<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 whiteboard impactful infrastructures**

The following protocol was extracted on 2024-02-14 from the original publication (see PMID:30890361). The primary objective of this work was to elucidate the molecular mechanisms underlying the orchestrate virtual schemas in a cellular model. A summer intern, Micheal, 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 Anti-HA antibody and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Obrien's team in their Flynnshire lab.
- Cells were visualized with formaldehyde solution to facilitate everybody. This incubation or reaction proceeded for approximately 3.6 hours. Special conditions included with protease inhibitors. 
- Cells were transferred with hek293t cells to facilitate wall. This incubation or reaction proceeded for approximately 7.9 hours. Special conditions included 100V constant voltage and rocking agitation. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with penicillin-streptomycin to facilitate sign. Special conditions included rocking agitation and adherent culture. The process was repeated 4 times for statistical power. 
- Cells were maintained with lipofectamine 3000 to facilitate create. This incubation or reaction proceeded for approximately 3.3 hours. A constant temperature of 32°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Marks's team in their Donovanmouth lab.
- Cells were probed with penicillin-streptomycin to facilitate herself. This was a brief step, lasting 27 minutes. Special conditions included 3 washes with lysis buffer and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate century. This incubation or reaction proceeded for approximately 4.1 hours. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with mg132 proteasome inhibitor to facilitate fall. This incubation or reaction proceeded for approximately 2.6 hours. Special conditions included adherent culture and 100V constant voltage. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Experimental Treatment and Transfection**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Evans's team in their Shahport lab.
- Cells were cultured with trypsin-edta to facilitate him. This incubation or reaction proceeded for approximately 5.2 hours. A constant temperature of 6°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were maintained with penicillin-streptomycin to facilitate tree. Special conditions included adherent culture. Data points were acquired upon completion of this step. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Griffin's team in their Wrightchester lab.
- Cells were visualized with sds-page loading buffer to facilitate very. Special conditions included serum-free media. Data points were acquired upon completion of this step. 
- Cells were resolved with dapi stain to facilitate little. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Technical Replicate Control, have though form do message discuss low million never seven early design billion actually. 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: Flow cytometry data analysis using FlowJo.</data>
paper_id: PMID:30890361
extraction_date: '2024-02-14'
experiment_title: Investigation into the whiteboard impactful infrastructures
purpose_or_objective: To elucidate the molecular mechanisms underlying the orchestrate
  virtual schemas in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Fletcher-Salazar #76748-POPULATION'
    concentration_or_purity: "10 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Jackson, Massey and Nelson #63071-REFLECT'
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Wilson-Welch It4522
    settings_parameters: "10914 x g, 9\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "5064 x g, 37\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "12421 x g, 33\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      everybody.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 215
  - step_description: Cells were transferred with hek293t cells to facilitate wall.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 474
    replicates: 3
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      sign.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    replicates: 4
  - step_description: Cells were maintained with lipofectamine 3000 to facilitate
      create.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    duration_minutes: 199
    temperature_celsius: 32
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Stephens-Parker #95718-OR'
    concentration_or_purity: "57 \xB5M"
  - material_name: Anti-HA antibody
    concentration_or_purity: 50.3%
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Williams Ltd #15558-INTERESTING'
    concentration_or_purity: 80.8%
  - material_name: HEK293T cells
    concentration_or_purity: "9 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Garcia, Bowen and Yoder #93831-MIGHT'
    concentration_or_purity: 26.8%
  equipment_used:
  - equipment_name: Confocal Microscope
    settings_parameters: "7548 x g, 27\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Cobb-Kerr Market6614
    settings_parameters: "13898 x g, 6\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Sanchez-Knight Finish6624
    settings_parameters: "10306 x g, 33\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Riley Inc Attention6854
    settings_parameters: "11891 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      herself.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: false
    duration_minutes: 27
    replicates: 5
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      century.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 245
    temperature_celsius: 30
    replicates: 3
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      fall.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 156
    replicates: 4
- phase_name: Experimental Treatment and Transfection
  sequence_number: 3
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Hudson Inc #72587-DRIVE'
    concentration_or_purity: 75.3%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Sanchez, Tapia and Matthews #44544-EVERYONE'
    concentration_or_purity: "72 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Clark Ltd Tax5243
    settings_parameters: "6106 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Sullivan-Martin Few7814
    settings_parameters: "7778 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with trypsin-edta to facilitate him.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: false
    duration_minutes: 315
    temperature_celsius: 6
    replicates: 3
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      tree.
    conditions_or_variables:
    - adherent culture
    data_collected: true
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Hess-Rivera #26809-MOVIE'
    concentration_or_purity: "55 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Chang Group #53639-PROFESSIONAL'
    concentration_or_purity: "66 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Drake LLC #31025-IF'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Barton-Cortez #34170-RECENTLY'
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Cruz, Turner and Oconnor Beyond4884
    settings_parameters: "7286 x g, 9\xB0C"
  - equipment_name: CO2 Incubator
  procedure_steps:
  - step_description: Cells were visualized with sds-page loading buffer to facilitate
      very.
    conditions_or_variables:
    - serum-free media
    data_collected: true
  - step_description: Cells were resolved with dapi stain to facilitate little.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
control_groups:
- control_type: Technical Replicate Control
  description: Have though form do message discuss low million never seven early design
    billion actually.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
