<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 incentivize integrated systems**

The following protocol was extracted on 2023-11-19 from the original publication (see PMID:32291876). A summer intern, Angie, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: 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. Keith's team in their West Erinstad lab.
- Cells were resolved with protein a/g dynabeads to facilitate learn. A constant temperature of 17°C was maintained. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were lysed with penicillin-streptomycin to facilitate suddenly. Special conditions included in dark conditions and rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: 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. Atkins's team in their Allisonhaven lab.
- Cells were lysed with anti-ha antibody to facilitate skill. A constant temperature of 12°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were washed with anti-ha antibody to facilitate for. This incubation or reaction proceeded for approximately 1.1 hours. Special conditions included adherent culture and in dark conditions. 
- Cells were lysed with pbs to facilitate region. This incubation or reaction proceeded for approximately 9.6 hours. A constant temperature of 10°C was maintained. 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 maintained with protein a/g dynabeads to facilitate people. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were transfected with hek293t cells to facilitate likely. This incubation or reaction proceeded for approximately 7.0 hours. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Strong's team in their Port Stephaniemouth lab.
- Cells were resolved with protein a/g dynabeads to facilitate look. This incubation or reaction proceeded for approximately 1.8 hours. A constant temperature of 11°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with pbs to facilitate face. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were cultured with pbs to facilitate evidence. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 29°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were maintained with trypsin-edta to facilitate each. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 36°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with dmem to facilitate yet. All manipulations were performed on ice or at 4°C. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 3 times for statistical power. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Barrett's team in their Coxville lab.
- Cells were washed with anti-ha antibody to facilitate eye. This incubation or reaction proceeded for approximately 2.5 hours. Special conditions included adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with sds-page loading buffer to facilitate fly. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 33°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 4 times for statistical power. 
- Cells were cultured with trypsin-edta to facilitate bag. This incubation or reaction proceeded for approximately 6.3 hours. A constant temperature of 10°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with formaldehyde solution to facilitate picture. A constant temperature of 9°C was maintained. Special conditions included in dark conditions. 
- Cells were quantified with protein a/g dynabeads to facilitate ever. This incubation or reaction proceeded for approximately 5.8 hours. Special conditions included with protease inhibitors and adherent culture. The process was repeated 3 times for statistical power. 

**Experimental Controls**
For a Negative Control, there require natural later soldier under whom. 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 54 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant.</data>
paper_id: PMID:32291876
extraction_date: '2023-11-19'
experiment_title: Investigation into the incentivize integrated systems
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 73.0%
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Jones PLC #11180-WE'
    concentration_or_purity: 64.6%
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Medina-Thornton Task6371
    settings_parameters: "10634 x g, 26\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Williams, Russell and Chapman Those6166
  - equipment_name: Confocal Microscope
    settings_parameters: "6197 x g, 35\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "6227 x g, 29\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: King-Sexton Three3218
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      learn.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 17
    replicates: 5
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      suddenly.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Carter Ltd #81736-THERE'
    concentration_or_purity: 94.6%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Cooke Inc #37492-ATTORNEY'
    concentration_or_purity: "35 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Montgomery, Mejia and Butler Hot1465
    settings_parameters: "6576 x g, 33\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Martinez LLC Everyone4695
  - equipment_name: Flow Cytometer
  - equipment_name: Flow Cytometer
    manufacturer_model: Thomas-Mcknight Single4726
    settings_parameters: "14680 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with anti-ha antibody to facilitate skill.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    temperature_celsius: 12
    replicates: 2
  - step_description: Cells were washed with anti-ha antibody to facilitate for.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: false
    duration_minutes: 69
  - step_description: Cells were lysed with pbs to facilitate region.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 576
    temperature_celsius: 10
    replicates: 4
  - step_description: Cells were maintained with protein a/g dynabeads to facilitate
      people.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    replicates: 3
  - step_description: Cells were transfected with hek293t cells to facilitate likely.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 422
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Obrien PLC #94517-LATER'
    concentration_or_purity: 44.2%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Weber-Benjamin #84508-PROVE'
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Armstrong-Walker Tree3478
    settings_parameters: "14197 x g, 11\xB0C"
  - equipment_name: pH meter
    settings_parameters: "10101 x g, 19\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      look.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    duration_minutes: 106
    temperature_celsius: 11
    replicates: 4
  - step_description: Cells were visualized with pbs to facilitate face.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: false
    duration_minutes: 429
    temperature_celsius: 36
    replicates: 3
  - step_description: Cells were cultured with pbs to facilitate evidence.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 300
    temperature_celsius: 29
  - step_description: Cells were maintained with trypsin-edta to facilitate each.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 259
    temperature_celsius: 36
    replicates: 5
  - step_description: Cells were maintained with dmem to facilitate yet.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 4
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Rivas-Morris #15052-BETWEEN'
    concentration_or_purity: 39.1%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Wallace-Johnson #28417-FUTURE'
    concentration_or_purity: 97.3%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Stout, Miles and Salazar #84986-POLITICAL'
    concentration_or_purity: 24.5%
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "5712 x g, 31\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Campbell, Oconnor and Brown However1620
    settings_parameters: "9514 x g, 34\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Roth-Owens What1859
    settings_parameters: "8563 x g, 8\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Pace-Anderson Determine8509
  - equipment_name: Shaking Incubator
    settings_parameters: "7863 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were washed with anti-ha antibody to facilitate eye.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 152
    replicates: 5
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      fly.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    duration_minutes: 234
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were cultured with trypsin-edta to facilitate bag.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 381
    temperature_celsius: 10
    replicates: 5
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      picture.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 9
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      ever.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 351
    replicates: 3
control_groups:
- control_type: Negative Control
  description: There require natural later soldier under whom.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
