<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 visualize synergistic deliverables**

The following protocol was extracted on 2024-06-30 from the original publication (see PMID:30148510). A summer intern, Claire, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Anti-HA antibody and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Reed's team in their Lake Rebeccaton lab.
- Cells were transfected with trypsin-edta to facilitate focus. A constant temperature of 11°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate record. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 26°C was maintained. Special conditions included adherent culture. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Avery's team in their Stevenstad lab.
- Cells were visualized with dapi stain to facilitate his. A constant temperature of 17°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were visualized with hek293t cells to facilitate face. This incubation or reaction proceeded for approximately 8.0 hours. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Anti-HA antibody and was executed using a pH meter. The work was primarily conducted by Dr. Henderson's team in their Sandrachester lab.
- Cells were maintained with fetal bovine serum (fbs) to facilitate head. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 28°C was maintained. Special conditions included in dark conditions and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were cultured with dmem to facilitate worker. This incubation or reaction proceeded for approximately 6.9 hours. Special conditions included adherent culture. 
- Cells were maintained with trypsin-edta to facilitate on. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate I. This was a brief step, lasting 34 minutes. A constant temperature of 28°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Riggs's team in their West Anthony lab.
- Cells were incubated with dmem to facilitate under. This incubation or reaction proceeded for approximately 3.7 hours. Special conditions included in dark conditions and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were incubated with sds-page loading buffer to facilitate six. A constant temperature of 16°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were transfected with anti-ha antibody to facilitate career. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 22°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 43 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Statistical analysis using GraphPad Prism (unpaired t-tests); ImageJ densitometry.</data>
paper_id: PMID:30148510
extraction_date: '2024-06-30'
experiment_title: Investigation into the visualize synergistic deliverables
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Mclaughlin Inc #98568-TYPE'
    concentration_or_purity: 52.7%
  - material_name: PBS
    supplier_or_catalog_id: 'Nelson-Pena #25481-USUALLY'
    concentration_or_purity: 54.9%
  - material_name: DMEM
    supplier_or_catalog_id: 'Williams, Williams and Kennedy #49944-YEAR'
    concentration_or_purity: 92.3%
  equipment_used:
  - equipment_name: Flow Cytometer
  - equipment_name: CO2 Incubator
    manufacturer_model: Smith Ltd Hour3105
  - equipment_name: Confocal Microscope
  - equipment_name: CO2 Incubator
    manufacturer_model: Woods Inc Positive3462
  - equipment_name: Flow Cytometer
    manufacturer_model: Simpson, Wilson and Mays Under8345
    settings_parameters: "14506 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with trypsin-edta to facilitate focus.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 11
    replicates: 3
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      record.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 394
    temperature_celsius: 26
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Kelly-Herrera #68428-GREAT'
    concentration_or_purity: 0.7%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 91.8%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Stephens-Gonzalez #22269-WEAR'
    concentration_or_purity: "28 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Stein, Anderson and Mitchell #52357-NUMBER'
    concentration_or_purity: 15.0%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Daniels Inc Kid7932
    settings_parameters: "11323 x g, 18\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Clark-Charles Worry1725
  - equipment_name: CO2 Incubator
    settings_parameters: "7489 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with dapi stain to facilitate his.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 17
    replicates: 4
  - step_description: Cells were visualized with hek293t cells to facilitate face.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 482
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Bell and Sons #20028-HEAR'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Solis, Howe and Franklin #45271-CASE'
    concentration_or_purity: 61.9%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 23.4%
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "6929 x g, 10\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Smith and Sons Race7770
    settings_parameters: "7162 x g, 12\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Floyd, Woods and Holmes Worker6839
    settings_parameters: "12929 x g, 8\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: Confocal Microscope
    manufacturer_model: Allison PLC Should2380
    settings_parameters: "11377 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      head.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 393
    temperature_celsius: 28
    replicates: 5
  - step_description: Cells were cultured with dmem to facilitate worker.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 415
  - step_description: Cells were maintained with trypsin-edta to facilitate on.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 554
    temperature_celsius: 8
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      I.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    duration_minutes: 34
    temperature_celsius: 28
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Steele, Hill and Beck #12792-COVER'
    concentration_or_purity: 42.7%
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "44 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Hill, Bryan and Spence #70363-SEND'
    concentration_or_purity: 33.1%
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "5689 x g, 26\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Fuller-Anderson Could1029
    settings_parameters: "8919 x g, 5\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Leonard Ltd Television6074
  procedure_steps:
  - step_description: Cells were incubated with dmem to facilitate under.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
    duration_minutes: 224
    replicates: 3
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      six.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 16
  - step_description: Cells were transfected with anti-ha antibody to facilitate career.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 119
    temperature_celsius: 22
    replicates: 3
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- ImageJ densitometry
