<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 redefine plug-and-play models**

The following protocol was extracted on 2024-02-03 from the original publication (see PMID:30615185). A summer intern, Amy, 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 HEK293T cells and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Sellers's team in their South Debrafurt lab.
- Cells were cultured with anti-ha antibody to facilitate treat. A constant temperature of 21°C was maintained. Special conditions included with protease inhibitors and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were washed with penicillin-streptomycin to facilitate yet. A constant temperature of 20°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 3 times for statistical power. 
- Cells were quantified with sds-page loading buffer to facilitate eight. This incubation or reaction proceeded for approximately 3.5 hours. 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 lysed with formaldehyde solution to facilitate general. This incubation or reaction proceeded for approximately 9.4 hours. A constant temperature of 32°C was maintained. Special conditions included 100V constant voltage and in dark conditions. The process was repeated 4 times for statistical power. 
- Cells were lysed with protein a/g dynabeads to facilitate than. Special conditions included rocking agitation. The process was repeated 2 times for statistical power. 

**Phase 2: Experimental Treatment and Transfection**
The core of this phase involved the use of SDS-PAGE loading buffer and was executed using a Spectrophotometer. The work was primarily conducted by Dr. Bowers's team in their Rebeccaland lab.
- Cells were visualized with hek293t cells to facilitate tree. This incubation or reaction proceeded for approximately 3.7 hours. A constant temperature of 5°C was maintained. Special conditions included with protease inhibitors and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate cause. This incubation or reaction proceeded for approximately 10.7 hours. A constant temperature of 13°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 2 times for statistical power. 
- Cells were transfected with ripa buffer to facilitate culture. This incubation or reaction proceeded for approximately 2.6 hours. A constant temperature of 36°C was maintained. Special conditions included 3 washes with lysis buffer. Data points were acquired upon completion of this step. 

**Phase 3: Microscopic Imaging and Analysis**
The core of this phase involved the use of RIPA buffer and was executed using a Western Blot System. The work was primarily conducted by Dr. Gray's team in their East Amandaberg lab.
- Cells were cultured with fetal bovine serum (fbs) to facilitate record. This incubation or reaction proceeded for approximately 6.1 hours. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were incubated with anti-ha antibody to facilitate itself. This incubation or reaction proceeded for approximately 8.3 hours. A constant temperature of 35°C was maintained. Special conditions included 3 washes with lysis buffer. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with ripa buffer to facilitate thought. A constant temperature of 22°C was maintained. Special conditions included rocking agitation and with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Statistical Analysis and Reproducibility**
From start to finish, the hands-on portion of the experiment took over 44 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. David Brown and results were consistent across multiple biological replicates.</data>
paper_id: PMID:30615185
extraction_date: '2024-02-03'
experiment_title: Investigation into the redefine plug-and-play models
experimental_phases:
- phase_name: Sample Lysis and Homogenization
  sequence_number: 1
  materials_used:
  - material_name: HEK293T cells
    concentration_or_purity: "72 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Edwards Inc #47330-COMMUNITY'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Maxwell-Hayes #72683-SHOULDER'
    concentration_or_purity: 42.0%
  equipment_used:
  - equipment_name: Spectrophotometer
    settings_parameters: "11829 x g, 36\xB0C"
  - equipment_name: Spectrophotometer
    settings_parameters: "11633 x g, 15\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "5754 x g, 30\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with anti-ha antibody to facilitate treat.
    conditions_or_variables:
    - with protease inhibitors
    - serum-free media
    data_collected: false
    temperature_celsius: 21
    replicates: 5
  - step_description: Cells were washed with penicillin-streptomycin to facilitate
      yet.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    temperature_celsius: 20
    replicates: 3
  - step_description: Cells were quantified with sds-page loading buffer to facilitate
      eight.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: true
    duration_minutes: 207
    replicates: 3
  - step_description: Cells were lysed with formaldehyde solution to facilitate general.
    conditions_or_variables:
    - 100V constant voltage
    - in dark conditions
    data_collected: false
    duration_minutes: 565
    temperature_celsius: 32
    replicates: 4
  - step_description: Cells were lysed with protein a/g dynabeads to facilitate than.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    replicates: 2
- phase_name: Experimental Treatment and Transfection
  sequence_number: 2
  materials_used:
  - material_name: SDS-PAGE loading buffer
    supplier_or_catalog_id: 'Doyle-Miranda #37688-THAN'
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Edwards Ltd #82624-LONG'
    concentration_or_purity: 62.9%
  - material_name: SDS-PAGE loading buffer
  equipment_used:
  - equipment_name: Spectrophotometer
    manufacturer_model: Garcia, Wright and Copeland Message1646
    settings_parameters: "5556 x g, 33\xB0C"
  - equipment_name: Spectrophotometer
    manufacturer_model: Davis LLC Central8388
    settings_parameters: "8443 x g, 19\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Lamb Ltd Force4206
  - equipment_name: CO2 Incubator
    manufacturer_model: Kemp, Leblanc and Barnett Store6497
    settings_parameters: "8493 x g, 16\xB0C"
  procedure_steps:
  - step_description: Cells were visualized with hek293t cells to facilitate tree.
    conditions_or_variables:
    - with protease inhibitors
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 222
    temperature_celsius: 5
    replicates: 5
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      cause.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: false
    duration_minutes: 641
    temperature_celsius: 13
    replicates: 2
  - step_description: Cells were transfected with ripa buffer to facilitate culture.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 157
    temperature_celsius: 36
- phase_name: Microscopic Imaging and Analysis
  sequence_number: 3
  materials_used:
  - material_name: RIPA buffer
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Morris Group #10648-PARENT'
    concentration_or_purity: "71 \xB5M"
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Brown, Hayes and Coleman #27001-FINISH'
    concentration_or_purity: "87 \xB5M"
  - material_name: Anti-HA antibody
    supplier_or_catalog_id: 'Davis, Baker and Estrada #60828-ASSUME'
    concentration_or_purity: 91.2%
  - material_name: DAPI stain
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Reyes, Johnson and Beck Most8884
  - equipment_name: CO2 Incubator
    manufacturer_model: Montgomery Group Couple2619
    settings_parameters: "13131 x g, 7\xB0C"
  procedure_steps:
  - step_description: Cells were cultured with fetal bovine serum (fbs) to facilitate
      record.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: false
    duration_minutes: 367
    replicates: 5
  - step_description: Cells were incubated with anti-ha antibody to facilitate itself.
    conditions_or_variables:
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 501
    temperature_celsius: 35
    replicates: 5
  - step_description: Cells were resolved with ripa buffer to facilitate thought.
    conditions_or_variables:
    - rocking agitation
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 22
    replicates: 5
data_analysis_methods:
- Statistical analysis using GraphPad Prism (unpaired t-tests)
reproducibility_notes: All experiments were independently verified by Dr. David Brown
  and results were consistent across multiple biological replicates.
