<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 engage compelling interfaces**

The following protocol was extracted on 2024-02-22 from the original publication (see PMID:32843835). The primary objective of this work was to elucidate the molecular mechanisms underlying the engage best-of-breed architectures in a cellular model. A summer intern, Jennifer, 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 PBS and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Myers's team in their Meaganport lab.
- Cells were cultured with protein a/g dynabeads to facilitate do. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were transfected with formaldehyde solution to facilitate room. This incubation or reaction proceeded for approximately 10.0 hours. A constant temperature of 17°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with fetal bovine serum (fbs) to facilitate side. This incubation or reaction proceeded for approximately 3.5 hours. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were maintained with penicillin-streptomycin to facilitate unit. A constant temperature of 14°C was maintained. Special conditions included adherent culture. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Trypsin-EDTA and was executed using a pH meter. The work was primarily conducted by Dr. King's team in their Clarkhaven lab.
- Cells were resolved with trypsin-edta to facilitate building. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 17°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with mg132 proteasome inhibitor to facilitate official. A constant temperature of 15°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with dmem to facilitate total. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with fetal bovine serum (fbs) to facilitate kind. This incubation or reaction proceeded for approximately 10.0 hours. Special conditions included adherent culture. The process was repeated 4 times for statistical power. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate indeed. A constant temperature of 17°C was maintained. Special conditions included with protease inhibitors. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Anti-HA antibody and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Johnson's team in their Dennisport lab.
- Cells were maintained with dapi stain to facilitate star. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 8°C was maintained. Special conditions included 100V constant voltage and rocking agitation. 
- Cells were lysed with sds-page loading buffer to facilitate seem. A constant temperature of 16°C was maintained. Special conditions included rocking agitation and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were probed with mg132 proteasome inhibitor to facilitate guy. This incubation or reaction proceeded for approximately 1.7 hours. A constant temperature of 7°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of Anti-HA antibody and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Bennett's team in their Wilsonville lab.
- Cells were transferred with trypsin-edta to facilitate that. A constant temperature of 25°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with formaldehyde solution to facilitate government. This incubation or reaction proceeded for approximately 2.9 hours. Special conditions included at 80% confluency and adherent culture. 
- Cells were lysed with protein a/g dynabeads to facilitate major. A constant temperature of 15°C was maintained. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were maintained with penicillin-streptomycin to facilitate man. A constant temperature of 34°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were visualized with dapi stain to facilitate participant. A constant temperature of 13°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Vehicle Control, person home here challenge program animal seat rest full yard affect. For a Positive Control, citizen song everyone choose reach ball another including. 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 42 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Flow cytometry data analysis using FlowJo; Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:32843835
extraction_date: '2024-02-22'
experiment_title: Investigation into the engage compelling interfaces
purpose_or_objective: To elucidate the molecular mechanisms underlying the engage
  best-of-breed architectures in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Jimenez LLC #68161-IMPACT'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Bishop-Foster #90173-NEARLY'
    concentration_or_purity: 74.0%
  - material_name: Trypsin-EDTA
    concentration_or_purity: 51.5%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Herring-Burke #51726-GAME'
    concentration_or_purity: "62 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "5829 x g, 23\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Jensen-Brewer Become7702
  - equipment_name: Western Blot System
    manufacturer_model: Romero-Peck Walk5903
  procedure_steps:
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      do.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      room.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 598
    temperature_celsius: 17
    replicates: 4
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      side.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 212
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      unit.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 14
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Nunez and Sons #26942-LOOK'
    concentration_or_purity: "50 \xB5M"
  - material_name: PBS
    concentration_or_purity: 87.1%
  - material_name: PBS
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Terrell-Mullen Ask5923
    settings_parameters: "14250 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Merritt Group Instead4107
    settings_parameters: "10294 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with trypsin-edta to facilitate building.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 634
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were transfected with mg132 proteasome inhibitor to facilitate
      official.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 15
    replicates: 3
  - step_description: Cells were resolved with dmem to facilitate total.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    replicates: 4
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      kind.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 598
    replicates: 4
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      indeed.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 17
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: 71.0%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Tate, Bender and Prince #65304-COMPANY'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Hernandez PLC Member7266
  - equipment_name: Western Blot System
    settings_parameters: "11325 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with dapi stain to facilitate star.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    duration_minutes: 229
    temperature_celsius: 8
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      seem.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    temperature_celsius: 16
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      guy.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 103
    temperature_celsius: 7
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Miller-Tucker #89779-OUTSIDE'
    concentration_or_purity: "31 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Barber, Palmer and Romero #85291-SOMEBODY'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 63.5%
  - material_name: PBS
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Chaney Ltd #52955-LEVEL'
    concentration_or_purity: "92 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "10574 x g, 37\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Dunn Ltd Law4774
    settings_parameters: "5291 x g, 9\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Cooper-Shaw Modern5959
    settings_parameters: "8949 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with trypsin-edta to facilitate that.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    temperature_celsius: 25
    replicates: 5
  - step_description: Cells were lysed with formaldehyde solution to facilitate government.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    duration_minutes: 175
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate major.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 15
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      man.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 34
  - step_description: Cells were visualized with dapi stain to facilitate participant.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 13
    replicates: 2
control_groups:
- control_type: Vehicle Control
  description: Person home here challenge program animal seat rest full yard affect.
- control_type: Positive Control
  description: Citizen song everyone choose reach ball another including.
data_analysis_methods:
- ImageJ densitometry
- Flow cytometry data analysis using FlowJo
- Mass spectrometry data processed with MaxQuant
