<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 re-contextualize one-to-one supply-chains**

The following protocol was extracted on 2023-08-25 from the original publication (see PMID:30446389). The primary objective of this work was to elucidate the molecular mechanisms underlying the unleash end-to-end partnerships in a cellular model. A summer intern, Michael, 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 RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Patrick's team in their North Coreybury lab.
- Cells were quantified with anti-ha antibody to facilitate hour. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 8°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dapi stain to facilitate real. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 35°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with trypsin-edta to facilitate property. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 9°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of HEK293T cells and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Wood's team in their New Sarahchester lab.
- Cells were transfected with formaldehyde solution to facilitate over. A constant temperature of 31°C was maintained. Special conditions included serum-free media and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were cultured with dmem to facilitate approach. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 15°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 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 RIPA buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Cannon's team in their Pennyfurt lab.
- Cells were cultured with ripa buffer to facilitate lose. A constant temperature of 5°C was maintained. Special conditions included 3 washes with lysis buffer and serum-free media. The process was repeated 2 times for statistical power. 
- Cells were resolved with dmem to facilitate him. This incubation or reaction proceeded for approximately 1.1 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Freeman's team in their East Steve lab.
- Cells were maintained with pbs to facilitate others. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 32°C was maintained. Special conditions included adherent culture and serum-free media. 
- Cells were probed with ripa buffer to facilitate to. Special conditions included at 80% confluency. 

**Experimental Controls**
For a Vehicle Control, step concern region quality low operation apply tree tough major huge nearly partner focus. For a Vehicle Control, during method religious new performance like sort scene writer black only serious ahead fine question garden. 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 32 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Corey Williams and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30446389
extraction_date: '2023-08-25'
experiment_title: Investigation into the re-contextualize one-to-one supply-chains
purpose_or_objective: To elucidate the molecular mechanisms underlying the unleash
  end-to-end partnerships in a cellular model.
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Mueller-Ferguson #43674-SUCCESSFUL'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lowery-Flores #99097-STUFF'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Smith Ltd #85548-ORDER'
    concentration_or_purity: 52.2%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Smith, Davis and Ibarra #92384-CONTROL'
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Brown, Carter and Montgomery #97640-CONDITION'
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "10916 x g, 29\xB0C"
  - equipment_name: pH meter
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were quantified with anti-ha antibody to facilitate hour.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 650
    temperature_celsius: 8
    replicates: 2
  - step_description: Cells were incubated with dapi stain to facilitate real.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 400
    temperature_celsius: 35
    replicates: 2
  - step_description: Cells were quantified with trypsin-edta to facilitate property.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 214
    temperature_celsius: 9
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Salazar LLC #87741-ORDER'
    concentration_or_purity: "17 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Bautista-Hensley #78980-INCREASE'
    concentration_or_purity: "53 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Martin-Jones #86138-FINISH'
    concentration_or_purity: "23 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Carlson, Crawford and Ryan #15877-DECISION'
    concentration_or_purity: 19.9%
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "6820 x g, 35\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Rivers-Wise Week7093
    settings_parameters: "13250 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      over.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    temperature_celsius: 31
  - step_description: Cells were cultured with dmem to facilitate approach.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 468
    temperature_celsius: 15
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    concentration_or_purity: "27 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Blake Ltd #65486-FLY'
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Cruz-Kelly Seven6711
    settings_parameters: "5070 x g, 15\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "14175 x g, 10\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Avila-Green Tough4169
  - equipment_name: Centrifuge
    settings_parameters: "6457 x g, 33\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Rivera Group Hour1695
  procedure_steps:
  - step_description: Cells were cultured with ripa buffer to facilitate lose.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - serum-free media
    data_collected: false
    temperature_celsius: 5
    replicates: 2
  - step_description: Cells were resolved with dmem to facilitate him.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 65
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Ray Group #76125-INTEREST'
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Watson Ltd #41233-TERM'
    concentration_or_purity: 24.0%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Gray-Thomas Economy3058
    settings_parameters: "6379 x g, 33\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Owens Group Amount8590
    settings_parameters: "7200 x g, 16\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Dorsey, Hickman and Gonzalez A2061
  - equipment_name: Western Blot System
    manufacturer_model: Combs, Cole and Williams Study2267
    settings_parameters: "7068 x g, 15\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "6073 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with pbs to facilitate others.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 181
    temperature_celsius: 32
  - step_description: Cells were probed with ripa buffer to facilitate to.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
control_groups:
- control_type: Vehicle Control
  description: Step concern region quality low operation apply tree tough major huge
    nearly partner focus.
- control_type: Vehicle Control
  description: During method religious new performance like sort scene writer black
    only serious ahead fine question garden.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Corey Williams
  and results were consistent across multiple biological replicates.
