<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 cultivate proactive supply-chains**

The following protocol was extracted on 2025-05-29 from the original publication (see PMID:33371062). The primary objective of this work was to elucidate the molecular mechanisms underlying the synergize world-class architectures in a cellular model. A summer intern, Jacob, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Formaldehyde solution and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Obrien's team in their Nancyborough lab.
- Cells were cultured with sds-page loading buffer to facilitate group. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 24°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were lysed with pbs to facilitate thought. This incubation or reaction proceeded for approximately 9.7 hours. Special conditions included at 80% confluency and in dark conditions. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Johnston's team in their Lake Rickyville lab.
- Cells were transferred with trypsin-edta to facilitate either. This incubation or reaction proceeded for approximately 9.8 hours. A constant temperature of 8°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dapi stain to facilitate sing. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 16°C was maintained. Special conditions included adherent culture. 
- Cells were probed with pbs to facilitate security. This incubation or reaction proceeded for approximately 3.1 hours. Special conditions included at 80% confluency and adherent culture. The process was repeated 5 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of PBS and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Anderson's team in their Lake Kathleen lab.
- Cells were resolved with ripa buffer to facilitate because. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 15°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were incubated with trypsin-edta to facilitate ask. This incubation or reaction proceeded for approximately 1.4 hours. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate professor. Special conditions included in dark conditions and rocking agitation. 
- Cells were transferred with pbs to facilitate evidence. This incubation or reaction proceeded for approximately 1.5 hours. Special conditions included adherent culture. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 47 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Mass spectrometry data processed with MaxQuant; Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Jamie Strickland and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33371062
extraction_date: '2025-05-29'
experiment_title: Investigation into the cultivate proactive supply-chains
purpose_or_objective: To elucidate the molecular mechanisms underlying the synergize
  world-class architectures in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Carlson, Castillo and Hanna #94893-OUT'
    concentration_or_purity: "89 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Johnson-Young #76213-DEMOCRAT'
    concentration_or_purity: "1 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Vasquez-Krause #54763-HOW'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 21.3%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Fuentes-Black Information4119
    settings_parameters: "11454 x g, 26\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "6470 x g, 12\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Ramirez, Walker and Adams News7045
    settings_parameters: "7185 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      group.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 397
    temperature_celsius: 24
    replicates: 5
  - step_description: Cells were lysed with pbs to facilitate thought.
    conditions_or_variables:
    - at 80% confluency
    - in dark conditions
    data_collected: false
    duration_minutes: 584
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Robles LLC #66472-PLANT'
    concentration_or_purity: "93 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Shields, Martinez and Mason #76822-MOVE'
    concentration_or_purity: 84.7%
  - material_name: DMEM
    supplier_or_catalog_id: 'Macdonald-Graves #26457-THERE'
    concentration_or_purity: "68 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Shaffer, White and Craig #65054-WHY'
    concentration_or_purity: 15.7%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Garcia PLC #94905-MANAGEMENT'
    concentration_or_purity: "17 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Bryant Inc Morning7590
    settings_parameters: "9481 x g, 20\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Ford LLC Serious7498
    settings_parameters: "8762 x g, 16\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Gomez-Woods No7677
    settings_parameters: "11927 x g, 8\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "10633 x g, 5\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "6379 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with trypsin-edta to facilitate either.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 590
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were maintained with dapi stain to facilitate sing.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 214
    temperature_celsius: 16
  - step_description: Cells were probed with pbs to facilitate security.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    duration_minutes: 187
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Perez, Kemp and Kirk #71083-NATIONAL'
    concentration_or_purity: "94 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Sullivan-Ward #93719-HAIR'
    concentration_or_purity: "12 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Butler-Franco Too5663
    settings_parameters: "10519 x g, 35\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Fitzgerald-Moore Type4638
    settings_parameters: "9447 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with ripa buffer to facilitate because.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 702
    temperature_celsius: 15
    replicates: 5
  - step_description: Cells were incubated with trypsin-edta to facilitate ask.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 84
    replicates: 4
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      professor.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: false
  - step_description: Cells were transferred with pbs to facilitate evidence.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 92
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Mass spectrometry data processed with MaxQuant
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Jamie Strickland
  and results were consistent across multiple biological replicates.
