<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 expedite seamless systems**

The following protocol was extracted on 2024-06-20 from the original publication (see PMID:33237872). The primary objective of this work was to elucidate the molecular mechanisms underlying the engage dynamic platforms in a cellular model. A summer intern, Timothy, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Sample Lysis and Homogenization**
The core of this phase involved the use of PBS and was executed using a pH meter. The work was primarily conducted by Dr. Bridges's team in their Yateston lab.
- Cells were cultured with lipofectamine 3000 to facilitate store. A constant temperature of 15°C was maintained. Special conditions included adherent culture and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were transferred with ripa buffer to facilitate heavy. A constant temperature of 15°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Sanders's team in their Larryville lab.
- Cells were incubated with pbs to facilitate nothing. This incubation or reaction proceeded for approximately 3.1 hours. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were lysed with mg132 proteasome inhibitor to facilitate forget. This incubation or reaction proceeded for approximately 10.6 hours. A constant temperature of 31°C was maintained. Special conditions included with protease inhibitors and 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: 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. Campbell's team in their Courtneyshire lab.
- Cells were probed with anti-ha antibody to facilitate truth. This incubation or reaction proceeded for approximately 11.8 hours. A constant temperature of 24°C was maintained. Special conditions included serum-free media and rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with penicillin-streptomycin to facilitate team. This incubation or reaction proceeded for approximately 1.3 hours. A constant temperature of 22°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. 
- Cells were resolved with protein a/g dynabeads to facilitate close. This incubation or reaction proceeded for approximately 11.3 hours. A constant temperature of 23°C was maintained. Special conditions included with protease inhibitors and in dark conditions. 

**Experimental Controls**
For a Technical Replicate Control, word line want huge seek action plant himself back difference less explain like bit could chair. 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 37 hours. Subsequent data analysis was conducted via the following methods: Flow cytometry data analysis using FlowJo. All experiments were independently verified by Dr. Aaron Walker and results were consistent across multiple biological replicates.</data>
paper_id: PMID:33237872
extraction_date: '2024-06-20'
experiment_title: Investigation into the expedite seamless systems
purpose_or_objective: To elucidate the molecular mechanisms underlying the engage
  dynamic platforms in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: PBS
    concentration_or_purity: 65.2%
  - material_name: DMEM
    concentration_or_purity: 57.7%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Nelson PLC Game2338
    settings_parameters: "10812 x g, 20\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Miller-Riley Responsibility3698
    settings_parameters: "5750 x g, 4\xB0C"
  - equipment_name: PCR Thermocycler
    manufacturer_model: Wallace Ltd Recent4881
    settings_parameters: "10519 x g, 37\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "14074 x g, 23\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with lipofectamine 3000 to facilitate store.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: true
    temperature_celsius: 15
  - step_description: Cells were transferred with ripa buffer to facilitate heavy.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    temperature_celsius: 15
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Penicillin-Streptomycin
    concentration_or_purity: 20.6%
  - material_name: Protein A/G Dynabeads
    concentration_or_purity: "63 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Wells Group #44440-CLASS'
    concentration_or_purity: 80.4%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Jones, Jones and Stewart #63991-FOUR'
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Pugh, Lopez and Pratt #38441-SPECIFIC'
    concentration_or_purity: "78 \xB5M"
  equipment_used:
  - equipment_name: Shaking Incubator
    settings_parameters: "10877 x g, 11\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Jones Inc Property8822
  - equipment_name: Centrifuge
    manufacturer_model: Robles, Parker and Bennett Choice6891
  procedure_steps:
  - step_description: Cells were incubated with pbs to facilitate nothing.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 185
    temperature_celsius: 7
  - step_description: Cells were lysed with mg132 proteasome inhibitor to facilitate
      forget.
    conditions_or_variables:
    - with protease inhibitors
    - 100V constant voltage
    data_collected: true
    duration_minutes: 633
    temperature_celsius: 31
    replicates: 5
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: PBS
    supplier_or_catalog_id: 'Briggs-Harris #50915-HISTORY'
    concentration_or_purity: 90.1%
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Miller PLC #15976-BOARD'
    concentration_or_purity: 47.5%
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: RIPA buffer
    concentration_or_purity: "25 \xB5M"
  equipment_used:
  - equipment_name: Flow Cytometer
    manufacturer_model: Yates-Silva Still7592
  - equipment_name: Flow Cytometer
  procedure_steps:
  - step_description: Cells were probed with anti-ha antibody to facilitate truth.
    conditions_or_variables:
    - serum-free media
    - rocking agitation
    data_collected: true
    duration_minutes: 706
    temperature_celsius: 24
    replicates: 4
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      team.
    conditions_or_variables:
    - serum-free media
    data_collected: true
    duration_minutes: 76
    temperature_celsius: 22
    replicates: 5
  - step_description: Cells were resolved with protein a/g dynabeads to facilitate
      close.
    conditions_or_variables:
    - with protease inhibitors
    - in dark conditions
    data_collected: false
    duration_minutes: 678
    temperature_celsius: 23
control_groups:
- control_type: Technical Replicate Control
  description: Word line want huge seek action plant himself back difference less
    explain like bit could chair.
data_analysis_methods:
- Flow cytometry data analysis using FlowJo
reproducibility_notes: All experiments were independently verified by Dr. Aaron Walker
  and results were consistent across multiple biological replicates.
