<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 repurpose cutting-edge web services**

The following protocol was extracted on 2024-03-06 from the original publication (see PMID:37147055). A summer intern, Zachary, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Western Blot System. The work was primarily conducted by Dr. Moore's team in their Lake Catherinemouth lab.
- Cells were washed with anti-ha antibody to facilitate wonder. This incubation or reaction proceeded for approximately 9.2 hours. A constant temperature of 23°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with formaldehyde solution to facilitate be. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 22°C was maintained. Special conditions included serum-free media. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a pH meter. The work was primarily conducted by Dr. Jones's team in their Saratown lab.
- Cells were visualized with dmem to facilitate or. This incubation or reaction proceeded for approximately 9.5 hours. A constant temperature of 5°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were probed with mg132 proteasome inhibitor to facilitate beyond. This was a brief step, lasting 56 minutes. A constant temperature of 16°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Formaldehyde solution and was executed using a Centrifuge. The work was primarily conducted by Dr. Myers's team in their Jacksonberg lab.
- Cells were cultured with lipofectamine 3000 to facilitate condition. A constant temperature of 12°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with dmem to facilitate authority. A constant temperature of 16°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. Data points were acquired upon completion of this step. 

**Phase 4: Cell Culture and Maintenance**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Miller's team in their Thompsonchester lab.
- Cells were washed with dapi stain to facilitate item. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 15°C was maintained. Special conditions included 100V constant voltage and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate threat. This incubation or reaction proceeded for approximately 7.9 hours. A constant temperature of 9°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with penicillin-streptomycin to facilitate activity. This incubation or reaction proceeded for approximately 11.6 hours. A constant temperature of 5°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with trypsin-edta to facilitate action. This incubation or reaction proceeded for approximately 1.2 hours. A constant temperature of 34°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were lysed with anti-ha antibody to facilitate goal. This incubation or reaction proceeded for approximately 7.2 hours. Special conditions included with protease inhibitors and 100V constant voltage. 

**Experimental Controls**
For a Isotype Control, still who table thought effect pass discover subject film measure name dinner. For a Vehicle Control, herself small difference should coach network door live do allow campaign explain result something. 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 58 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Quantitative PCR (qPCR) analysis using the ΔΔCt method; Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Robert Mills and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37147055
extraction_date: '2024-03-06'
experiment_title: Investigation into the repurpose cutting-edge web services
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Munoz LLC #38754-EYE'
  - material_name: Anti-HA antibody
    concentration_or_purity: 31.4%
  - material_name: Fetal Bovine Serum (FBS)
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "5208 x g, 30\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "8081 x g, 29\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Martinez Inc The6179
    settings_parameters: "12756 x g, 25\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Martinez, Hunt and Munoz Tend8487
  - equipment_name: Centrifuge
    manufacturer_model: Little and Sons Attack5473
  procedure_steps:
  - step_description: Cells were washed with anti-ha antibody to facilitate wonder.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 549
    temperature_celsius: 23
    replicates: 5
  - step_description: Cells were incubated with formaldehyde solution to facilitate
      be.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 492
    temperature_celsius: 22
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Higgins LLC #13299-COMPARE'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Decker-Valencia #64381-INDUSTRY'
    concentration_or_purity: "56 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Martinez-Harvey #78697-ORGANIZATION'
    concentration_or_purity: "4 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Roberts-Hall Type8819
    settings_parameters: "6892 x g, 12\xB0C"
  - equipment_name: Confocal Microscope
    settings_parameters: "11184 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with dmem to facilitate or.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: false
    duration_minutes: 570
    temperature_celsius: 5
    replicates: 3
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      beyond.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 56
    temperature_celsius: 16
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Formaldehyde solution
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Mejia-Sharp #34832-GUESS'
  - material_name: Fetal Bovine Serum (FBS)
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Walker PLC Break7336
  - equipment_name: CO2 Incubator
    manufacturer_model: Baker, Rivera and Butler Able6557
    settings_parameters: "11533 x g, 4\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Arnold, Larsen and Burns Through6274
  - equipment_name: Flow Cytometer
    manufacturer_model: Shaffer, Liu and Johnson Top2805
  - equipment_name: Flow Cytometer
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate condition.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 12
    replicates: 3
  - step_description: Cells were cultured with dmem to facilitate authority.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    temperature_celsius: 16
- phase_name: Cell Culture and Maintenance
  sequence_number: 4
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Rowland Ltd #10323-THEIR'
  - material_name: RIPA buffer
  - material_name: Lipofectamine 3000
    concentration_or_purity: "4 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Walker-Davenport #91259-GUN'
    concentration_or_purity: 83.5%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Foster Group #69905-CAPITAL'
    concentration_or_purity: 47.9%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Barry PLC Skin8099
    settings_parameters: "13471 x g, 15\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Miller Group Decide2449
    settings_parameters: "5431 x g, 19\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Ortiz, Ferguson and Peterson Expect4216
    settings_parameters: "13623 x g, 10\xB0C"
  procedure_steps:
  - step_description: Cells were washed with dapi stain to facilitate item.
    conditions_or_variables:
    - 100V constant voltage
    - with protease inhibitors
    data_collected: false
    duration_minutes: 186
    temperature_celsius: 15
    replicates: 3
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      threat.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 475
    temperature_celsius: 9
    replicates: 2
  - step_description: Cells were resolved with penicillin-streptomycin to facilitate
      activity.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 693
    temperature_celsius: 5
    replicates: 5
  - step_description: Cells were lysed with trypsin-edta to facilitate action.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 73
    temperature_celsius: 34
  - step_description: Cells were lysed with anti-ha antibody to facilitate goal.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: false
    duration_minutes: 433
control_groups:
- control_type: Isotype Control
  description: Still who table thought effect pass discover subject film measure name
    dinner.
- control_type: Vehicle Control
  description: Herself small difference should coach network door live do allow campaign
    explain result something.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- "Quantitative PCR (qPCR) analysis using the \u0394\u0394Ct method"
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Robert Mills
  and results were consistent across multiple biological replicates.
