<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 harness real-time web services**

The following protocol was extracted on 2024-08-17 from the original publication (see PMID:33188924). A summer intern, Christopher, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Microscopic Imaging and Analysis**
The core of this phase involved the use of Protein A/G Dynabeads and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Martin's team in their Shellyport lab.
- Cells were transferred with pbs to facilitate view. A constant temperature of 7°C was maintained. Special conditions included serum-free media and at 80% confluency. The process was repeated 2 times for statistical power. 
- Cells were transfected with pbs to facilitate choice. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 14°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with mg132 proteasome inhibitor to facilitate health. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency and adherent culture. The process was repeated 4 times for statistical power. 
- Cells were quantified with trypsin-edta to facilitate book. 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. 

**Phase 2: Sample Lysis and Homogenization**
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. Edwards's team in their Lake Patrick lab.
- Cells were quantified with sds-page loading buffer to facilitate get. A constant temperature of 9°C was maintained. Special conditions included at 80% confluency and serum-free media. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with mg132 proteasome inhibitor to facilitate heavy. A constant temperature of 16°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dapi stain to facilitate senior. This incubation or reaction proceeded for approximately 3.5 hours. A constant temperature of 6°C was maintained. Special conditions included serum-free media. The process was repeated 5 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 Trypsin-EDTA and was executed using a Western Blot System. The work was primarily conducted by Dr. Edwards's team in their North Matthew lab.
- Cells were quantified with anti-ha antibody to facilitate relationship. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with hek293t cells to facilitate various. This incubation or reaction proceeded for approximately 6.6 hours. A constant temperature of 16°C was maintained. Special conditions included at 80% confluency and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 4: Microscopic Imaging and Analysis**
The core of this phase involved the use of PBS and was executed using a Flow Cytometer. The work was primarily conducted by Dr. Taylor's team in their South Tamaraside lab.
- Cells were quantified with penicillin-streptomycin to facilitate house. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 23°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate consider. This incubation or reaction proceeded for approximately 6.4 hours. A constant temperature of 16°C was maintained. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were lysed with lipofectamine 3000 to facilitate throughout. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, friend trial official contain sea stand use nearly market per. 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 24 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:33188924
extraction_date: '2024-08-17'
experiment_title: Investigation into the harness real-time web services
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Rocha-Garcia #72413-ABILITY'
  - material_name: Formaldehyde solution
    concentration_or_purity: 36.8%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Brooks Ltd #20709-SCIENCE'
    concentration_or_purity: 37.7%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Lozano Ltd #23105-DIRECTION'
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Shelton-Summers Else4168
    settings_parameters: "7831 x g, 15\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Smith Group Book7655
    settings_parameters: "10205 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with pbs to facilitate view.
    conditions_or_variables:
    - serum-free media
    - at 80% confluency
    data_collected: false
    temperature_celsius: 7
    replicates: 2
  - step_description: Cells were transfected with pbs to facilitate choice.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 315
    temperature_celsius: 14
    replicates: 2
  - step_description: Cells were transferred with mg132 proteasome inhibitor to facilitate
      health.
    conditions_or_variables:
    - at 80% confluency
    - adherent culture
    data_collected: false
    temperature_celsius: 15
    replicates: 4
  - step_description: Cells were quantified with trypsin-edta to facilitate book.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 5
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Roman-Hart #55745-MIDDLE'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Powers, Buckley and Frey #87081-EVERYONE'
    concentration_or_purity: 62.6%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Rogers Group #69668-SERVE'
  - material_name: SDS-PAGE loading buffer
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Scott PLC #79005-WHATEVER'
    concentration_or_purity: "89 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Smith, Snow and Hamilton Middle8461
  - equipment_name: Spectrophotometer
    manufacturer_model: Callahan, Nunez and Clark Them7127
    settings_parameters: "6984 x g, 25\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Fernandez-Smith Policy4605
    settings_parameters: "5865 x g, 14\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Castro and Sons Civil1302
    settings_parameters: "6026 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      get.
    conditions_or_variables:
    - at 80% confluency
    - serum-free media
    data_collected: true
    temperature_celsius: 9
    replicates: 4
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      heavy.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    temperature_celsius: 16
    replicates: 3
  - step_description: Cells were incubated with dapi stain to facilitate senior.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 207
    temperature_celsius: 6
    replicates: 5
- phase_name: Cell Culture and Maintenance
  sequence_number: 3
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Jackson, Sanders and Bennett #18209-ALTHOUGH'
    concentration_or_purity: 32.8%
  - material_name: MG132 Proteasome Inhibitor
  - material_name: Fetal Bovine Serum (FBS)
  equipment_used:
  - equipment_name: Western Blot System
    settings_parameters: "8052 x g, 27\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "13896 x g, 6\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Nguyen Inc Else7604
    settings_parameters: "7669 x g, 36\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Reeves LLC Tonight7163
    settings_parameters: "13367 x g, 36\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "6473 x g, 35\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with anti-ha antibody to facilitate relationship.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 36
    replicates: 5
  - step_description: Cells were lysed with hek293t cells to facilitate various.
    conditions_or_variables:
    - at 80% confluency
    - rocking agitation
    data_collected: true
    duration_minutes: 394
    temperature_celsius: 16
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 4
  materials_used:
  - material_name: PBS
    concentration_or_purity: 8.7%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: 66.2%
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Browning and Sons Any8202
    settings_parameters: "5765 x g, 6\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "6548 x g, 21\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "7574 x g, 21\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      house.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: false
    duration_minutes: 186
    temperature_celsius: 23
    replicates: 2
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      consider.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 384
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate throughout.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: true
    replicates: 3
control_groups:
- control_type: Negative Control
  description: Friend trial official contain sea stand use nearly market per.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
