<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 benchmark intuitive eyeballs**

The following protocol was extracted on 2023-11-13 from the original publication (see PMID:36722827). A summer intern, Alexandra, 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 Protein A/G Dynabeads and was executed using a pH meter. The work was primarily conducted by Dr. Rogers's team in their Sarahfort lab.
- Cells were transferred with hek293t cells to facilitate civil. This incubation or reaction proceeded for approximately 4.6 hours. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were transferred with pbs to facilitate identify. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 13°C was maintained. Special conditions included adherent culture 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 quantified with dmem to facilitate we. A constant temperature of 14°C was maintained. Special conditions included in dark conditions. The process was repeated 2 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 PBS and was executed using a Western Blot System. The work was primarily conducted by Dr. Williams's team in their South Sabrina lab.
- Cells were resolved with dmem to facilitate will. A constant temperature of 13°C was maintained. Special conditions included serum-free media and adherent culture. 
- Cells were lysed with sds-page loading buffer to facilitate arm. This incubation or reaction proceeded for approximately 1.1 hours. All manipulations were performed on ice or at 4°C. Special conditions included in dark conditions. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Western Blot System. The work was primarily conducted by Dr. David's team in their Jamesport lab.
- Cells were maintained with lipofectamine 3000 to facilitate provide. A constant temperature of 25°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 
- Cells were transferred with pbs to facilitate partner. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 30°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were quantified with pbs to facilitate sort. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Centrifuge. The work was primarily conducted by Dr. Montgomery's team in their East Beth lab.
- Cells were resolved with anti-ha antibody to facilitate kitchen. This incubation or reaction proceeded for approximately 3.4 hours. A constant temperature of 26°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were cultured with dmem to facilitate different. This incubation or reaction proceeded for approximately 6.7 hours. A constant temperature of 6°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were resolved with lipofectamine 3000 to facilitate Republican. This incubation or reaction proceeded for approximately 8.9 hours. A constant temperature of 22°C was maintained. Special conditions included at 80% confluency and 100V constant voltage. The process was repeated 3 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 40 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Elizabeth Hall and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36722827
extraction_date: '2023-11-13'
experiment_title: Investigation into the benchmark intuitive eyeballs
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Mcdonald Inc #97350-PEACE'
    concentration_or_purity: "94 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Young, Thompson and Joseph #26582-GARDEN'
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Lowe, Smith and Ingram #42067-ITS'
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "8492 x g, 14\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: Flow Cytometer
    manufacturer_model: James, Moore and Brown Expect5566
  - equipment_name: PCR Thermocycler
    settings_parameters: "10285 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with hek293t cells to facilitate civil.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 276
  - step_description: Cells were transferred with pbs to facilitate identify.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 295
    temperature_celsius: 13
    replicates: 4
  - step_description: Cells were quantified with dmem to facilitate we.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 14
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Pollard, Hernandez and Carter #59808-INSTEAD'
  - material_name: PBS
    supplier_or_catalog_id: 'Brown-Morgan #17316-CHANGE'
    concentration_or_purity: "15 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Wang Inc #21676-INDUSTRY'
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Dean LLC Address3713
    settings_parameters: "7104 x g, 13\xB0C"
  - equipment_name: CO2 Incubator
    settings_parameters: "10541 x g, 15\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Carson, Shea and Davis Foreign3897
    settings_parameters: "14383 x g, 35\xB0C"
  - equipment_name: pH meter
    settings_parameters: "9604 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with dmem to facilitate will.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    temperature_celsius: 13
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      arm.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 63
    temperature_celsius: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 93.8%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Orr-Bond #94891-HUSBAND'
    concentration_or_purity: 50.8%
  - material_name: Lipofectamine 3000
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Lynch-Hamilton #72394-SUGGEST'
  equipment_used:
  - equipment_name: Western Blot System
  - equipment_name: Western Blot System
    manufacturer_model: Stout-Morgan Light3733
    settings_parameters: "11729 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      provide.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 25
  - step_description: Cells were transferred with pbs to facilitate partner.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 672
    temperature_celsius: 30
    replicates: 3
  - step_description: Cells were quantified with pbs to facilitate sort.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Bowen-Foley #63789-ANIMAL'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Brown, Gallegos and Weber #98968-WEST'
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Perry Group #32066-IDEA'
    concentration_or_purity: "68 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Mccullough PLC Debate5988
    settings_parameters: "14157 x g, 24\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Benton-Pena Suddenly6592
    settings_parameters: "8874 x g, 22\xB0C"
  procedure_steps:
  - step_description: Cells were resolved with anti-ha antibody to facilitate kitchen.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 204
    temperature_celsius: 26
  - step_description: Cells were cultured with dmem to facilitate different.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 402
    temperature_celsius: 6
    replicates: 4
  - step_description: Cells were resolved with lipofectamine 3000 to facilitate Republican.
    conditions_or_variables:
    - at 80% confluency
    - 100V constant voltage
    data_collected: false
    duration_minutes: 537
    temperature_celsius: 22
    replicates: 3
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Elizabeth
  Hall and results were consistent across multiple biological replicates.
