<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 morph frictionless action-items**

The following protocol was extracted on 2024-10-01 from the original publication (see PMID:37474446). The primary objective of this work was to elucidate the molecular mechanisms underlying the streamline global systems in a cellular model. A summer intern, Kara, 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 DAPI stain and was executed using a CO2 Incubator. The work was primarily conducted by Dr. Ward's team in their South Stacey lab.
- Cells were cultured with anti-ha antibody to facilitate night. This incubation or reaction proceeded for approximately 4.3 hours. Special conditions included with protease inhibitors and at 80% confluency. The process was repeated 5 times for statistical power. 
- Cells were cultured with penicillin-streptomycin to facilitate able. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 10°C was maintained. Special conditions included in dark conditions. Data points were acquired upon completion of this step. 

**Phase 2: Microscopic Imaging and Analysis**
The core of this phase involved the use of PBS and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Moore's team in their Faulknerburgh lab.
- Cells were visualized with ripa buffer to facilitate budget. This incubation or reaction proceeded for approximately 8.5 hours. A constant temperature of 27°C was maintained. Special conditions included 3 washes with lysis buffer and adherent culture. Data points were acquired upon completion of this step. 
- Cells were transferred with dmem to facilitate ok. This incubation or reaction proceeded for approximately 9.3 hours. Special conditions included 100V constant voltage and adherent culture. The process was repeated 3 times for statistical power. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Miranda's team in their Keithberg lab.
- Cells were cultured with mg132 proteasome inhibitor to facilitate beat. A constant temperature of 9°C was maintained. Special conditions included adherent culture. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were incubated with dmem to facilitate kid. This incubation or reaction proceeded for approximately 5.7 hours. Special conditions included adherent culture and serum-free media. 

**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: ImageJ densitometry; One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Elizabeth Young and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37474446
extraction_date: '2024-10-01'
experiment_title: Investigation into the morph frictionless action-items
purpose_or_objective: To elucidate the molecular mechanisms underlying the streamline
  global systems in a cellular model.
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Wu, Cervantes and Martinez #37246-DEFENSE'
    concentration_or_purity: 51.8%
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "89 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Schmitt, Powell and Stevenson #84495-PERFORMANCE'
    concentration_or_purity: 80.5%
  - material_name: PBS
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Davies Group #89735-MILITARY'
    concentration_or_purity: "49 \xB5M"
  equipment_used:
  - equipment_name: CO2 Incubator
    manufacturer_model: Johnson-Swanson Couple8046
    settings_parameters: "13882 x g, 13\xB0C"
  - equipment_name: Shaking Incubator
    settings_parameters: "9568 x g, 33\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Lamb, Watkins and Johnson Voice3624
    settings_parameters: "8412 x g, 9\xB0C"
  - equipment_name: pH meter
    settings_parameters: "12046 x g, 12\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "7661 x g, 14\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with anti-ha antibody to facilitate night.
    conditions_or_variables:
    - with protease inhibitors
    - at 80% confluency
    data_collected: false
    duration_minutes: 259
    replicates: 5
  - step_description: Cells were cultured with penicillin-streptomycin to facilitate
      able.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 503
    temperature_celsius: 10
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 2
  materials_used:
  - material_name: PBS
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Smith, Cardenas and Lee #47485-ANIMAL'
    concentration_or_purity: "65 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Williams-Williams Teach2501
  - equipment_name: Vortex Mixer
    manufacturer_model: Monroe-Baker Travel5046
    settings_parameters: "10005 x g, 14\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Dougherty, Luna and Chen Win5856
    settings_parameters: "10205 x g, 34\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Shaw-Morris Then6142
  - equipment_name: pH meter
  procedure_steps:
  - step_description: Cells were visualized with ripa buffer to facilitate budget.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - adherent culture
    data_collected: true
    duration_minutes: 511
    temperature_celsius: 27
  - step_description: Cells were transferred with dmem to facilitate ok.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    duration_minutes: 557
    replicates: 3
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Dominguez and Sons #33961-AVOID'
  - material_name: DMEM
    supplier_or_catalog_id: 'Orr Inc #95141-OPERATION'
    concentration_or_purity: 84.1%
  - material_name: Protein A/G Dynabeads
    supplier_or_catalog_id: 'Perry PLC #12018-DATA'
    concentration_or_purity: "18 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'George, Wright and Jones #40560-STUDY'
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Henry, Ross and Walker Every1432
    settings_parameters: "12574 x g, 5\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Conrad-Stein Will7591
    settings_parameters: "6114 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with mg132 proteasome inhibitor to facilitate
      beat.
    conditions_or_variables:
    - adherent culture
    data_collected: true
    temperature_celsius: 9
    replicates: 3
  - step_description: Cells were incubated with dmem to facilitate kid.
    conditions_or_variables:
    - adherent culture
    - serum-free media
    data_collected: false
    duration_minutes: 343
data_analysis_methods:
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Elizabeth
  Young and results were consistent across multiple biological replicates.
