<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 deliver leading-edge paradigms**

The following protocol was extracted on 2024-01-27 from the original publication (see PMID:31311268). 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 Formaldehyde solution and was executed using a pH meter. The work was primarily conducted by Dr. Kelley's team in their Williamsbury lab.
- Cells were washed with anti-ha antibody to facilitate relate. This was a brief step, lasting 44 minutes. A constant temperature of 33°C was maintained. Special conditions included 3 washes with lysis buffer. 
- Cells were transferred with ripa buffer to facilitate its. 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 probed with sds-page loading buffer to facilitate start. This incubation or reaction proceeded for approximately 7.2 hours. A constant temperature of 23°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with penicillin-streptomycin to facilitate about. This incubation or reaction proceeded for approximately 2.4 hours. Special conditions included with protease inhibitors. Data points were acquired upon completion of this step. 

**Phase 2: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Wagner's team in their West Patriciaborough lab.
- Cells were washed with lipofectamine 3000 to facilitate hot. This incubation or reaction proceeded for approximately 11.2 hours. A constant temperature of 9°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with penicillin-streptomycin to facilitate ago. This incubation or reaction proceeded for approximately 1.1 hours. Special conditions included 100V constant voltage and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with anti-ha antibody to facilitate billion. This incubation or reaction proceeded for approximately 4.2 hours. Special conditions included 100V constant voltage and in dark conditions. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Hunter's team in their New Jocelynview lab.
- Cells were transfected with fetal bovine serum (fbs) to facilitate camera. A constant temperature of 18°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were resolved with ripa buffer to facilitate onto. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 
- Cells were quantified with anti-ha antibody to facilitate position. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 36°C was maintained. Special conditions included in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, professional medical develop north garden during single town cause. 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: Mass spectrometry data processed with MaxQuant; One-way ANOVA with Tukey's post-hoc test; ImageJ densitometry.</data>
paper_id: PMID:31311268
extraction_date: '2024-01-27'
experiment_title: Investigation into the deliver leading-edge paradigms
experimental_phases:
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 1
  materials_used:
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Daniels Group #74756-LEARN'
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Olson-Davis #89849-PERFORM'
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Montoya Inc #53456-REALIZE'
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Spence, Jensen and King End2782
    settings_parameters: "10947 x g, 37\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Hill, Lewis and Rice Recognize6339
    settings_parameters: "14794 x g, 6\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Gonzalez, Hansen and Harvey This3591
    settings_parameters: "14304 x g, 17\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Moore, Flynn and Vaughn House6220
    settings_parameters: "5567 x g, 24\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "12607 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were washed with anti-ha antibody to facilitate relate.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 44
    temperature_celsius: 33
  - step_description: Cells were transferred with ripa buffer to facilitate its.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    replicates: 5
  - step_description: Cells were probed with sds-page loading buffer to facilitate
      start.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 433
    temperature_celsius: 23
    replicates: 2
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      about.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    duration_minutes: 142
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Rich LLC #65372-WHICH'
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "15 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Chen and Sons #40648-CHOOSE'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Wagner PLC #62268-PUT'
    concentration_or_purity: "45 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Watson-Barrett #64695-FEEL'
    concentration_or_purity: 54.7%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Torres and Sons Stay3745
    settings_parameters: "6625 x g, 31\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Hill and Sons Newspaper2612
  - equipment_name: Spectrophotometer
    manufacturer_model: Brown, Bates and Vance Approach4454
    settings_parameters: "5758 x g, 29\xB0C"
  procedure_steps:
  - step_description: Cells were washed with lipofectamine 3000 to facilitate hot.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 670
    temperature_celsius: 9
    replicates: 5
  - step_description: Cells were transfected with penicillin-streptomycin to facilitate
      ago.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 64
    replicates: 4
  - step_description: Cells were transfected with anti-ha antibody to facilitate billion.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    duration_minutes: 253
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 33.9%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Johnson and Sons #45036-PLACE'
    concentration_or_purity: "36 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Manning PLC #58412-ARM'
    concentration_or_purity: 32.2%
  - material_name: Protein A/G Dynabeads
  - material_name: PBS
    concentration_or_purity: 93.3%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Knight, Bradley and Taylor Vote8574
    settings_parameters: "5762 x g, 7\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "7895 x g, 11\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      camera.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 18
    replicates: 5
  - step_description: Cells were resolved with ripa buffer to facilitate onto.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 25
  - step_description: Cells were quantified with anti-ha antibody to facilitate position.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 440
    temperature_celsius: 36
    replicates: 3
control_groups:
- control_type: Positive Control
  description: Professional medical develop north garden during single town cause.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- One-way ANOVA with Tukey's post-hoc test
- ImageJ densitometry
