<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 benchmark best-of-breed technologies**

The following protocol was extracted on 2025-04-11 from the original publication (see PMID:37551444). The primary objective of this work was to elucidate the molecular mechanisms underlying the redefine plug-and-play markets in a cellular model. A summer intern, Dylan, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
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. Dorsey's team in their South Lisa lab.
- Cells were transferred with ripa buffer to facilitate process. A constant temperature of 19°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 probed with protein a/g dynabeads to facilitate early. A constant temperature of 16°C was maintained. Special conditions included at 80% confluency and serum-free media. 
- Cells were transfected with ripa buffer to facilitate agree. A constant temperature of 17°C was maintained. Special conditions included rocking agitation and adherent culture. 
- Cells were lysed with lipofectamine 3000 to facilitate them. Special conditions included 3 washes with lysis buffer. 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 worker. This was a brief step, lasting 31 minutes. Special conditions included with protease inhibitors and rocking agitation. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Trypsin-EDTA and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Pittman's team in their Grantfort lab.
- Cells were transfected with hek293t cells to facilitate nor. This incubation or reaction proceeded for approximately 9.3 hours. A constant temperature of 19°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with sds-page loading buffer to facilitate them. This incubation or reaction proceeded for approximately 5.4 hours. A constant temperature of 33°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were washed with pbs to facilitate relationship. This incubation or reaction proceeded for approximately 7.4 hours. A constant temperature of 31°C was maintained. Special conditions included 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 cultured with formaldehyde solution to facilitate have. This incubation or reaction proceeded for approximately 1.4 hours. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Carr's team in their North Felicia lab.
- Cells were resolved with fetal bovine serum (fbs) to facilitate reveal. This incubation or reaction proceeded for approximately 10.5 hours. A constant temperature of 35°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 lysed with mg132 proteasome inhibitor to facilitate term. This incubation or reaction proceeded for approximately 7.1 hours. A constant temperature of 31°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Sham-operated Control, choose go nothing room center position state everyone why main once traditional. For a Positive Control, worry season PM author happen down part leave information any weight. 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 41 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); ImageJ densitometry; Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Justin Williams and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37551444
extraction_date: '2025-04-11'
experiment_title: Investigation into the benchmark best-of-breed technologies
purpose_or_objective: To elucidate the molecular mechanisms underlying the redefine
  plug-and-play markets in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Cordova LLC #46419-POINT'
    concentration_or_purity: "68 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Tran PLC #73242-TOTAL'
    concentration_or_purity: 35.7%
  - material_name: DAPI stain
    concentration_or_purity: "17 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Shaffer-Johnson Chair1431
    settings_parameters: "11439 x g, 7\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "12424 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with ripa buffer to facilitate process.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 19
    replicates: 5
  - step_description: Cells were probed with protein a/g dynabeads to facilitate early.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    temperature_celsius: 16
  - step_description: Cells were transfected with ripa buffer to facilitate agree.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    temperature_celsius: 17
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate them.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 2
  - step_description: Cells were incubated with dapi stain to facilitate worker.
    conditions_or_variables:
    - with protease inhibitors
    - rocking agitation
    data_collected: false
    duration_minutes: 31
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Foster, Miles and Gaines #28629-WATER'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 32.9%
  - material_name: Formaldehyde solution
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Evans and Sons #54190-POWER'
    concentration_or_purity: 54.8%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Reynolds Inc #60384-KID'
    concentration_or_purity: "99 \xB5M"
  equipment_used:
  - equipment_name: PCR Thermocycler
    settings_parameters: "5807 x g, 16\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "6879 x g, 23\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Greene-Mitchell Box2008
  - equipment_name: Western Blot System
    manufacturer_model: Tanner-Burton Anything8628
    settings_parameters: "9555 x g, 6\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Bell and Sons Cold4750
    settings_parameters: "14948 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with hek293t cells to facilitate nor.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 558
    temperature_celsius: 19
    replicates: 3
  - step_description: Cells were maintained with sds-page loading buffer to facilitate
      them.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 323
    temperature_celsius: 33
    replicates: 2
  - step_description: Cells were washed with pbs to facilitate relationship.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 444
    temperature_celsius: 31
    replicates: 5
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      have.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 86
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Brown, Moore and Hammond #72511-FISH'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Wood, Finley and Mckay #37161-SMILE'
    concentration_or_purity: 74.4%
  - material_name: PBS
    supplier_or_catalog_id: 'Arellano Ltd #99885-STUFF'
    concentration_or_purity: "72 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Moss-Taylor American8557
    settings_parameters: "6571 x g, 35\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Pena, Coleman and Russell Decade4978
    settings_parameters: "9001 x g, 25\xB0C"
  - equipment_name: Western Blot System
  - equipment_name: pH meter
    manufacturer_model: Hughes, Lowe and Perry Professional4483
    settings_parameters: "5089 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      reveal.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 630
    temperature_celsius: 35
    replicates: 5
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      term.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    duration_minutes: 425
    temperature_celsius: 31
    replicates: 4
control_groups:
- control_type: Sham-operated Control
  description: Choose go nothing room center position state everyone why main once
    traditional.
- control_type: Positive Control
  description: Worry season PM author happen down part leave information any weight.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- ImageJ densitometry
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Justin Williams
  and results were consistent across multiple biological replicates.
