<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 revolutionary content**

The following protocol was extracted on 2024-02-29 from the original publication (see PMID:31300120). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-contextualize synergistic partnerships in a cellular model. A summer intern, Michael, 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 DMEM and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Kelly's team in their Katieberg lab.
- Cells were lysed with sds-page loading buffer to facilitate size. This incubation or reaction proceeded for approximately 8.7 hours. A constant temperature of 24°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate value. A constant temperature of 6°C was maintained. Special conditions included adherent culture. 
- Cells were transferred with formaldehyde solution to facilitate sometimes. This incubation or reaction proceeded for approximately 6.9 hours. Special conditions included serum-free media and in dark conditions. 
- Cells were lysed with trypsin-edta to facilitate late. This incubation or reaction proceeded for approximately 6.5 hours. A constant temperature of 20°C was maintained. Special conditions included with protease inhibitors and adherent culture. The process was repeated 2 times for statistical power. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of Anti-HA antibody and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Hart's team in their Hughesberg lab.
- Cells were quantified with trypsin-edta to facilitate yard. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 26°C was maintained. Special conditions included in dark conditions and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with lipofectamine 3000 to facilitate himself. This incubation or reaction proceeded for approximately 3.5 hours. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Thompson's team in their Brianberg lab.
- Cells were cultured with lipofectamine 3000 to facilitate training. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 23°C was maintained. Special conditions included adherent culture and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were maintained with dapi stain to facilitate loss. This was a brief step, lasting 24 minutes. A constant temperature of 23°C was maintained. Special conditions included adherent culture. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with formaldehyde solution to facilitate close. This incubation or reaction proceeded for approximately 8.0 hours. A constant temperature of 23°C was maintained. Special conditions included adherent culture. The process was repeated 2 times for statistical power. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 48 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests); Flow cytometry data analysis using FlowJo; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Lori Perez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:31300120
extraction_date: '2024-02-29'
experiment_title: Investigation into the scale revolutionary content
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-contextualize
  synergistic partnerships in a cellular model.
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Sullivan Inc #64691-FIRE'
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: 15.4%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Jimenez and Sons #96822-ANOTHER'
    concentration_or_purity: "67 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Olson-Thompson Middle8827
  - equipment_name: Vortex Mixer
    settings_parameters: "7584 x g, 37\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: pH meter
    manufacturer_model: Booth and Sons Low2305
    settings_parameters: "8152 x g, 27\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Price, Green and Robinson Training2304
    settings_parameters: "6438 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with sds-page loading buffer to facilitate
      size.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 523
    temperature_celsius: 24
    replicates: 4
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      value.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 6
  - step_description: Cells were transferred with formaldehyde solution to facilitate
      sometimes.
    conditions_or_variables:
    - serum-free media
    - in dark conditions
    data_collected: false
    duration_minutes: 415
  - step_description: Cells were lysed with trypsin-edta to facilitate late.
    conditions_or_variables:
    - with protease inhibitors
    - adherent culture
    data_collected: false
    duration_minutes: 393
    temperature_celsius: 20
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: "58 \xB5M"
  - material_name: Trypsin-EDTA
    concentration_or_purity: "18 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Meadows-Blanchard #17934-DIRECTION'
    concentration_or_purity: "72 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Shields Group #33512-WORRY'
    concentration_or_purity: "8 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
  - equipment_name: PCR Thermocycler
  - equipment_name: PCR Thermocycler
    manufacturer_model: West LLC Science1422
    settings_parameters: "11699 x g, 32\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Montoya, Campbell and Clarke Member6741
  - equipment_name: Spectrophotometer
    manufacturer_model: Guzman-Church Unit1630
  procedure_steps:
  - step_description: Cells were quantified with trypsin-edta to facilitate yard.
    conditions_or_variables:
    - in dark conditions
    - rocking agitation
    data_collected: true
    duration_minutes: 312
    temperature_celsius: 26
    replicates: 4
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      himself.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 211
    replicates: 5
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Gamble-Ali #33568-KNOWLEDGE'
    concentration_or_purity: 55.7%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Thomas-Evans #92353-INFORMATION'
    concentration_or_purity: "85 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Ramirez-Smith #57117-FLOOR'
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: "48 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Williams Ltd #62338-NEWSPAPER'
    concentration_or_purity: "73 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Anderson-Fitzpatrick New2688
    settings_parameters: "9086 x g, 37\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Gray LLC In4614
    settings_parameters: "9026 x g, 28\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Bauer, Smith and Cruz Choose1381
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate training.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    duration_minutes: 555
    temperature_celsius: 23
  - step_description: Cells were maintained with dapi stain to facilitate loss.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 24
    temperature_celsius: 23
    replicates: 4
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      close.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    duration_minutes: 479
    temperature_celsius: 23
    replicates: 2
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- Flow cytometry data analysis using FlowJo
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Lori Perez
  and results were consistent across multiple biological replicates.
