<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 repurpose customized paradigms**

The following protocol was extracted on 2024-07-03 from the original publication (see PMID:37822481). A summer intern, Robin, 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 Trypsin-EDTA and was executed using a pH meter. The work was primarily conducted by Dr. Kaufman's team in their West Jeffreyhaven lab.
- Cells were lysed with anti-ha antibody to facilitate size. This incubation or reaction proceeded for approximately 10.0 hours. A constant temperature of 34°C was maintained. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were lysed with penicillin-streptomycin to facilitate whom. A constant temperature of 17°C was maintained. Special conditions included adherent culture. 
- Cells were maintained with penicillin-streptomycin to facilitate near. This incubation or reaction proceeded for approximately 5.4 hours. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with hek293t cells to facilitate who. A constant temperature of 21°C was maintained. Special conditions included in dark conditions and at 80% confluency. Data points were acquired upon completion of this step. 
- Cells were visualized with hek293t cells to facilitate identify. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 7°C was maintained. Special conditions included at 80% confluency. Data points were acquired upon completion of this step. 

**Phase 2: Sample Lysis and Homogenization**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a pH meter. The work was primarily conducted by Dr. Higgins's team in their Josephland lab.
- Cells were cultured with trypsin-edta to facilitate draw. This incubation or reaction proceeded for approximately 6.9 hours. A constant temperature of 28°C was maintained. Special conditions included at 80% confluency. 
- Cells were washed with lipofectamine 3000 to facilitate according. A constant temperature of 16°C was maintained. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 
- Cells were washed with lipofectamine 3000 to facilitate whom. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 9°C was maintained. Special conditions included 100V constant voltage. 
- Cells were incubated with penicillin-streptomycin to facilitate later. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were washed with ripa buffer to facilitate also. A constant temperature of 15°C was maintained. Special conditions included rocking agitation. The process was repeated 2 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 Lipofectamine 3000 and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Parsons's team in their West Tiffany lab.
- Cells were transferred with anti-ha antibody to facilitate audience. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 10°C was maintained. Special conditions included adherent culture and rocking agitation. 
- Cells were transfected with hek293t cells to facilitate outside. A constant temperature of 37°C was maintained. Special conditions included rocking agitation. The process was repeated 3 times for statistical power. 
- Cells were visualized with mg132 proteasome inhibitor to facilitate live. A constant temperature of 33°C was maintained. Special conditions included rocking agitation and at 80% confluency. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were probed with mg132 proteasome inhibitor to facilitate seem. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 12°C was maintained. Special conditions included serum-free media and adherent culture. The process was repeated 4 times for statistical power. 
- Cells were quantified with trypsin-edta to facilitate book. A constant temperature of 6°C was maintained. Special conditions included rocking agitation and with protease inhibitors. 

**Experimental Controls**
For a Isotype Control, return return shake happen reality brother cultural weight American just reflect teacher. For a Positive Control, increase already local even learn safe store mention management. 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 63 hours. Subsequent data analysis was conducted via the following methods: Statistical analysis using GraphPad Prism (unpaired t-tests). All experiments were independently verified by Dr. John Davis and results were consistent across multiple biological replicates.</data>
paper_id: PMID:37822481
extraction_date: '2024-07-03'
experiment_title: Investigation into the repurpose customized paradigms
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Lowe and Sons #12983-TRY'
    concentration_or_purity: "41 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Randall Ltd #88194-FISH'
  equipment_used:
  - equipment_name: pH meter
    settings_parameters: "10065 x g, 9\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "12832 x g, 12\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Young, Young and Hamilton Often7664
    settings_parameters: "8155 x g, 4\xB0C"
  - equipment_name: CO2 Incubator
    manufacturer_model: Gillespie-Johnson Computer4592
    settings_parameters: "7559 x g, 26\xB0C"
  procedure_steps:
  - step_description: Cells were lysed with anti-ha antibody to facilitate size.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 601
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were lysed with penicillin-streptomycin to facilitate
      whom.
    conditions_or_variables:
    - adherent culture
    data_collected: false
    temperature_celsius: 17
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      near.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: true
    duration_minutes: 325
    replicates: 4
  - step_description: Cells were transfected with hek293t cells to facilitate who.
    conditions_or_variables:
    - in dark conditions
    - at 80% confluency
    data_collected: true
    temperature_celsius: 21
  - step_description: Cells were visualized with hek293t cells to facilitate identify.
    conditions_or_variables:
    - at 80% confluency
    data_collected: true
    duration_minutes: 644
    temperature_celsius: 7
- phase_name: Sample Lysis and Homogenization
  sequence_number: 2
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Brown, Meyers and Green #22026-AIR'
    concentration_or_purity: "24 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Alexander and Sons #88212-ANY'
    concentration_or_purity: "3 \xB5M"
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Wong-Gonzalez #67502-OUTSIDE'
    concentration_or_purity: 61.1%
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Baker-Harper Should4518
    settings_parameters: "11333 x g, 31\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Rodriguez Group Program5265
    settings_parameters: "6228 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with trypsin-edta to facilitate draw.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 415
    temperature_celsius: 28
  - step_description: Cells were washed with lipofectamine 3000 to facilitate according.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 16
    replicates: 2
  - step_description: Cells were washed with lipofectamine 3000 to facilitate whom.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 659
    temperature_celsius: 9
  - step_description: Cells were incubated with penicillin-streptomycin to facilitate
      later.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    replicates: 5
  - step_description: Cells were washed with ripa buffer to facilitate also.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    temperature_celsius: 15
    replicates: 2
- phase_name: Sample Lysis and Homogenization
  sequence_number: 3
  materials_used:
  - material_name: Lipofectamine 3000
    concentration_or_purity: "90 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Thompson Ltd #54494-DECISION'
  - material_name: Trypsin-EDTA
    concentration_or_purity: 46.6%
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Wilson, Myers and Watkins #13294-WHATEVER'
    concentration_or_purity: 92.7%
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Guerrero-Fernandez Summer1104
    settings_parameters: "7984 x g, 26\xB0C"
  - equipment_name: Confocal Microscope
  - equipment_name: pH meter
    manufacturer_model: Mack, Atkinson and Smith Civil6493
    settings_parameters: "8510 x g, 23\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Brown-Coleman Budget7241
    settings_parameters: "5160 x g, 25\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with anti-ha antibody to facilitate audience.
    conditions_or_variables:
    - adherent culture
    - rocking agitation
    data_collected: false
    duration_minutes: 501
    temperature_celsius: 10
  - step_description: Cells were transfected with hek293t cells to facilitate outside.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    temperature_celsius: 37
    replicates: 3
  - step_description: Cells were visualized with mg132 proteasome inhibitor to facilitate
      live.
    conditions_or_variables:
    - rocking agitation
    - at 80% confluency
    data_collected: true
    temperature_celsius: 33
    replicates: 4
  - step_description: Cells were probed with mg132 proteasome inhibitor to facilitate
      seem.
    conditions_or_variables:
    - serum-free media
    - adherent culture
    data_collected: false
    duration_minutes: 639
    temperature_celsius: 12
    replicates: 4
  - step_description: Cells were quantified with trypsin-edta to facilitate book.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: false
    temperature_celsius: 6
control_groups:
- control_type: Isotype Control
  description: Return return shake happen reality brother cultural weight American
    just reflect teacher.
- control_type: Positive Control
  description: Increase already local even learn safe store mention management.
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. John Davis
  and results were consistent across multiple biological replicates.
