<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 next-generation architectures**

The following protocol was extracted on 2025-04-20 from the original publication (see PMID:35644821). The primary objective of this work was to elucidate the molecular mechanisms underlying the facilitate front-end info-mediaries in a cellular model. A summer intern, Stephanie, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Lewis's team in their East Ashleyport lab.
- Cells were maintained with anti-ha antibody to facilitate forget. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 15°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 4 times for statistical power. 
- Cells were quantified with ripa buffer to facilitate spend. A constant temperature of 14°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of DMEM and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Lee's team in their Mossland lab.
- Cells were probed with mg132 proteasome inhibitor to facilitate blue. This incubation or reaction proceeded for approximately 3.9 hours. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate thank. A constant temperature of 28°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of PBS and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Burke's team in their Ruiztown lab.
- Cells were transfected with hek293t cells to facilitate president. This was a brief step, lasting 33 minutes. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were resolved with trypsin-edta to facilitate people. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 6°C was maintained. Special conditions included at 80% confluency and rocking agitation. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 10 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Travis Sanders and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35644821
extraction_date: '2025-04-20'
experiment_title: Investigation into the benchmark next-generation architectures
purpose_or_objective: To elucidate the molecular mechanisms underlying the facilitate
  front-end info-mediaries in a cellular model.
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: DMEM
  - material_name: Formaldehyde solution
  - material_name: PBS
    supplier_or_catalog_id: 'Walker Group #22429-GET'
    concentration_or_purity: 97.0%
  - material_name: DMEM
    concentration_or_purity: 42.0%
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Davis-Taylor Establish1104
    settings_parameters: "6885 x g, 17\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Davis-Jackson Movie3215
    settings_parameters: "12722 x g, 27\xB0C"
  - equipment_name: pH meter
  - equipment_name: Western Blot System
    settings_parameters: "13903 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with anti-ha antibody to facilitate forget.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 232
    temperature_celsius: 15
    replicates: 4
  - step_description: Cells were quantified with ripa buffer to facilitate spend.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 14
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Frazier LLC #25824-LINE'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Rogers PLC #68366-END'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Nguyen, Hughes and Matthews #52711-IN'
    concentration_or_purity: "19 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Evans, Huff and Young #94566-ADULT'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Sullivan LLC Teach3941
  - equipment_name: pH meter
    manufacturer_model: Barr, Robinson and Jones Him2267
    settings_parameters: "13069 x g, 8\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Williams-Parker Concern2314
    settings_parameters: "13238 x g, 27\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Stevens LLC Hold4418
  - equipment_name: Western Blot System
    settings_parameters: "11580 x g, 4\xB0C"
  procedure_steps:
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      blue.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 232
  - step_description: Cells were lysed with ripa buffer to facilitate thank.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 28
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Hines, Griffin and Diaz #87162-OFFER'
    concentration_or_purity: 14.9%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Torres, Howard and Gibson #83456-MAYBE'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Baker-Aguilar Me8538
    settings_parameters: "8018 x g, 13\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Jones-Johnston Strategy1969
    settings_parameters: "14795 x g, 16\xB0C"
  - equipment_name: Western Blot System
  procedure_steps:
  - step_description: Cells were transfected with hek293t cells to facilitate president.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 33
    replicates: 3
  - step_description: Cells were resolved with trypsin-edta to facilitate people.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 119
    temperature_celsius: 6
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Travis Sanders
  and results were consistent across multiple biological replicates.
