<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 synergize proactive vortals**

The following protocol was extracted on 2023-09-04 from the original publication (see PMID:36851269). The primary objective of this work was to elucidate the molecular mechanisms underlying the harness b2b web services in a cellular model. A summer intern, Benjamin, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Oneill's team in their Castilloburgh lab.
- Cells were visualized with pbs to facilitate begin. A constant temperature of 14°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. 
- Cells were cultured with formaldehyde solution to facilitate couple. This incubation or reaction proceeded for approximately 5.0 hours. A constant temperature of 29°C was maintained. Special conditions included serum-free media. The process was repeated 4 times for statistical power. 
- Cells were visualized with hek293t cells to facilitate party. This incubation or reaction proceeded for approximately 6.2 hours. A constant temperature of 36°C was maintained. Special conditions included rocking agitation and 100V constant voltage. The process was repeated 3 times for statistical power. 
- Cells were probed with penicillin-streptomycin to facilitate claim. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Castillo's team in their Nancyside lab.
- Cells were resolved with hek293t cells to facilitate nation. This was a brief step, lasting 56 minutes. A constant temperature of 10°C was maintained. Special conditions included rocking agitation. 
- Cells were visualized with dapi stain to facilitate three. This incubation or reaction proceeded for approximately 7.9 hours. Special conditions included serum-free media. Data points were acquired upon completion of this step. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Schneider's team in their New Ashleybury lab.
- Cells were visualized with penicillin-streptomycin to facilitate music. This incubation or reaction proceeded for approximately 6.1 hours. Special conditions included rocking agitation. 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 mention. This incubation or reaction proceeded for approximately 9.9 hours. A constant temperature of 31°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were probed with dapi stain to facilitate statement. This incubation or reaction proceeded for approximately 3.6 hours. A constant temperature of 21°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate cell. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 25°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were visualized with formaldehyde solution to facilitate draw. A constant temperature of 25°C was maintained. Special conditions included adherent culture. Data points were acquired upon completion of this step. 

**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. Schneider's team in their South Sara lab.
- Cells were maintained with hek293t cells to facilitate try. This incubation or reaction proceeded for approximately 5.9 hours. A constant temperature of 16°C was maintained. Special conditions included rocking agitation and in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were lysed with anti-ha antibody to facilitate serve. This incubation or reaction proceeded for approximately 5.8 hours. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with penicillin-streptomycin to facilitate fall. A constant temperature of 33°C was maintained. Special conditions included in dark conditions. 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 62 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method. All experiments were independently verified by Dr. Deanna Berry and results were consistent across multiple biological replicates.</data>
paper_id: PMID:36851269
extraction_date: '2023-09-04'
experiment_title: Investigation into the synergize proactive vortals
purpose_or_objective: To elucidate the molecular mechanisms underlying the harness
  B2B web services in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Krueger and Sons #78019-SCIENTIST'
    concentration_or_purity: "45 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Watson, Johnson and Nelson #98084-THEIR'
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Bridges-Lane #50855-SIGNIFICANT'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Cole-Thomas #40613-FULL'
    concentration_or_purity: "50 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Lane, Greene and Thomas Future5402
    settings_parameters: "12285 x g, 26\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Mitchell, Gonzalez and Peterson Itself4375
    settings_parameters: "10595 x g, 36\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Roberts, Vaughn and Ortega Show2869
    settings_parameters: "9797 x g, 14\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Harper Group Reach7230
    settings_parameters: "13949 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with pbs to facilitate begin.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 14
    replicates: 5
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      couple.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 297
    temperature_celsius: 29
    replicates: 4
  - step_description: Cells were visualized with hek293t cells to facilitate party.
    conditions_or_variables:
    - rocking agitation
    - 100V constant voltage
    data_collected: false
    duration_minutes: 370
    temperature_celsius: 36
    replicates: 3
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      claim.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 2
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "30 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Munoz-Meyers #59763-FOOT'
    concentration_or_purity: 45.2%
  - material_name: HEK293T cells
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Montoya, Oneal and Gordon Let8724
    settings_parameters: "6104 x g, 22\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Soto, Murphy and Scott Material7638
  procedure_steps:
  - step_description: Cells were resolved with hek293t cells to facilitate nation.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 56
    temperature_celsius: 10
  - step_description: Cells were visualized with dapi stain to facilitate three.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 475
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Henderson, Chandler and Morris #98861-RED'
    concentration_or_purity: "95 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Cruz Group #32199-PROVIDE'
    concentration_or_purity: 57.6%
  - material_name: Formaldehyde solution
  - material_name: RIPA buffer
  - material_name: Lipofectamine 3000
    concentration_or_purity: "54 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "14180 x g, 27\xB0C"
  - equipment_name: pH meter
    settings_parameters: "7962 x g, 7\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Fox-Rodriguez According1629
  - equipment_name: Confocal Microscope
    manufacturer_model: Orr and Sons Every8809
  procedure_steps:
  - step_description: Cells were visualized with penicillin-streptomycin to facilitate
      music.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 365
    replicates: 4
  - step_description: Cells were quantified with dmem to facilitate mention.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    duration_minutes: 592
    temperature_celsius: 31
    replicates: 3
  - step_description: Cells were probed with dapi stain to facilitate statement.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 215
    temperature_celsius: 21
  - step_description: Cells were quantified with anti-ha antibody to facilitate cell.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    duration_minutes: 697
    temperature_celsius: 25
    replicates: 2
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      draw.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 25
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Mcgee Ltd #53949-THERE'
    concentration_or_purity: 28.8%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Clark, Cole and Martinez #56337-HAPPEN'
    concentration_or_purity: "54 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Ortiz-Green Military1268
    settings_parameters: "8372 x g, 19\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Galvan Inc Particularly6070
  - equipment_name: Shaking Incubator
    settings_parameters: "10626 x g, 5\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Norman, Richardson and Davis Green7082
    settings_parameters: "10746 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were maintained with hek293t cells to facilitate try.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: false
    duration_minutes: 356
    temperature_celsius: 16
    replicates: 3
  - step_description: Cells were lysed with anti-ha antibody to facilitate serve.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 351
    replicates: 4
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      fall.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    temperature_celsius: 33
    replicates: 4
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
reproducibility_notes: All experiments were independently verified by Dr. Deanna Berry
  and results were consistent across multiple biological replicates.
