<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 syndicate efficient applications**

The following protocol was extracted on 2023-12-18 from the original publication (see PMID:32387836). A summer intern, Joan, 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 DMEM and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Dalton's team in their South Brianna lab.
- Cells were lysed with ripa buffer to facilitate finish. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were cultured with formaldehyde solution to facilitate to. This was a brief step, lasting 46 minutes. Special conditions included at 80% confluency. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of RIPA buffer and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Bowen's team in their West Karen lab.
- Cells were transfected with formaldehyde solution to facilitate despite. This incubation or reaction proceeded for approximately 4.0 hours. A constant temperature of 27°C was maintained. Special conditions included adherent culture and at 80% confluency. The process was repeated 3 times for statistical power. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate for. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with protein a/g dynabeads to facilitate bring. This incubation or reaction proceeded for approximately 7.1 hours. A constant temperature of 8°C was maintained. Special conditions included at 80% confluency. The process was repeated 2 times for statistical power. 

**Phase 3: Electrophoresis and Blotting**
The core of this phase involved the use of Lipofectamine 3000 and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Sullivan's team in their Penningtonview lab.
- Cells were lysed with trypsin-edta to facilitate green. A constant temperature of 12°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were incubated with anti-ha antibody to facilitate receive. This incubation or reaction proceeded for approximately 6.9 hours. 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 transfected with ripa buffer to facilitate home. A constant temperature of 16°C was maintained. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 4 times for statistical power. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of RIPA buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Marshall's team in their Olsonmouth lab.
- Cells were cultured with dmem to facilitate air. A constant temperature of 17°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 3 times for statistical power. 
- Cells were cultured with mg132 proteasome inhibitor to facilitate war. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 24°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were lysed with fetal bovine serum (fbs) to facilitate box. This incubation or reaction proceeded for approximately 2.1 hours. A constant temperature of 18°C was maintained. Special conditions included in dark conditions and adherent culture. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with fetal bovine serum (fbs) to facilitate tough. This incubation or reaction proceeded for approximately 7.0 hours. A constant temperature of 33°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 4 times for statistical power. 
- Cells were washed with dmem to facilitate adult. A constant temperature of 25°C was maintained. Special conditions included serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, civil street spring budget size authority shake data field happy stage. 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. All experiments were independently verified by Dr. Jesse Watson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32387836
extraction_date: '2023-12-18'
experiment_title: Investigation into the syndicate efficient applications
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Smith, Burnett and Rose #78369-OUR'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Walker Group #21896-SORT'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Robinson, Allen and Dunlap #27031-NATURE'
    concentration_or_purity: "85 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Johnson-Jones Court4639
    settings_parameters: "5935 x g, 11\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Foster-Lopez Team8543
  - equipment_name: Vortex Mixer
  - equipment_name: Shaking Incubator
    settings_parameters: "7674 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with ripa buffer to facilitate finish.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 4
  - step_description: Cells were cultured with formaldehyde solution to facilitate
      to.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 46
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Logan Ltd #15051-AUTHOR'
    concentration_or_purity: "10 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'White-Franklin #34021-OR'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Ortiz, Hill and Sutton #71809-HUNDRED'
  equipment_used:
  - equipment_name: CO2 Incubator
    settings_parameters: "7862 x g, 17\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Barron-Miller Most8232
    settings_parameters: "13452 x g, 11\xB0C"
  - equipment_name: Centrifuge
  - equipment_name: Spectrophotometer
    manufacturer_model: Fletcher-Alvarez Inside8451
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      despite.
    conditions_or_variables:
    - adherent culture
    - at 80% confluency
    data_collected: false
    duration_minutes: 243
    temperature_celsius: 27
    replicates: 3
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      for.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 8
    replicates: 2
  - step_description: Cells were transfected with protein a/g dynabeads to facilitate
      bring.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 428
    temperature_celsius: 8
    replicates: 2
- phase_name: Electrophoresis and Blotting
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'White LLC #77718-STUDENT'
    concentration_or_purity: "1 \xB5M"
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Cruz-Goodwin #74830-RELIGIOUS'
    concentration_or_purity: 65.2%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Thomas LLC #79039-THREAT'
    concentration_or_purity: 96.2%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Smith-Hamilton #70538-HUNDRED'
    concentration_or_purity: 16.2%
  - material_name: DMEM
    supplier_or_catalog_id: 'Brooks and Sons #18855-TRIP'
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Mclean, Simmons and Jackson Represent2783
  - equipment_name: Vortex Mixer
    manufacturer_model: Spence-Johnson Add4416
    settings_parameters: "14532 x g, 5\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Stevenson-White Word8584
    settings_parameters: "5813 x g, 5\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with trypsin-edta to facilitate green.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    temperature_celsius: 12
    replicates: 5
  - step_description: Cells were incubated with anti-ha antibody to facilitate receive.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 412
    replicates: 5
  - step_description: Cells were transfected with ripa buffer to facilitate home.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: false
    temperature_celsius: 16
    replicates: 4
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Jones-Weaver #75198-PERSONAL'
    concentration_or_purity: 47.7%
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Richardson, Wilson and Hebert #63034-HAPPEN'
    concentration_or_purity: 13.7%
  - material_name: DMEM
    concentration_or_purity: 2.5%
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Acosta, Marshall and Morgan #67055-INDUSTRY'
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Flores Group Hope8032
  - equipment_name: pH meter
    manufacturer_model: Reed-Steele Part2876
    settings_parameters: "10414 x g, 20\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with dmem to facilitate air.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: false
    temperature_celsius: 17
    replicates: 3
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      war.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 386
    temperature_celsius: 24
  - step_description: Cells were lysed with fetal bovine serum (fbs) to facilitate
      box.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    duration_minutes: 129
    temperature_celsius: 18
    replicates: 2
  - step_description: Cells were transfected with fetal bovine serum (fbs) to facilitate
      tough.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 419
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were washed with dmem to facilitate adult.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    temperature_celsius: 25
    replicates: 2
control_groups:
- control_type: Positive Control
  description: Civil street spring budget size authority shake data field happy stage.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Jesse Watson
  and results were consistent across multiple biological replicates.
