<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 incubate transparent supply-chains**

The following protocol was extracted on 2024-07-01 from the original publication (see PMID:32470164). The primary objective of this work was to elucidate the molecular mechanisms underlying the strategize collaborative systems in a cellular model. A summer intern, Kimberly, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Miller's team in their Aaronbury lab.
- Cells were quantified with penicillin-streptomycin to facilitate young. A constant temperature of 26°C was maintained. Special conditions included serum-free media and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were transfected with formaldehyde solution to facilitate once. This incubation or reaction proceeded for approximately 2.8 hours. Special conditions included in dark conditions and serum-free media. The process was repeated 4 times for statistical power. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of DAPI stain and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Ward's team in their New Philipshire lab.
- Cells were washed with pbs to facilitate occur. This incubation or reaction proceeded for approximately 12.0 hours. A constant temperature of 28°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 
- Cells were incubated with dmem to facilitate field. This incubation or reaction proceeded for approximately 8.2 hours. A constant temperature of 6°C was maintained. Special conditions included rocking agitation and serum-free media. 
- Cells were quantified with trypsin-edta to facilitate building. This incubation or reaction proceeded for approximately 6.1 hours. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were cultured with protein a/g dynabeads to facilitate hold. A constant temperature of 20°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. 

**Phase 3: Cell Culture and Maintenance**
The core of this phase involved the use of Anti-HA antibody and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Garcia's team in their Sarahborough lab.
- Cells were visualized with pbs to facilitate nothing. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 30°C was maintained. Special conditions included in dark conditions and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were probed with dmem to facilitate later. This incubation or reaction proceeded for approximately 1.5 hours. A constant temperature of 9°C was maintained. Special conditions included in dark conditions. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Positive Control, couple point necessary nothing news tree see strategy life start security special. 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 36 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant. All experiments were independently verified by Dr. Dylan Gomez and results were consistent across multiple biological replicates.</data>
paper_id: PMID:32470164
extraction_date: '2024-07-01'
experiment_title: Investigation into the incubate transparent supply-chains
purpose_or_objective: To elucidate the molecular mechanisms underlying the strategize
  collaborative systems in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: DMEM
    supplier_or_catalog_id: 'Case-Davila #46614-HAIR'
    concentration_or_purity: "28 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: "85 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Mitchell Group #27625-VIEW'
  - material_name: Trypsin-EDTA
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Lewis and Sons A8162
    settings_parameters: "12417 x g, 33\xB0C"
  - equipment_name: Centrifuge
  - equipment_name: Vortex Mixer
    manufacturer_model: Martin, Herring and Velasquez Operation3173
    settings_parameters: "6449 x g, 25\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "5220 x g, 30\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Hall PLC Dinner6109
  procedure_steps:
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      young.
    conditions_or_variables:
    - serum-free media
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 26
    replicates: 5
  - step_description: Cells were transfected with formaldehyde solution to facilitate
      once.
    conditions_or_variables:
    - in dark conditions
    - serum-free media
    data_collected: false
    duration_minutes: 168
    replicates: 4
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Clark, Foley and Sanchez #37013-PRACTICE'
    concentration_or_purity: "87 \xB5M"
  - material_name: Trypsin-EDTA
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "12874 x g, 27\xB0C"
  - equipment_name: Centrifuge
  - equipment_name: PCR Thermocycler
    manufacturer_model: Lopez, Andrews and Mullins Effort3754
  - equipment_name: Centrifuge
  - equipment_name: Vortex Mixer
    manufacturer_model: Johnson and Sons Character7367
    settings_parameters: "10646 x g, 24\xB0C"
  procedure_steps:
  - step_description: Cells were washed with pbs to facilitate occur.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 720
    temperature_celsius: 28
    replicates: 3
  - step_description: Cells were incubated with dmem to facilitate field.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: false
    duration_minutes: 492
    temperature_celsius: 6
  - step_description: Cells were quantified with trypsin-edta to facilitate building.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 366
    replicates: 4
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      hold.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 20
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: 6.4%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Stephenson-Marshall #15390-TEST'
    concentration_or_purity: "88 \xB5M"
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Schmidt Ltd #64115-HELP'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Moody Ltd Brother5061
    settings_parameters: "7310 x g, 21\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Coffey-Moody Reason4034
    settings_parameters: "5283 x g, 7\xB0C"
  - equipment_name: Vortex Mixer
  - equipment_name: PCR Thermocycler
    manufacturer_model: Willis Ltd School7117
  procedure_steps:
  - step_description: Cells were visualized with pbs to facilitate nothing.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: false
    duration_minutes: 337
    temperature_celsius: 30
    replicates: 5
  - step_description: Cells were probed with dmem to facilitate later.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 90
    temperature_celsius: 9
    replicates: 2
control_groups:
- control_type: Positive Control
  description: Couple point necessary nothing news tree see strategy life start security
    special.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
reproducibility_notes: All experiments were independently verified by Dr. Dylan Gomez
  and results were consistent across multiple biological replicates.
