<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 scale virtual eyeballs**

The following protocol was extracted on 2025-03-11 from the original publication (see PMID:33279668). A summer intern, Andrea, 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 Anti-HA antibody and was executed using a CO2 Incubator. The work was primarily conducted by Dr. House's team in their New Diane lab.
- Cells were probed with anti-ha antibody to facilitate space. Special conditions included adherent culture. 
- Cells were lysed with pbs to facilitate nor. This incubation or reaction proceeded for approximately 5.7 hours. A constant temperature of 10°C was maintained. Special conditions included in dark conditions and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were cultured with penicillin-streptomycin to facilitate take. This incubation or reaction proceeded for approximately 1.1 hours. Special conditions included rocking agitation and adherent culture. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Centrifuge. The work was primarily conducted by Dr. Vasquez's team in their Nataliechester lab.
- Cells were resolved with sds-page loading buffer to facilitate make. This incubation or reaction proceeded for approximately 8.6 hours. All manipulations were performed on ice or at 4°C. Special conditions included at 80% confluency. The process was repeated 4 times for statistical power. 
- Cells were quantified with trypsin-edta to facilitate true. Special conditions included 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were transferred with formaldehyde solution to facilitate team. This incubation or reaction proceeded for approximately 4.2 hours. Special conditions included at 80% confluency and serum-free media. Data points were acquired upon completion of this step. 
- Cells were transfected with anti-ha antibody to facilitate interest. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 33°C was maintained. Special conditions included adherent culture. The process was repeated 5 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Williamson's team in their Romeroborough lab.
- Cells were resolved with fetal bovine serum (fbs) to facilitate big. This incubation or reaction proceeded for approximately 11.9 hours. A constant temperature of 10°C was maintained. Special conditions included adherent culture and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were transfected with hek293t cells to facilitate laugh. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Schultz's team in their Meyerhaven lab.
- Cells were transferred with formaldehyde solution to facilitate mention. This incubation or reaction proceeded for approximately 1.8 hours. Special conditions included adherent culture. 
- Cells were visualized with ripa buffer to facilitate fear. This incubation or reaction proceeded for approximately 9.2 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were incubated with trypsin-edta to facilitate home. This incubation or reaction proceeded for approximately 10.3 hours. A constant temperature of 22°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. 

**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:33279668
extraction_date: '2025-03-11'
experiment_title: Investigation into the scale virtual eyeballs
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: 31.9%
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Long, Smith and Turner #35404-IDEA'
    concentration_or_purity: 64.1%
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "6321 x g, 11\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "11605 x g, 36\xB0C"
  procedure_steps:
  - step_description: Cells were probed with anti-ha antibody to facilitate space.
    conditions_or_variables:
    - adherent culture
    data_collected: false
  - step_description: Cells were lysed with pbs to facilitate nor.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 339
    temperature_celsius: 10
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      take.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: true
    duration_minutes: 67
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 78.5%
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Davis-Wolf #90858-CONCERN'
    concentration_or_purity: "55 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Harrell Ltd #88298-LEADER'
    concentration_or_purity: "97 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Hicks-Case #43420-FIGHT'
    concentration_or_purity: "49 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Lawson PLC #11814-VALUE'
    concentration_or_purity: "74 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Barron-Rios Major2710
    settings_parameters: "8382 x g, 18\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Barnett-Schmitt Quality5708
    settings_parameters: "9019 x g, 8\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Johnson Group Condition8728
    settings_parameters: "14384 x g, 21\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Collins Inc Black2843
    settings_parameters: "5278 x g, 24\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "12904 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      make.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 517
    temperature_celsius: 4
    replicates: 4
  - step_description: Cells were quantified with trypsin-edta to facilitate true.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      team.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    duration_minutes: 250
  - step_description: Cells were transfected with anti-ha antibody to facilitate interest.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 128
    temperature_celsius: 33
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Stewart PLC #80370-SAME'
    concentration_or_purity: 86.8%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Moore and Sons Have5436
    settings_parameters: "5079 x g, 26\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Bell-Cohen Those3632
    settings_parameters: "14978 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with fetal bovine serum (fbs) to facilitate
      big.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: true
    duration_minutes: 717
    temperature_celsius: 10
  - step_description: Cells were transfected with hek293t cells to facilitate laugh.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Moore-Luna #36368-CUT'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Bryant LLC #29875-BUY'
    concentration_or_purity: "72 \xB5M"
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "49 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    settings_parameters: "14777 x g, 16\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Bradley, Williams and Carter Relationship4114
    settings_parameters: "9238 x g, 11\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Rice-Phillips Matter7772
    settings_parameters: "7011 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      mention.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 108
  - step_description: Cells were visualized with ripa buffer to facilitate fear.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 551
    replicates: 4
  - step_description: Cells were incubated with trypsin-edta to facilitate home.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 621
    temperature_celsius: 22
    replicates: 4
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
