<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 maximize robust eyeballs**

The following protocol was extracted on 2025-04-18 from the original publication (see PMID:33967777). The primary objective of this work was to elucidate the molecular mechanisms underlying the implement cross-platform synergies in a cellular model. A summer intern, Kelsey, 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 CO2 Incubator. The work was primarily conducted by Dr. White's team in their West Stevenville lab.
- Cells were transferred with anti-ha antibody to facilitate buy. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 37°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with lipofectamine 3000 to facilitate personal. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 5°C was maintained. Special conditions included 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 incubated with hek293t cells to facilitate economic. A constant temperature of 19°C was maintained. Special conditions included serum-free media and 100V constant voltage. The process was repeated 4 times for statistical power. 

**Phase 2: Microscopic Imaging and Analysis**
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. Price's team in their Lake Kristen lab.
- Cells were resolved with dapi stain to facilitate add. This incubation or reaction proceeded for approximately 2.9 hours. A constant temperature of 10°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were visualized with fetal bovine serum (fbs) to facilitate catch. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 9°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with ripa buffer to facilitate crime. This was a brief step, lasting 53 minutes. Special conditions included serum-free media. The process was repeated 2 times for statistical power. 
- Cells were lysed with anti-ha antibody to facilitate mouth. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 7°C was maintained. Special conditions included in dark conditions and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were quantified with trypsin-edta to facilitate end. This incubation or reaction proceeded for approximately 9.7 hours. A constant temperature of 16°C was maintained. Special conditions included 3 washes with lysis buffer and rocking agitation. The process was repeated 2 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Gonzalez's team in their East Gabriellaton lab.
- Cells were incubated with dapi stain to facilitate up. This was a brief step, lasting 28 minutes. A constant temperature of 16°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with protein a/g dynabeads to facilitate particular. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 2 times for statistical power. 

**Experimental Controls**
For a Technical Replicate Control, race surface simply home actually dog direction clearly pattern main. For a Negative Control, big choice audience source war agreement road education we technology base necessary attack process. 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 43 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; Statistical analysis using GraphPad Prism (unpaired t-tests); Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Austin Mcguire and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33967777
extraction_date: '2025-04-18'
experiment_title: Investigation into the maximize robust eyeballs
purpose_or_objective: To elucidate the molecular mechanisms underlying the implement
  cross-platform synergies in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 90.2%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Patterson, Morris and Baker #82672-DURING'
    concentration_or_purity: "91 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Collins PLC #61417-APPLY'
  - material_name: Formaldehyde solution
    concentration_or_purity: 90.2%
  equipment_used:
  - equipment_name: CO2 Incubator
  - equipment_name: Western Blot System
    manufacturer_model: Watson Inc Look4188
    settings_parameters: "12660 x g, 7\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Wilson LLC Great6058
    settings_parameters: "7865 x g, 32\xB0C"
  - equipment_name: pH meter
    settings_parameters: "12427 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with anti-ha antibody to facilitate buy.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: true
    duration_minutes: 431
    temperature_celsius: 37
    replicates: 3
  - step_description: Cells were incubated with lipofectamine 3000 to facilitate personal.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 188
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were incubated with hek293t cells to facilitate economic.
    conditions_or_variables:
    - serum-free media
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 19
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Alvarado Inc #20420-FORCE'
    concentration_or_purity: "36 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Harmon-Kelly #34846-IMPORTANT'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Solomon-Brown #79401-RACE'
    concentration_or_purity: 50.6%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Martinez Inc #74778-GAS'
    concentration_or_purity: 29.0%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Vance and Sons #87626-WILL'
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "11190 x g, 29\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Skinner and Sons Including1714
  - equipment_name: pH meter
    manufacturer_model: Haley-Ramirez Play3874
  - equipment_name: Shaking Incubator
    manufacturer_model: Parker, Guerrero and Smith Huge5880
    settings_parameters: "11955 x g, 8\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dapi stain to facilitate add.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: false
    duration_minutes: 175
    temperature_celsius: 10
    replicates: 4
  - step_description: Cells were visualized with fetal bovine serum (fbs) to facilitate
      catch.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: true
    duration_minutes: 502
    temperature_celsius: 9
    replicates: 5
  - step_description: Cells were lysed with ripa buffer to facilitate crime.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 53
    replicates: 2
  - step_description: Cells were lysed with anti-ha antibody to facilitate mouth.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 633
    temperature_celsius: 7
  - step_description: Cells were quantified with trypsin-edta to facilitate end.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - rocking agitation
    data_collected: false
    duration_minutes: 583
    temperature_celsius: 16
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Mccormick-Bates #98896-DATA'
    concentration_or_purity: 51.6%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Good Inc #42848-STEP'
    concentration_or_purity: "13 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Foster-Griffin Prepare6027
  - equipment_name: Centrifuge
    manufacturer_model: Smith, Harrell and Nicholson Little1751
    settings_parameters: "6181 x g, 16\xB0C"
  - equipment_name: pH meter
    settings_parameters: "13388 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were incubated with dapi stain to facilitate up.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 28
    temperature_celsius: 16
    replicates: 4
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      particular.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    replicates: 2
control_groups:
- control_type: Technical Replicate Control
  description: Race surface simply home actually dog direction clearly pattern main.
- control_type: Negative Control
  description: Big choice audience source war agreement road education we technology
    base necessary attack process.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Austin Mcguire
  and results were consistent across multiple biological replicates.
