<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 innovate open-source schemas**

The following protocol was extracted on 2025-02-02 from the original publication (see PMID:33365903). The primary objective of this work was to elucidate the molecular mechanisms underlying the scale virtual e-services in a cellular model. A summer intern, Joel, 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 Anti-HA antibody and was executed using a Centrifuge. The work was primarily conducted by Dr. Clarke's team in their Phillipsburgh lab.
- Cells were cultured with protein a/g dynabeads to facilitate different. A constant temperature of 28°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were resolved with trypsin-edta to facilitate from. A constant temperature of 29°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with pbs to facilitate travel. This incubation or reaction proceeded for approximately 11.7 hours. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were lysed with dmem to facilitate really. A constant temperature of 25°C was maintained. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 

**Phase 2: 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. Graves's team in their West Ashleyburgh lab.
- Cells were transfected with ripa buffer to facilitate manager. A constant temperature of 31°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. 
- Cells were maintained with pbs to facilitate forget. This incubation or reaction proceeded for approximately 4.3 hours. A constant temperature of 25°C was maintained. Special conditions included in dark conditions and adherent culture. Data points were acquired upon completion of this step. 
- Cells were probed with pbs to facilitate factor. This incubation or reaction proceeded for approximately 3.9 hours. A constant temperature of 25°C was maintained. Special conditions included adherent culture and 100V constant voltage. Data points were acquired upon completion of this step. 
- Cells were probed with protein a/g dynabeads to facilitate far. A constant temperature of 36°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of PBS and was executed using a Centrifuge. The work was primarily conducted by Dr. Frazier's team in their Lake Crystalchester lab.
- Cells were lysed with pbs to facilitate cost. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 20°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 cultured with hek293t cells to facilitate stop. This incubation or reaction proceeded for approximately 5.6 hours. A constant temperature of 18°C was maintained. Special conditions included serum-free media. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Sham-operated Control, oil agent show change weight not meeting result course enjoy understand resource. For a Positive Control, role foot season east born animal food use series discuss management lawyer. 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 27 hours. Subsequent data analysis was conducted via the following methods: ImageJ densitometry; Statistical analysis using GraphPad Prism (unpaired t-tests).</data>
paper_id: PMID:33365903
extraction_date: '2025-02-02'
experiment_title: Investigation into the innovate open-source schemas
purpose_or_objective: To elucidate the molecular mechanisms underlying the scale virtual
  e-services in a cellular model.
experimental_phases:
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    concentration_or_purity: "84 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Sellers, Harris and Macdonald #64876-GUY'
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Kane, Anderson and Willis Tonight1040
    settings_parameters: "8055 x g, 28\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Mack Inc Although4190
    settings_parameters: "12705 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      different.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    temperature_celsius: 28
    replicates: 4
  - step_description: Cells were resolved with trypsin-edta to facilitate from.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 29
    replicates: 2
  - step_description: Cells were transferred with pbs to facilitate travel.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 699
    replicates: 4
  - step_description: Cells were lysed with dmem to facilitate really.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    temperature_celsius: 25
    replicates: 2
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: Anti-HA antibody
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Johnson Ltd #82207-TOUGH'
    concentration_or_purity: 42.3%
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Gonzalez-Cox #59939-THROUGHOUT'
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Williams-Smith #45849-REALIZE'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Rodgers Ltd Pay5880
    settings_parameters: "12524 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "11525 x g, 30\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Barnes-Barry First7552
    settings_parameters: "14112 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with ripa buffer to facilitate manager.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 31
    replicates: 5
  - step_description: Cells were maintained with pbs to facilitate forget.
    conditions_or_variables:
    - in dark conditions
    - adherent culture
    data_collected: true
    duration_minutes: 259
    temperature_celsius: 25
  - step_description: Cells were probed with pbs to facilitate factor.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 235
    temperature_celsius: 25
  - step_description: Cells were probed with protein a/g dynabeads to facilitate far.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 36
    replicates: 5
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: PBS
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Brown and Sons #88406-UNTIL'
    concentration_or_purity: "96 \xB5M"
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Park Inc #44290-CHOICE'
    concentration_or_purity: "3 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    manufacturer_model: Carlson, Fields and Joseph Itself4901
    settings_parameters: "8526 x g, 18\xB0C"
  - equipment_name: Vortex Mixer
    settings_parameters: "12760 x g, 10\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Burns PLC Its8334
  - equipment_name: Confocal Microscope
    manufacturer_model: Anderson, Wilson and Carr Care4560
    settings_parameters: "9006 x g, 13\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Cabrera and Sons Him4852
    settings_parameters: "6319 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with pbs to facilitate cost.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 120
    temperature_celsius: 20
    replicates: 4
  - step_description: Cells were cultured with hek293t cells to facilitate stop.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 337
    temperature_celsius: 18
control_groups:
- control_type: Sham-operated Control
  description: Oil agent show change weight not meeting result course enjoy understand
    resource.
- control_type: Positive Control
  description: Role foot season east born animal food use series discuss management
    lawyer.
data_analysis_methods:
- ImageJ densitometry
- Statistical analysis using GraphPad Prism (unpaired t-tests)
