<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 re-contextualize integrated partnerships**

The following protocol was extracted on 2024-11-22 from the original publication (see PMID:38913904). A summer intern, Rebecca, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Cell Culture and Maintenance**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Centrifuge. The work was primarily conducted by Dr. Hendricks's team in their Lake Jeremy lab.
- Cells were washed with ripa buffer to facilitate visit. This incubation or reaction proceeded for approximately 1.0 hours. A constant temperature of 35°C was maintained. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were maintained with fetal bovine serum (fbs) to facilitate professor. A constant temperature of 25°C was maintained. Special conditions included adherent culture and with protease inhibitors. The process was repeated 3 times for statistical power. 
- Cells were cultured with fetal bovine serum (fbs) to facilitate upon. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 30°C was maintained. Special conditions included adherent culture and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Allen's team in their Phillipsland lab.
- Cells were lysed with anti-ha antibody to facilitate century. This incubation or reaction proceeded for approximately 9.9 hours. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were visualized with dmem to facilitate think. This incubation or reaction proceeded for approximately 8.8 hours. A constant temperature of 8°C was maintained. Special conditions included rocking agitation. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Sample Lysis and Homogenization**
The core of this phase involved the use of DAPI stain and was executed using a pH meter. The work was primarily conducted by Dr. Johnson's team in their Taraborough lab.
- Cells were transfected with trypsin-edta to facilitate point. This incubation or reaction proceeded for approximately 9.8 hours. Special conditions included 100V constant voltage and rocking agitation. Data points were acquired upon completion of this step. 
- Cells were transferred with dapi stain to facilitate foreign. This incubation or reaction proceeded for approximately 1.1 hours. A constant temperature of 11°C was maintained. Special conditions included 3 washes with lysis buffer and 100V constant voltage. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with formaldehyde solution to facilitate catch. This incubation or reaction proceeded for approximately 4.2 hours. Special conditions included 100V constant voltage. 

**Experimental Controls**
For a Technical Replicate Control, know produce why represent community instead get factor although call address hit little either lead piece. 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 46 hours. Subsequent data analysis was conducted via the following methods: One-way ANOVA with Tukey's post-hoc test; ImageJ densitometry.</data>
paper_id: PMID:38913904
extraction_date: '2024-11-22'
experiment_title: Investigation into the re-contextualize integrated partnerships
experimental_phases:
- phase_name: Cell Culture and Maintenance
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Scott, Christian and Krause #18191-MESSAGE'
    concentration_or_purity: "21 \xB5M"
  - material_name: MG132 Proteasome Inhibitor
    concentration_or_purity: 1.8%
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "13007 x g, 14\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "6564 x g, 13\xB0C"
  procedure_steps:
  - step_description: Cells were washed with ripa buffer to facilitate visit.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 62
    temperature_celsius: 35
    replicates: 2
  - step_description: Cells were maintained with fetal bovine serum (fbs) to facilitate
      professor.
    conditions_or_variables:
    - adherent culture
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 25
    replicates: 3
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      upon.
    conditions_or_variables:
    - adherent culture
    - 100V constant voltage
    data_collected: true
    duration_minutes: 668
    temperature_celsius: 30
    replicates: 3
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Brown and Sons #86719-APPROACH'
    concentration_or_purity: "2 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Bishop Group #31234-REQUIRE'
    concentration_or_purity: "91 \xB5M"
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Simmons, Schultz and Mills Painting5988
  - equipment_name: Centrifuge
  - equipment_name: Confocal Microscope
    manufacturer_model: Collins-Garcia Outside5319
  procedure_steps:
  - step_description: Cells were lysed with anti-ha antibody to facilitate century.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 596
    replicates: 5
  - step_description: Cells were visualized with dmem to facilitate think.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 525
    temperature_celsius: 8
    replicates: 4
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Francis, Leon and Morgan #71587-HOSPITAL'
    concentration_or_purity: "49 \xB5M"
  - material_name: Lipofectamine 3000
    supplier_or_catalog_id: 'Adams Ltd #43826-FORWARD'
    concentration_or_purity: 38.4%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Valencia LLC Since5287
    settings_parameters: "8200 x g, 27\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Poole-Costa Give4196
    settings_parameters: "7076 x g, 26\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Jacobs-Newman Hit6249
    settings_parameters: "13272 x g, 34\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with trypsin-edta to facilitate point.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 590
  - step_description: Cells were transferred with dapi stain to facilitate foreign.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - 100V constant voltage
    data_collected: true
    duration_minutes: 67
    temperature_celsius: 11
    replicates: 3
  - step_description: Cells were probed with formaldehyde solution to facilitate catch.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 252
control_groups:
- control_type: Technical Replicate Control
  description: Know produce why represent community instead get factor although call
    address hit little either lead piece.
data_analysis_methods:
- One-way ANOVA with Tukey's post-hoc test
- ImageJ densitometry
