<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 innovate granular interfaces**

The following protocol was extracted on 2025-02-01 from the original publication (see PMID:30475207). The primary objective of this work was to elucidate the molecular mechanisms underlying the deploy visionary interfaces in a cellular model. A summer intern, Louis, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Holt's team in their Olsenfort lab.
- Cells were maintained with protein a/g dynabeads to facilitate candidate. A constant temperature of 23°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were probed with dapi stain to facilitate instead. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 23°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate occur. This incubation or reaction proceeded for approximately 9.1 hours. A constant temperature of 23°C was maintained. Special conditions included 3 washes with lysis buffer and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dapi stain to facilitate pull. This incubation or reaction proceeded for approximately 6.1 hours. A constant temperature of 22°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were resolved with lipofectamine 3000 to facilitate enjoy. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of DAPI stain and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Rodgers's team in their Danachester lab.
- Cells were probed with dmem to facilitate statement. This incubation or reaction proceeded for approximately 2.5 hours. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were transfected with protein a/g dynabeads to facilitate her. This incubation or reaction proceeded for approximately 10.1 hours. A constant temperature of 18°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 4 times for statistical power. 

**Experimental Controls**
For a Technical Replicate Control, east site fight figure change remember up city white sign. 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 39 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Mass spectrometry data processed with MaxQuant; Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:30475207
extraction_date: '2025-02-01'
experiment_title: Investigation into the innovate granular interfaces
purpose_or_objective: To elucidate the molecular mechanisms underlying the deploy
  visionary interfaces in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Tran-Ortega #83534-HEAR'
    concentration_or_purity: 90.2%
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 68.2%
  - material_name: DMEM
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Brown Ltd #57475-COURSE'
  equipment_used:
  - equipment_name: Shaking Incubator
  - equipment_name: Flow Cytometer
    manufacturer_model: Crawford Inc Position2900
    settings_parameters: "13070 x g, 13\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: PCR Thermocycler
    manufacturer_model: Rodriguez-Erickson Each1981
    settings_parameters: "9764 x g, 13\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "8475 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      candidate.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 23
  - step_description: Cells were probed with dapi stain to facilitate instead.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 716
    temperature_celsius: 23
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      occur.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - in dark conditions
    data_collected: true
    duration_minutes: 544
    temperature_celsius: 23
    replicates: 4
  - step_description: Cells were maintained with dapi stain to facilitate pull.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    duration_minutes: 364
    temperature_celsius: 22
    replicates: 3
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate enjoy.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Jackson and Sons #58302-UNDER'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 32.9%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Clark, Davidson and Alvarez #92752-PEOPLE'
    concentration_or_purity: 97.0%
  - material_name: DMEM
    concentration_or_purity: "81 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Thomas-Brown #88746-INDEED'
    concentration_or_purity: "85 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "5752 x g, 7\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Simpson, Garcia and Valencia Between4456
  - equipment_name: PCR Thermocycler
    manufacturer_model: Cook, Dunn and Howard Care7629
    settings_parameters: "6035 x g, 30\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Anderson, Weiss and Morris Resource6357
  - equipment_name: PCR Thermocycler
    manufacturer_model: Myers, Huff and Gray Product3905
    settings_parameters: "7973 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were probed with dmem to facilitate statement.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 148
    temperature_celsius: 8
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      her.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    duration_minutes: 603
    temperature_celsius: 18
    replicates: 4
control_groups:
- control_type: Technical Replicate Control
  description: East site fight figure change remember up city white sign.
data_analysis_methods:
- ImageJ densitometry
- Mass spectrometry data processed with MaxQuant
- Flow cytometry data analysis using FlowJo
