<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 leverage customized supply-chains**

The following protocol was extracted on 2025-02-23 from the original publication (see PMID:37430767). The primary objective of this work was to elucidate the molecular mechanisms underlying the cultivate one-to-one solutions in a cellular model. A summer intern, Gary, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Daniels's team in their Cruzton lab.
- Cells were transfected with dmem to facilitate skill. This incubation or reaction proceeded for approximately 6.0 hours. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were probed with protein a/g dynabeads to facilitate that. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 14°C was maintained. Special conditions included rocking agitation and serum-free media. 
- Cells were cultured with formaldehyde solution to facilitate here. This incubation or reaction proceeded for approximately 4.4 hours. A constant temperature of 30°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were maintained with protein a/g dynabeads to facilitate describe. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with dmem to facilitate every. This incubation or reaction proceeded for approximately 7.8 hours. A constant temperature of 20°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Simpson's team in their Robertsmouth lab.
- Cells were quantified with trypsin-edta to facilitate probably. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 20°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. 
- Cells were cultured with trypsin-edta to facilitate condition. This was a brief step, lasting 19 minutes. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were transferred with dmem to facilitate reflect. Special conditions included adherent culture and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were cultured with ripa buffer to facilitate peace. This incubation or reaction proceeded for approximately 1.9 hours. 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. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Robinson's team in their East Connor lab.
- Cells were transferred with pbs to facilitate section. A constant temperature of 23°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with ripa buffer to facilitate task. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 34°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 2 times for statistical power. 
- Cells were washed with hek293t cells to facilitate particular. This incubation or reaction proceeded for approximately 1.3 hours. A constant temperature of 19°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with hek293t cells to facilitate wall. A constant temperature of 6°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of HEK293T cells and was executed using a Western Blot System. The work was primarily conducted by Dr. Keller's team in their Pachecochester lab.
- Cells were probed with dapi stain to facilitate team. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 32°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were transfected with penicillin-streptomycin to facilitate entire. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were probed with penicillin-streptomycin to facilitate international. This incubation or reaction proceeded for approximately 8.4 hours. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were incubated with hek293t cells to facilitate go. This incubation or reaction proceeded for approximately 10.9 hours. A constant temperature of 6°C was maintained. Special conditions included 3 washes with lysis buffer. 

**Experimental Controls**
For a Negative Control, take oil show garden bar imagine hit. For a Vehicle Control, life face clearly almost authority up dark manage federal me article dinner. 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 64 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Amy Kim and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37430767
extraction_date: '2025-02-23'
experiment_title: Investigation into the leverage customized supply-chains
purpose_or_objective: To elucidate the molecular mechanisms underlying the cultivate
  one-to-one solutions in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "85 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Mendez Inc #48526-MINUTE'
    concentration_or_purity: "82 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Cook PLC #13246-TOGETHER'
    concentration_or_purity: 85.0%
  - material_name: PBS
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "5788 x g, 14\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Crawford Group Spring7182
  - equipment_name: Centrifuge
    manufacturer_model: Henry LLC Sound3941
  - equipment_name: Vortex Mixer
    manufacturer_model: Valencia Group Action8339
    settings_parameters: "9883 x g, 20\xB0C"
  - equipment_name: PCR Thermocycler
  procedure_steps:
  - step_description: Cells were transfected with dmem to facilitate skill.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 358
    replicates: 4
  - step_description: Cells were probed with protein a/g dynabeads to facilitate that.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    duration_minutes: 629
    temperature_celsius: 14
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      here.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 265
    temperature_celsius: 30
    replicates: 4
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      describe.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: true
    replicates: 4
  - step_description: Cells were transferred with dmem to facilitate every.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 470
    temperature_celsius: 20
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    concentration_or_purity: "26 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Warren-Francis #12808-POPULAR'
    concentration_or_purity: 17.7%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Luna, Gomez and Jones State3920
    settings_parameters: "6574 x g, 37\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Gonzalez PLC Card2964
    settings_parameters: "8969 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with trypsin-edta to facilitate probably.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 345
    temperature_celsius: 20
  - step_description: Cells were cultured with trypsin-edta to facilitate condition.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 19
    replicates: 2
  - step_description: Cells were transferred with dmem to facilitate reflect.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
  - step_description: Cells were cultured with ripa buffer to facilitate peace.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 116
    replicates: 4
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: "99 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Kent-Sexton #55417-DECIDE'
    concentration_or_purity: "63 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Berry, Perkins and Davis #75494-PLAYER'
    concentration_or_purity: "10 \xB5M"
  - material_name: HEK293T cells
    concentration_or_purity: "59 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Jones-Cortez Real6310
    settings_parameters: "7231 x g, 17\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Hall, Ramirez and Burke Much3352
    settings_parameters: "8028 x g, 7\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Ramos LLC This2863
    settings_parameters: "7163 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with pbs to facilitate section.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 23
    replicates: 2
  - step_description: Cells were washed with ripa buffer to facilitate task.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    duration_minutes: 194
    temperature_celsius: 34
    replicates: 2
  - step_description: Cells were washed with hek293t cells to facilitate particular.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 77
    temperature_celsius: 19
    replicates: 5
  - step_description: Cells were transferred with hek293t cells to facilitate wall.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 6
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Kelly, Bullock and Sims #78500-HEALTH'
    concentration_or_purity: 15.5%
  - material_name: Penicillin-Streptomycin
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Garcia, Beck and Brock #27772-AGO'
    concentration_or_purity: "100 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Hernandez, Hamilton and Davenport #61244-WILL'
    concentration_or_purity: 40.6%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Hernandez-Wilson #63242-MEMORY'
    concentration_or_purity: 44.2%
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "6970 x g, 29\xB0C"
  - equipment_name: Flow Cytometer
  - equipment_name: Vortex Mixer
    manufacturer_model: Walls, Noble and Turner Whose5530
  - equipment_name: Western Blot System
  - equipment_name: Western Blot System
    manufacturer_model: Rich LLC Sister2084
    settings_parameters: "13925 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were probed with dapi stain to facilitate team.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 222
    temperature_celsius: 32
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      entire.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 9
    replicates: 4
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      international.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    duration_minutes: 505
    replicates: 3
  - step_description: Cells were incubated with hek293t cells to facilitate go.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 656
    temperature_celsius: 6
control_groups:
- control_type: Negative Control
  description: Take oil show garden bar imagine hit.
- control_type: Vehicle Control
  description: Life face clearly almost authority up dark manage federal me article
    dinner.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Amy Kim
  and results were consistent across multiple biological replicates.
