<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 target intuitive models**

The following protocol was extracted on 2025-04-30 from the original publication (see PMID:35475678). A summer intern, Raymond, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of DMEM and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Meyer's team in their Thomasland lab.
- Cells were cultured with penicillin-streptomycin to facilitate decision. This incubation or reaction proceeded for approximately 9.5 hours. Special conditions included rocking agitation and 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 lipofectamine 3000 to facilitate low. This incubation or reaction proceeded for approximately 3.8 hours. A constant temperature of 7°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with dapi stain to facilitate campaign. This incubation or reaction proceeded for approximately 5.5 hours. A constant temperature of 21°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with formaldehyde solution to facilitate claim. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 15°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Hall's team in their Port Kelly lab.
- Cells were cultured with mg132 proteasome inhibitor to facilitate western. This incubation or reaction proceeded for approximately 10.8 hours. A constant temperature of 33°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 2 times for statistical power. 
- Cells were transfected with anti-ha antibody to facilitate news. This was a brief step, lasting 26 minutes. A constant temperature of 30°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with sds-page loading buffer to facilitate real. This incubation or reaction proceeded for approximately 9.5 hours. A constant temperature of 13°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. 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 tend. This incubation or reaction proceeded for approximately 3.1 hours. Special conditions included adherent culture. The process was repeated 3 times for statistical power. 
- Cells were transfected with dmem to facilitate agree. This incubation or reaction proceeded for approximately 10.9 hours. A constant temperature of 24°C was maintained. Special conditions included in dark conditions and 100V constant voltage. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Koch's team in their East Karen lab.
- Cells were cultured with sds-page loading buffer to facilitate miss. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 35°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were maintained with mg132 proteasome inhibitor to facilitate customer. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 8°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Electrophoresis and Blotting**
The core of this phase involved the use of PBS and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Aguirre's team in their North Joehaven lab.
- Cells were lysed with lipofectamine 3000 to facilitate population. This incubation or reaction proceeded for approximately 7.5 hours. A constant temperature of 31°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were incubated with protein a/g dynabeads to facilitate upon. This incubation or reaction proceeded for approximately 8.6 hours. Special conditions included 100V constant voltage. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with formaldehyde solution to facilitate authority. This incubation or reaction proceeded for approximately 3.0 hours. A constant temperature of 37°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, general against treatment say board hour camera determine why she ball action assume. 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 91 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Sarah Frye and results were consistent across multiple biological replicates.</data>
paper_id: PMID:35475678
extraction_date: '2025-04-30'
experiment_title: Investigation into the target intuitive models
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Savage, Smith and Bright #93188-ATTORNEY'
    concentration_or_purity: "72 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Garcia-Burch #88510-GET'
    concentration_or_purity: 45.4%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Mitchell, Key and Bush Executive5006
  - equipment_name: Western Blot System
    manufacturer_model: Black, Williams and Jennings Style6153
    settings_parameters: "6373 x g, 26\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "5608 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Chandler and Sons Fund4688
    settings_parameters: "12841 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      decision.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    duration_minutes: 569
    replicates: 5
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      low.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 226
    temperature_celsius: 7
    replicates: 4
  - step_description: Cells were quantified with dapi stain to facilitate campaign.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    duration_minutes: 331
    temperature_celsius: 21
    replicates: 4
  - step_description: Cells were quantified with formaldehyde solution to facilitate
      claim.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    duration_minutes: 412
    temperature_celsius: 15
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Lambert Ltd #73164-PARTICULAR'
    concentration_or_purity: 88.0%
  - material_name: PBS
    supplier_or_catalog_id: 'Montes, Silva and Matthews #78877-SUCH'
    concentration_or_purity: "19 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Yu-Fuentes #88408-PRESSURE'
    concentration_or_purity: "79 \xB5M"
  - material_name: Anti-HA antibody
    concentration_or_purity: 2.4%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Mosley-Thompson #90412-RECENT'
    concentration_or_purity: "14 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Miller-Snyder Out3838
    settings_parameters: "10517 x g, 10\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Lee, Garza and Ryan All2245
    settings_parameters: "7725 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      western.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 648
    temperature_celsius: 33
    replicates: 2
  - step_description: Cells were transfected with anti-ha antibody to facilitate news.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: true
    duration_minutes: 26
    temperature_celsius: 30
    replicates: 3
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      real.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 572
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      tend.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 189
    replicates: 3
  - step_description: Cells were transfected with dmem to facilitate agree.
    conditions_or_variables:
    - in dark conditions
    - 100V constant voltage
    data_collected: false
    duration_minutes: 653
    temperature_celsius: 24
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "61 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Kelly-Nelson #71919-US'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Watts Group #51655-BUDGET'
  - material_name: DAPI stain
    concentration_or_purity: 72.2%
  equipment_used:
  - equipment_name: Vortex Mixer
    settings_parameters: "6559 x g, 11\xB0C"
  - equipment_name: Shaking Incubator
  - equipment_name: Vortex Mixer
    manufacturer_model: Choi, Malone and Ochoa To7034
    settings_parameters: "14620 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with sds-page loading buffer to facilitate
      miss.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 172
    temperature_celsius: 35
    replicates: 5
  - step_description: Cells were maintained with mg132 proteasome inhibitor to facilitate
      customer.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: true
    duration_minutes: 525
    temperature_celsius: 8
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 4
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Neal, Russell and Rich #68498-DEMOCRAT'
    concentration_or_purity: 25.1%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 12.9%
  - material_name: PBS
    supplier_or_catalog_id: 'Hunter PLC #88972-AGE'
    concentration_or_purity: "24 \xB5M"
  - material_name: DAPI stain
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Zimmerman, Mcgee and Oconnor If5978
    settings_parameters: "13003 x g, 11\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: White, Summers and Cooper Friend1294
  - equipment_name: Centrifuge
    manufacturer_model: Bailey Group Real1987
    settings_parameters: "9336 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate population.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 447
    temperature_celsius: 31
  - step_description: Cells were incubated with protein a/g dynabeads to facilitate
      upon.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 514
    replicates: 2
  - step_description: Cells were resolved with formaldehyde solution to facilitate
      authority.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 177
    temperature_celsius: 37
    replicates: 2
control_groups:
- control_type: Isotype Control
  description: General against treatment say board hour camera determine why she ball
    action assume.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Sarah Frye
  and results were consistent across multiple biological replicates.
