth, Australia).
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10

Bile Flow Measurement in Mice

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The common bile duct was cannulated and the bile flow rate was measured in live three to four month-old, male and female, WT and YAP1 KO mice. The bile duct was cannulated with a microfil tubing according to previously described techniques. (Plaa and Becker, 1965; Tonsberg et al., 2010) In brief, mice were anesthetized with Avertin 0.5 mg/g intraperitoneally (IP). The common bile duct was incised with a pair of fine iridectomy scissors about 6 mm below the hilum of the liver. A microfil tube (WPI, Sarasota, FL, MF28G-5) was passed through the incision and propelled towards the hilum for a distance of about 3 mm. Bile flow rate was recorded (µl/min/100g body weight) and bile was collected in CryoTube vials (Thermo Fisher Scientific) and immediately placed in liquid nitrogen. Animal work described in this manuscript has been approved and conducted under the oversight of the University of Pittsburgh Institutional Animal Care and Use Committee.
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