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MB Sample ID: SA211443
| Local Sample ID: | Maryam_2nd-set_Urine_DC_Vaccine_D5_Post |
| Subject ID: | SU002294 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6J |
| Gender: | Not applicable |
| Animal Animal Supplier: | Jackson Labs (Bar Harbor, ME) |
| Animal Housing: | Housed in a temperature of 22 oC |
| Animal Light Cycle: | 12-hour light/12-hour dark |
| Animal Water: | free access to food and water (3-5 animals per cage). |
Select appropriate tab below to view additional metadata details:
Subject:
| Subject ID: | SU002294 |
| Subject Type: | Mammal |
| Subject Species: | Mus musculus |
| Taxonomy ID: | 10090 |
| Genotype Strain: | C57BL/6J |
| Gender: | Not applicable |
| Animal Animal Supplier: | Jackson Labs (Bar Harbor, ME) |
| Animal Housing: | Housed in a temperature of 22 oC |
| Animal Light Cycle: | 12-hour light/12-hour dark |
| Animal Water: | free access to food and water (3-5 animals per cage). |
Factors:
| Local Sample ID | MB Sample ID | Factor Level ID | Level Value | Factor Name |
|---|---|---|---|---|
| Maryam_2nd-set_Urine_DC_Vaccine_D5_Post | SA211443 | FL025791 | DC_Vaccine_Day 0 to 1 | Group |
Collection:
| Collection ID: | CO002287 |
| Collection Summary: | Intakt urine samples were collected from C57/Bl6 mice. Urine is collected from a clean surface after urination. |
| Sample Type: | Urine |
| Collection Method: | Each animal was in a separate chamber individually. The chamber bottom was covered with clean parafilm. Animals were kept in the chamber until urination. Urine drops were collected using sterile syringes. Samples were stored at -80 °C until further analysis. |
| Collection Location: | University of Florida, Neurosurgery Department, Medical college, University of Florida |
| Collection Frequency: | Post-vaccination day 1, day 8, day 12, day 16, and day 20 |
| Collection Duration: | ~30 minutes |
| Volumeoramount Collected: | ~100 uL |
| Storage Conditions: | -80℃ |
| Collection Vials: | cryovials |
| Storage Vials: | cryovials |
Treatment:
| Treatment ID: | TR002306 |
| Treatment Summary: | DC vaccine treatment Naïve C57/BL6 mice were used for tumor implantation. B16F10-OVA (2 × 104 cells/brain) tumor cell lines were injected intracranially. Antigen specific T cells (3 × 107 cells/50 µL of PBS) were infused into the animals intravenous (IV) five days after tumor implantation and the DC vaccine (1x106 cells/50 µL of PBS per animal) was injected intradermally on the same day. Both antigen-specific T cells and DC vaccine were administered once. Urine samples were collected after DC vaccination at several timepoints. Finally, animals were euthanized when they reached the endpoints. Sample collection Each animal was in a separate chamber individually. The chamber bottom was covered with clean parafilm. Animals were kept in the chamber until urination. Urine drops were collected using sterile syringes. Samples were stored at -80 °C until further analysis. Serum samples were collected from peripheral blood. |
| Animal Anesthesia: | isoflurane |
| Animal Fasting: | non-fasted |
| Animal Endp Euthanasia: | Euthanasia was carried out by thoracotomy followed by cervical dislocation. |
Sample Preparation:
| Sampleprep ID: | SP002300 |
| Sampleprep Summary: | No filtration was performed for urine samples. The urine samples were centrifuged at 4 oC, with 13.2 K rpm speed before mixing it with an internal reference and phosphate buffer system. |
| Sampleprep Protocol Filename: | DC_Vaccine_treated_NMR_urine_Procedures.docx |
| Processing Method: | None |
| Processing Storage Conditions: | -80℃ |
| Extraction Method: | None |
| Extract Storage: | -80℃ |
| Sample Resuspension: | In 500 microliter of 150 mM phosphate buffer (pH 7.2) with 2 mM EDTA, 0.5 mM DSS and 0.2% sodium azide for aqueous phase samples. |
| Sample Spiking: | 0.5 mM DSS for urine samples |
Analysis:
| MB Sample ID: | SA211443 |
| Analysis ID: | AN003611 |
| Laboratory Name: | McKnight Brain Institute |
| Analysis Type: | NMR |
| Acquisition Date: | 4/12/2018 |
| Acquisition Parameters File: | DC_Vaccine_treated_NMR_urine_Procedures.docx |
| Software Version: | Topspin |
| Operator Name: | Ram Khattri |
| Processing Parameters File: | DC_Vaccine_treated_NMR_urine_Procedures.docx |
| Detector Type: | Bruker 600 MHz |
| Data Format: | fid, 1r |
| Num Factors: | 10 |
| Num Metabolites: | 33 |
| Units: | mM |
NMR:
| NMR ID: | NM000244 |
| Analysis ID: | AN003611 |
| Instrument Name: | Bruker 600 MHz |
| Instrument Type: | FT-NMR |
| NMR Experiment Type: | 1D-1H |
| Field Frequency Lock: | Deuterium |
| Standard Concentration: | 0.5mM DSS |
| Spectrometer Frequency: | 600 MHz |
| NMR Probe: | Z44866_0026 (CP TXI 600S3 H-C/N-D-05 Z) |
| NMR Solvent: | Phosphate buffer (pH 7.2) + 2 mM EDTA + 0.5 mM DSS + 0.2% of sodium azide in deuterated environment |
| NMR Tube Size: | 5 mm O.D. |
| Shimming Method: | Topshim |
| Pulse Sequence: | noesypr1d |
| Water Suppression: | presat |
| Pulse Width: | 90-degree |
| Receiver Gain: | 101 |
| Offset Frequency: | 4.78 ppm |
| Chemical Shift Ref Cpd: | DSS |
| Temperature: | 298.2 oK |
| Number Of Scans: | 64 |
| Dummy Scans: | 8 |
| Acquisition Time: | 4s |
| Relaxation Delay: | 1s |
| Spectral Width: | 7142.9 Hz |
| Num Data Points Acquired: | 28572 |
| Real Data Points: | 65536 |
| Line Broadening: | 0.22 Hz |
| Zero Filling: | 65,536 points |
| Apodization: | Exponential |
| Baseline Correction Method: | Spline |
| Chemical Shift Ref Std: | 0 ppm for DSS |
