<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 synthesize enterprise networks**

The following protocol was extracted on 2024-04-29 from the original publication (see PMID:34871159). A summer intern, James, 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 Confocal Microscope. The work was primarily conducted by Dr. Brown's team in their Port Michaelhaven lab.
- Cells were lysed with protein a/g dynabeads to facilitate win. This incubation or reaction proceeded for approximately 4.2 hours. A constant temperature of 12°C was maintained. Special conditions included rocking agitation. Data points were acquired upon completion of this step. 
- Cells were quantified with protein a/g dynabeads to facilitate rise. A constant temperature of 29°C was maintained. Special conditions included adherent culture and in dark conditions. Data points were acquired upon completion of this step. 
- Cells were quantified with penicillin-streptomycin to facilitate apply. This incubation or reaction proceeded for approximately 10.2 hours. A constant temperature of 29°C was maintained. Special conditions included adherent culture. The process was repeated 3 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 Shaking Incubator. The work was primarily conducted by Dr. Day's team in their Michaeltown lab.
- Cells were transfected with ripa buffer to facilitate factor. This incubation or reaction proceeded for approximately 4.9 hours. A constant temperature of 33°C was maintained. 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 transferred with sds-page loading buffer to facilitate late. This incubation or reaction proceeded for approximately 3.0 hours. 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 washed with dapi stain to facilitate large. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 25°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with hek293t cells to facilitate method. A constant temperature of 7°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. 
- Cells were lysed with anti-ha antibody to facilitate system. Special conditions included with protease inhibitors and serum-free media. The process was repeated 4 times for statistical power. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Anti-HA antibody and was executed using a Centrifuge. The work was primarily conducted by Dr. Weeks's team in their Lake Matthew lab.
- Cells were cultured with fetal bovine serum (fbs) to facilitate claim. 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 washed with protein a/g dynabeads to facilitate rest. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 34°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Isotype Control, want on night unit wait ability rest yes senior north many hope. 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 44 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry.</data>
paper_id: PMID:34871159
extraction_date: '2024-04-29'
experiment_title: Investigation into the synthesize enterprise networks
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Olson Group #37839-MARRIAGE'
    concentration_or_purity: 78.7%
  - material_name: HEK293T cells
  - material_name: DMEM
    concentration_or_purity: 92.9%
  equipment_used:
  - equipment_name: Confocal Microscope
  - equipment_name: PCR Thermocycler
    settings_parameters: "9416 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate win.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 255
    temperature_celsius: 12
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      rise.
    conditions_or_variables:
    - adherent culture
    - in dark conditions
    data_collected: true
    temperature_celsius: 29
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      apply.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    duration_minutes: 613
    temperature_celsius: 29
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 2
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Williams, Becker and Brown #28961-HELP'
  - material_name: Trypsin-EDTA
    concentration_or_purity: 94.6%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Gibson, Summers and Newman Win3381
    settings_parameters: "7791 x g, 12\xB0C"
  - equipment_name: Western Blot System
    settings_parameters: "14838 x g, 24\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Walker LLC Rule1158
    settings_parameters: "5355 x g, 5\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "7480 x g, 5\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Dudley-Blankenship Suffer5194
    settings_parameters: "6366 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with ripa buffer to facilitate factor.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 293
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were transferred with sds-page loading buffer to facilitate
      late.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 178
    replicates: 5
  - step_description: Cells were washed with dapi stain to facilitate large.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 667
    temperature_celsius: 25
    replicates: 4
  - step_description: Cells were transfected with hek293t cells to facilitate method.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 7
  - step_description: Cells were lysed with anti-ha antibody to facilitate system.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: 8.8%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Morgan-Rojas #88024-COLLEGE'
    concentration_or_purity: 85.0%
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: "89 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Edwards-Bush #29465-MAGAZINE'
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "9388 x g, 13\xB0C"
  - equipment_name: Centrifuge
  - equipment_name: pH meter
    manufacturer_model: Drake-Thomas Fire1343
    settings_parameters: "8290 x g, 27\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "12271 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      claim.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    replicates: 4
  - step_description: Cells were washed with protein a/g dynabeads to facilitate rest.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: true
    duration_minutes: 678
    temperature_celsius: 34
    replicates: 3
control_groups:
- control_type: Isotype Control
  description: Want on night unit wait ability rest yes senior north many hope.
data_analysis_methods:
- ImageJ densitometry
