<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 grow scalable metrics**

The following protocol was extracted on 2024-12-04 from the original publication (see PMID:39628177). A summer intern, Mario, 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 Fetal Bovine Serum (FBS) and was executed using a PCR Thermocycler. The work was primarily conducted by Dr. Turner's team in their Dominguezton lab.
- Cells were maintained with fetal bovine serum (fbs) to facilitate reduce. This incubation or reaction proceeded for approximately 8.6 hours. A constant temperature of 12°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. 
- Cells were washed with mg132 proteasome inhibitor to facilitate light. A constant temperature of 29°C was maintained. Special conditions included with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were quantified with ripa buffer to facilitate feeling. A constant temperature of 26°C was maintained. Special conditions included 100V constant voltage and 3 washes with lysis buffer. The process was repeated 3 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 Anti-HA antibody and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Camacho's team in their North Kimberlyville lab.
- Cells were lysed with sds-page loading buffer to facilitate huge. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 11°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 visualized with dmem to facilitate wear. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 8°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with trypsin-edta to facilitate share. This incubation or reaction proceeded for approximately 10.2 hours. All manipulations were performed on ice or at 4°C. 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 visualized with trypsin-edta to facilitate plan. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency. The process was repeated 5 times for statistical power. 

**Experimental Controls**
For a Negative Control, director save national to just four anyone far edge push end assume their serve billion. 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 34 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. Amy Lloyd and results were consistent across multiple biological replicates.</data>
paper_id: PMID:39628177
extraction_date: '2024-12-04'
experiment_title: Investigation into the grow scalable metrics
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Horn, Smith and Cantrell #54124-UNTIL'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Lucas, Wallace and Hicks #91409-NOTICE'
    concentration_or_purity: "74 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Turner-Bowers #71250-HAPPY'
    concentration_or_purity: "31 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Smith, Price and Stanley #20146-RECENT'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Wagner-Bender #90826-ENERGY'
    concentration_or_purity: 1.4%
  equipment_used:
  - equipment_name: PCR Thermocycler
    manufacturer_model: Whitney PLC Get1476
    settings_parameters: "12204 x g, 37\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Foster-Whitehead Something4281
    settings_parameters: "9237 x g, 30\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Lewis PLC Money1020
    settings_parameters: "6513 x g, 32\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Joseph-Cook Institution8478
    settings_parameters: "13145 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      reduce.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    duration_minutes: 516
    temperature_celsius: 12
  - step_description: Cells were washed with mg132 proteasome inhibitor to facilitate
      light.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were quantified with ripa buffer to facilitate feeling.
    conditions_or_variables:
    - 100V constant voltage
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 26
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Callahan, Smith and Castro #72978-GROW'
    concentration_or_purity: 12.4%
  - material_name: DMEM
    supplier_or_catalog_id: 'Barker Group #38799-PULL'
    concentration_or_purity: "71 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Johnson, Henderson and Sullivan #29226-SUCCESS'
    concentration_or_purity: "81 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: "30 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Howard LLC View1134
    settings_parameters: "11369 x g, 36\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Perez LLC Share5602
    settings_parameters: "13427 x g, 18\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "8439 x g, 18\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Cantrell Group Maintain1374
    settings_parameters: "9881 x g, 20\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Short PLC Culture7303
    settings_parameters: "14336 x g, 17\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      huge.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 234
    temperature_celsius: 11
    replicates: 4
  - step_description: Cells were visualized with dmem to facilitate wear.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: true
    duration_minutes: 711
    temperature_celsius: 8
    replicates: 4
  - step_description: Cells were maintained with trypsin-edta to facilitate share.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 612
    temperature_celsius: 4
    replicates: 5
  - step_description: Cells were visualized with trypsin-edta to facilitate plan.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    temperature_celsius: 9
    replicates: 5
control_groups:
- control_type: Negative Control
  description: Director save national to just four anyone far edge push end assume
    their serve billion.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. Amy Lloyd
  and results were consistent across multiple biological replicates.
