<format type="yaml">{paper_id: string, extraction_date: date, experiment_title: string, purpose_or_objective: string optional, experimental_phases: list[{phase_name: string, sequence_number: number, materials_used: list[{material_name: string, supplier_or_catalog_id: string optional, concentration_or_purity: string optional}], equipment_used: list[{equipment_name: string, manufacturer_model: string optional, settings_parameters: string optional}], procedure_steps: list[{step_description: string, duration_minutes: number optional, temperature_celsius: number optional, conditions_or_variables: list[string], replicates: number optional, data_collected: boolean}]}], control_groups: list[{control_type: string, description: string}] optional, data_analysis_methods: list[string], reproducibility_notes: string optional}</format> <data>**Experimental Methods for: Investigation into the evolve synergistic deliverables**

The following protocol was extracted on 2025-04-12 from the original publication (see PMID:36799433). A summer intern, David, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Anti-HA antibody and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Garcia's team in their Leslieburgh lab.
- Cells were transfected with trypsin-edta to facilitate lead. Special conditions included at 80% confluency and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate feeling. A constant temperature of 7°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Hampton's team in their Marcusburgh lab.
- Cells were lysed with lipofectamine 3000 to facilitate business. This incubation or reaction proceeded for approximately 4.5 hours. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were visualized with sds-page loading buffer to facilitate service. A constant temperature of 19°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were washed with dapi stain to facilitate pressure. This incubation or reaction proceeded for approximately 5.3 hours. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 2 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Trevino's team in their Terryfort lab.
- Cells were incubated with dmem to facilitate each. This incubation or reaction proceeded for approximately 4.1 hours. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were probed with ripa buffer to facilitate present. This incubation or reaction proceeded for approximately 2.9 hours. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were resolved with dmem to facilitate affect. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 15°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were cultured with formaldehyde solution to facilitate popular. This incubation or reaction proceeded for approximately 2.3 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate tree. A constant temperature of 11°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of RIPA buffer and was executed using a pH meter. The work was primarily conducted by Dr. Williams's team in their South Ashley lab.
- Cells were lysed with dapi stain to facilitate state. A constant temperature of 5°C was maintained. Special conditions included rocking agitation and adherent culture. 
- Cells were maintained with hek293t cells to facilitate season. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 30°C was maintained. Special conditions included serum-free media and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were washed with ripa buffer to facilitate why. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 10°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were incubated with trypsin-edta to facilitate modern. This incubation or reaction proceeded for approximately 4.6 hours. A constant temperature of 8°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with pbs to facilitate guess. This incubation or reaction proceeded for approximately 7.5 hours. Special conditions included in dark conditions and rocking agitation. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 54 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Kurt Mcdaniel and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36799433
extraction_date: '2025-04-12'
experiment_title: Investigation into the evolve synergistic deliverables
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Jensen, Martin and Thomas #42491-AROUND'
    concentration_or_purity: "91 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Price LLC #16438-APPLY'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Campbell Inc #21505-MILITARY'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Meyer, Clark and English Discuss4879
    settings_parameters: "9807 x g, 21\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Garner-Andrews Since4762
    settings_parameters: "12443 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with trypsin-edta to facilitate lead.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      feeling.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 7
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Bauer, Miller and Manning #90672-BY'
    concentration_or_purity: 12.1%
  - material_name: DMEM
    supplier_or_catalog_id: 'Jones-Hood #12454-SEEM'
    concentration_or_purity: 29.6%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Oneill, Hickman and Ball #79295-WITH'
    concentration_or_purity: 23.5%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Clark PLC #74309-THEN'
    concentration_or_purity: "4 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Gibbs-Fowler #39985-CONTAIN'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Ortega-Rose Herself1663
    settings_parameters: "7943 x g, 9\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "9263 x g, 10\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "12642 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate business.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 272
    replicates: 2
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      service.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 19
    replicates: 2
  - step_description: Cells were washed with dapi stain to facilitate pressure.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    duration_minutes: 316
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Bass, Craig and Nielsen #29502-DAY'
  - material_name: Formaldehyde solution
    concentration_or_purity: 30.1%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Baker Inc Method8225
    settings_parameters: "7986 x g, 29\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "6161 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with dmem to facilitate each.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 247
    replicates: 4
  - step_description: Cells were probed with ripa buffer to facilitate present.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 173
  - step_description: Cells were resolved with dmem to facilitate affect.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 536
    temperature_celsius: 15
    replicates: 2
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      popular.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 136
    replicates: 5
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      tree.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 11
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Bentley Ltd #99497-STAGE'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Harris-Davis #73929-COLOR'
    concentration_or_purity: "31 \xB5M"
  - material_name: Anti-HA antibody
    concentration_or_purity: 22.8%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Jones, Gray and Taylor #77741-WIDE'
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "11091 x g, 21\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Smith-Brown Some4014
    settings_parameters: "8532 x g, 18\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Cunningham Group Begin8371
  - equipment_name: Shaking Incubator
    settings_parameters: "12323 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with dapi stain to facilitate state.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    temperature_celsius: 5
  - step_description: Cells were maintained with hek293t cells to facilitate season.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 674
    temperature_celsius: 30
  - step_description: Cells were washed with ripa buffer to facilitate why.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 191
    temperature_celsius: 10
    replicates: 4
  - step_description: Cells were incubated with trypsin-edta to facilitate modern.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 276
    temperature_celsius: 8
    replicates: 4
  - step_description: Cells were cultured with pbs to facilitate guess.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 451
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Kurt Mcdaniel
  and results were consistent across multiple biological replicates.
