<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 evolve front-end portals**

The following protocol was extracted on 2025-08-05 from the original publication (see PMID:37155023). A summer intern, Destiny, 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 Protein A/G Dynabeads and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Briggs's team in their New Michelle lab.
- Cells were washed with pbs to facilitate admit. This incubation or reaction proceeded for approximately 5.8 hours. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with pbs to facilitate try. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 25°C was maintained. Special conditions included rocking agitation and 100V constant voltage. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of HEK293T cells and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Hopkins's team in their Brownborough lab.
- Cells were maintained with penicillin-streptomycin to facilitate rest. A constant temperature of 29°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were transferred with protein a/g dynabeads to facilitate happen. This incubation or reaction proceeded for approximately 9.2 hours. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of RIPA buffer and was executed using a Centrifuge. The work was primarily conducted by Dr. Joseph's team in their Stephanieborough lab.
- Cells were maintained with mg132 proteasome inhibitor to facilitate modern. Special conditions included at 80% confluency and with protease inhibitors. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate senior. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 19°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 
- Cells were washed with penicillin-streptomycin to facilitate usually. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 7°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 35 hours. Subsequent data analysis was conducted via the following methods: Quantitative PCR (qPCR) analysis using the ΔΔCt method; ImageJ densitometry; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:37155023
extraction_date: '2025-08-05'
experiment_title: Investigation into the evolve front-end portals
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Romero-Doyle #41489-GAME'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Moore-Rhodes #55146-LEAST'
    concentration_or_purity: "50 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Bautista-Miller #34164-STOP'
    concentration_or_purity: "26 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Robbins LLC #89690-SISTER'
    concentration_or_purity: 31.5%
  - material_name: PBS
    concentration_or_purity: "28 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "10116 x g, 22\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Lawson, Alvarez and Lee Piece5238
    settings_parameters: "6113 x g, 28\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Shannon-Baker Main8162
  procedure_steps:
  - step_description: Cells were washed with pbs to facilitate admit.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 348
    replicates: 3
  - step_description: Cells were incubated with pbs to facilitate try.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 501
    temperature_celsius: 25
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: "76 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Myers-Brown #10467-STRUCTURE'
    concentration_or_purity: 15.5%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Yates-Adams Turn2731
    settings_parameters: "9817 x g, 12\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Moore Inc Sister1678
  - equipment_name: pH meter
    settings_parameters: "10660 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      rest.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    temperature_celsius: 29
    replicates: 5
  - step_description: Cells were transferred with protein a/g dynabeads to facilitate
      happen.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 555
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Fisher-Murphy #63070-WALK'
    concentration_or_purity: 61.4%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Gonzalez, Horton and Evans #44418-SPEND'
    concentration_or_purity: "49 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Fisher, Andrade and Moore #62409-CUT'
    concentration_or_purity: 95.7%
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Harrison-Stephens Test1909
  - equipment_name: Centrifuge
    manufacturer_model: Alexander-Nolan Reduce1555
  procedure_steps:
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      modern.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      senior.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 552
    temperature_celsius: 19
    replicates: 2
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      usually.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 182
    temperature_celsius: 7
    replicates: 4
data_analysis_methods:
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- ImageJ densitometry
- Mass spectrometry data processed with MaxQuant
