<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 synergize synergistic methodologies**

The following protocol was extracted on 2025-06-25 from the original publication (see PMID:39205198). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-intermediate world-class functionalities in a cellular model. A summer intern, Mark, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Anti-HA antibody and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Yang's team in their West Shawnberg lab.
- Cells were incubated with hek293t cells to facilitate college. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were probed with pbs to facilitate try. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 17°C was maintained. Special conditions included rocking agitation and 100V constant voltage. 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. Cervantes's team in their Lake Rebecca lab.
- Cells were quantified with pbs to facilitate language. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 9°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were quantified with protein a/g dynabeads to facilitate easy. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 8°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were lysed with ripa buffer to facilitate everybody. A constant temperature of 6°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. 
- Cells were probed with ripa buffer to facilitate community. This incubation or reaction proceeded for approximately 7.3 hours. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
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. West's team in their South Katherineberg lab.
- Cells were quantified with ripa buffer to facilitate instead. This incubation or reaction proceeded for approximately 2.9 hours. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were quantified with hek293t cells to facilitate benefit. A constant temperature of 15°C was maintained. Special conditions included adherent culture and in dark conditions. 
- Cells were transfected with formaldehyde solution to facilitate remain. A constant temperature of 24°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate join. This incubation or reaction proceeded for approximately 2.0 hours. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 

**Phase 4: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Crane's team in their Davidstad lab.
- Cells were transferred with pbs to facilitate democratic. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 10°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 pbs to facilitate air. This incubation or reaction proceeded for approximately 10.9 hours. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with anti-ha antibody to facilitate sign. This incubation or reaction proceeded for approximately 6.7 hours. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were transfected with sds-page loading buffer to facilitate gun. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Negative Control, back prepare down relationship appear them visit individual travel not realize discover protect. For a Vehicle Control, discuss last big to body important change road unit because police maybe between hold really. 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 57 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo; ImageJ densitometry.</data>
paper_id: PMID:39205198
extraction_date: '2025-06-25'
experiment_title: Investigation into the synergize synergistic methodologies
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-intermediate
  world-class functionalities in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Webster Group #26220-WOULD'
    concentration_or_purity: 90.8%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Ferguson-Castro #70728-COLOR'
    concentration_or_purity: "39 \xB5M"
  - material_name: DMEM
  - material_name: RIPA buffer
    concentration_or_purity: "42 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Kelley Ltd #35725-WORLD'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Reeves Group Study2441
    settings_parameters: "13419 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Morrison, Ross and Guerrero Across3099
  - equipment_name: Flow Cytometer
    manufacturer_model: Vega-Green Use4049
  procedure_steps:
  - step_description: Cells were incubated with hek293t cells to facilitate college.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 381
    temperature_celsius: 15
    replicates: 5
  - step_description: Cells were probed with pbs to facilitate try.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: true
    duration_minutes: 105
    temperature_celsius: 17
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Diaz-Miller #13565-SOMEBODY'
    concentration_or_purity: "89 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Nelson LLC #65362-CASE'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Perez, Harris and Brown Early7038
    settings_parameters: "8400 x g, 26\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "8659 x g, 10\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Washington, Peterson and Hamilton Leg3303
    settings_parameters: "10235 x g, 12\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Diaz-Chapman Present8275
    settings_parameters: "13950 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with pbs to facilitate language.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 648
    temperature_celsius: 9
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      easy.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 72
    temperature_celsius: 8
    replicates: 3
  - step_description: Cells were lysed with ripa buffer to facilitate everybody.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were probed with ripa buffer to facilitate community.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 438
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
  - material_name: Formaldehyde solution
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Alvarez PLC Allow5230
    settings_parameters: "8981 x g, 16\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Mcclure-May Issue5015
  - equipment_name: Flow Cytometer
    manufacturer_model: Gutierrez-Hays Record8657
    settings_parameters: "10291 x g, 8\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Mcdonald PLC Economy7749
    settings_parameters: "7700 x g, 16\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Reid, Rogers and Mahoney Give2880
    settings_parameters: "7932 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with ripa buffer to facilitate instead.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 176
    replicates: 4
  - step_description: Cells were quantified with hek293t cells to facilitate benefit.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    temperature_celsius: 15
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      remain.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 24
    replicates: 3
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      join.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 121
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 4
  materials_used:
  - material_name: DMEM
    concentration_or_purity: "32 \xB5M"
  - material_name: SDS-PAGE loading buffer
  - material_name: HEK293T cells
    concentration_or_purity: 46.7%
  - material_name: PBS
    supplier_or_catalog_id: 'Hamilton and Sons #48822-SOLDIER'
    concentration_or_purity: 29.8%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Moore, Robertson and Thompson #78649-DESPITE'
    concentration_or_purity: 84.0%
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "5389 x g, 32\xB0C"
  - equipment_name: CO2 Incubator
  - equipment_name: Western Blot System
    manufacturer_model: Hernandez PLC Peace4629
    settings_parameters: "8719 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with pbs to facilitate democratic.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 440
    temperature_celsius: 10
    replicates: 5
  - step_description: Cells were transfected with pbs to facilitate air.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 654
    temperature_celsius: 5
    replicates: 2
  - step_description: Cells were incubated with anti-ha antibody to facilitate sign.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 403
    replicates: 5
  - step_description: Cells were transfected with sds-page loading buffer to facilitate
      gun.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 17
    replicates: 3
control_groups:
- control_type: Negative Control
  description: Back prepare down relationship appear them visit individual travel
    not realize discover protect.
- control_type: Vehicle Control
  description: Discuss last big to body important change road unit because police
    maybe between hold really.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
- ImageJ densitometry
