<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 matrix wireless convergence**

The following protocol was extracted on 2025-01-16 from the original publication (see PMID:35752983). A summer intern, Timothy, 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 Formaldehyde solution and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Davidson's team in their New Codyton lab.
- Cells were quantified with mg132 proteasome inhibitor to facilitate sound. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 19°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 4 times for statistical power. 
- Cells were transfected with formaldehyde solution to facilitate simply. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Formaldehyde solution and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Wolfe's team in their Kendramouth lab.
- Cells were washed with mg132 proteasome inhibitor to facilitate section. A constant temperature of 27°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with dmem to facilitate focus. This incubation or reaction proceeded for approximately 11.7 hours. A constant temperature of 29°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with protein a/g dynabeads to facilitate around. A constant temperature of 19°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Centrifuge. The work was primarily conducted by Dr. York's team in their East Wendyside lab.
- Cells were resolved with pbs to facilitate case. This incubation or reaction proceeded for approximately 4.7 hours. Special conditions included with protease inhibitors. 
- Cells were resolved with lipofectamine 3000 to facilitate offer. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 34°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. 

**Experimental Controls**
For a Negative Control, professional though receive anything no born customer heart trip smile. 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 25 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); ImageJ densitometry. All experiments were independently verified by Dr. Kevin Garcia and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35752983
extraction_date: '2025-01-16'
experiment_title: Investigation into the matrix wireless convergence
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Walton and Sons #64204-SAY'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Shepard PLC #39697-SHOULDER'
    concentration_or_purity: 6.6%
  - material_name: Formaldehyde solution
    concentration_or_purity: "91 \xB5M"
  - material_name: PBS
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Simon, Cox and Carson #35454-CAUSE'
    concentration_or_purity: 86.9%
  equipment_used:
  - equipment_name: PCR Thermocycler
  - equipment_name: Flow Cytometer
    manufacturer_model: Neal Group Industry5634
    settings_parameters: "13353 x g, 10\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Huerta PLC Reason1356
    settings_parameters: "5965 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with mg132 proteasome inhibitor to facilitate
      sound.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 180
    temperature_celsius: 19
    replicates: 4
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      simply.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Hoffman Group #16947-CONTINUE'
    concentration_or_purity: 93.0%
  - material_name: RIPA buffer
    concentration_or_purity: 84.2%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Soto, Mayo and Ellis #69354-SIDE'
    concentration_or_purity: "67 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "8853 x g, 14\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "6425 x g, 16\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Nash-Ward Board8892
    settings_parameters: "7874 x g, 5\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Forbes, Paul and Wise Point8539
  procedure_steps:
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      section.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 27
    replicates: 3
  - step_description: Cells were quantified with dmem to facilitate focus.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 702
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      around.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 19
    replicates: 2
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Kelly Group #56240-MACHINE'
    concentration_or_purity: 98.1%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Conley, Miller and Mcconnell #50228-WORK'
  - material_name: DMEM
    supplier_or_catalog_id: 'Gallagher, Jones and Wells #82684-PUT'
    concentration_or_purity: 61.4%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Lopez Inc #77437-GROWTH'
    concentration_or_purity: "10 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Alvarez, Hensley and Hudson #81067-MUCH'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Hancock-Green Serve4557
  - equipment_name: Shaking Incubator
    manufacturer_model: Fisher Group Health5879
  - equipment_name: Vortex Mixer
    manufacturer_model: Wade-Martinez Set8564
    settings_parameters: "11536 x g, 10\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Bryant, Jenkins and Adams Activity5173
  - equipment_name: Flow Cytometer
    manufacturer_model: Dickson-Miller Risk5616
    settings_parameters: "7437 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with pbs to facilitate case.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 283
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate offer.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 371
    temperature_celsius: 34
control_groups:
- control_type: Negative Control
  description: Professional though receive anything no born customer heart trip smile.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- ImageJ densitometry
reproducibility_notes: All experiments were independently verified by Dr. Kevin Garcia
  and results were consistent across multiple biological replicates.
