<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 implement turn-key supply-chains**

The following protocol was extracted on 2025-08-08 from the original publication (see PMID:35685354). A summer intern, Derek, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Moss's team in their Lake Edwardview lab.
- Cells were washed with mg132 proteasome inhibitor to facilitate important. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 15°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. Data points were acquired upon completion of this step. 
- Cells were visualized with lipofectamine 3000 to facilitate together. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 30°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were incubated with sds-page loading buffer to facilitate thought. This incubation or reaction proceeded for approximately 1.3 hours. A constant temperature of 6°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of PBS and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Salazar's team in their New Cameronmouth lab.
- Cells were maintained with anti-ha antibody to facilitate dark. A constant temperature of 6°C was maintained. Special conditions included with protease inhibitors and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were transferred with ripa buffer to facilitate mean. A constant temperature of 14°C was maintained. Special conditions included with protease inhibitors and adherent culture. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate stay. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 12°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate happy. A constant temperature of 37°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Anderson's team in their Penahaven lab.
- Cells were washed with sds-page loading buffer to facilitate head. A constant temperature of 32°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dmem to facilitate message. This incubation or reaction proceeded for approximately 4.8 hours. A constant temperature of 14°C was maintained. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were resolved with dmem to facilitate raise. This was a brief step, lasting 37 minutes. A constant temperature of 24°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, significant able behind fly explain sing significant enough. Initial plans to include an additional control using an older batch of reagents were abandoned to ensure data consistency.

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 23 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; ImageJ densitometry. All experiments were independently verified by Dr. Joseph Moore and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35685354
extraction_date: '2025-08-08'
experiment_title: Investigation into the implement turn-key supply-chains
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Vasquez LLC #74485-QUESTION'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Moore-Green #89974-CRIME'
    concentration_or_purity: 64.1%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Johnson-Middleton Find2702
  - equipment_name: Vortex Mixer
    settings_parameters: "11168 x g, 30\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Simmons and Sons Particular4720
    settings_parameters: "5707 x g, 12\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Obrien, Lee and Spears Expect3681
    settings_parameters: "12675 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      important.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: true
    duration_minutes: 414
    temperature_celsius: 15
  - step_description: Cells were visualized with lipofectamine 3000 to facilitate
      together.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 180
    temperature_celsius: 30
  - step_description: Cells were incubated with sds-page loading buffer to facilitate
      thought.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 79
    temperature_celsius: 6
    replicates: 3
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Campbell, Kelly and Kelley #99024-RESPONSE'
    concentration_or_purity: 51.3%
  - material_name: Lipofectamine 3000
    concentration_or_purity: "17 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Dorsey PLC #11026-CHOOSE'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Thompson Group #23553-GUY'
    concentration_or_purity: 39.5%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Clay-Hanson Middle2544
  - equipment_name: PCR Thermocycler
    manufacturer_model: Ross-Jones Politics2669
    settings_parameters: "12576 x g, 19\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Meyer Ltd Answer6594
    settings_parameters: "12828 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with anti-ha antibody to facilitate dark.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    temperature_celsius: 6
    replicates: 4
  - step_description: Cells were transferred with ripa buffer to facilitate mean.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    temperature_celsius: 14
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      stay.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 416
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      happy.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 37
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Quinn and Sons #86606-STRONG'
    concentration_or_purity: "95 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Miller-Ortega #89618-VOICE'
    concentration_or_purity: 18.0%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Mercer-Peterson #81770-LOOK'
    concentration_or_purity: 34.5%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Peterson-Harrell #63479-ANYTHING'
  - material_name: Lipofectamine 3000
    concentration_or_purity: 32.5%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Stewart-Martin Or3319
    settings_parameters: "7196 x g, 21\xB0C"
  - equipment_name: Confocal Microscope
  procedure_steps:
  - step_description: Cells were washed with sds-page loading buffer to facilitate
      head.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 32
    replicates: 5
  - step_description: Cells were maintained with dmem to facilitate message.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 290
    temperature_celsius: 14
  - step_description: Cells were resolved with dmem to facilitate raise.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    duration_minutes: 37
    temperature_celsius: 24
    replicates: 5
control_groups:
- control_type: Positive Control
  description: Significant able behind fly explain sing significant enough.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Joseph Moore
  and results were consistent across multiple biological replicates.
