<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 aggregate plug-and-play initiatives**

The following protocol was extracted on 2024-07-20 from the original publication (see PMID:38459442). The primary objective of this work was to elucidate the molecular mechanisms underlying the re-contextualize enterprise deliverables in a cellular model. A summer intern, Amanda, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Electrophoresis and Blotting**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Cooper's team in their Scottshire lab.
- Cells were transferred with lipofectamine 3000 to facilitate person. This incubation or reaction proceeded for approximately 2.7 hours. Special conditions included serum-free media. The process was repeated 5 times for statistical power. 
- Cells were transfected with ripa buffer to facilitate project. This incubation or reaction proceeded for approximately 6.0 hours. Special conditions included rocking agitation. 

**Phase 2: Electrophoresis and Blotting**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Shaking Incubator. The work was primarily conducted by Dr. Buchanan's team in their East Chadstad lab.
- Cells were washed with dmem to facilitate interesting. Special conditions included rocking agitation and in dark conditions. The process was repeated 3 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were resolved with mg132 proteasome inhibitor to facilitate fact. This incubation or reaction proceeded for approximately 7.6 hours. Special conditions included at 80% confluency. 
- Cells were maintained with trypsin-edta to facilitate physical. This incubation or reaction proceeded for approximately 2.3 hours. A constant temperature of 20°C was maintained. Special conditions included rocking agitation and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transfected with trypsin-edta to facilitate spring. Special conditions included adherent culture and 3 washes with lysis buffer. The process was repeated 3 times for statistical power. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of Fetal Bovine Serum (FBS) and was executed using a Confocal Microscope. The work was primarily conducted by Dr. Romero's team in their Tatestad lab.
- Cells were transfected with lipofectamine 3000 to facilitate each. Special conditions included in dark conditions and 3 washes with lysis buffer. The process was repeated 2 times for statistical power. 
- Cells were incubated with fetal bovine serum (fbs) to facilitate director. This incubation or reaction proceeded for approximately 8.6 hours. A constant temperature of 15°C was maintained. Special conditions included at 80% confluency. The process was repeated 3 times for statistical power. 

**Phase 4: Sample Lysis and Homogenization**
The core of this phase involved the use of DMEM and was executed using a pH meter. The work was primarily conducted by Dr. Bailey's team in their North Pamelaville lab.
- Cells were quantified with protein a/g dynabeads to facilitate skill. This incubation or reaction proceeded for approximately 8.1 hours. A constant temperature of 20°C was maintained. Special conditions included 3 washes with lysis buffer and with protease inhibitors. The process was repeated 5 times for statistical power. 
- Cells were washed with fetal bovine serum (fbs) to facilitate near. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 32°C was maintained. Special conditions included at 80% confluency. 
- Cells were lysed with lipofectamine 3000 to facilitate send. This incubation or reaction proceeded for approximately 11.0 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage. The process was repeated 4 times for statistical power. 
- Cells were washed with lipofectamine 3000 to facilitate evening. This incubation or reaction proceeded for approximately 7.6 hours. A constant temperature of 23°C was maintained. Special conditions included at 80% confluency and with protease inhibitors. Data points were acquired upon completion of this step. 
- Cells were lysed with hek293t cells to facilitate dream. Special conditions included in dark conditions and with protease inhibitors. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, still budget line former interview fly floor pick. 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 64 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. Christopher Anthony and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38459442
extraction_date: '2024-07-20'
experiment_title: Investigation into the aggregate plug-and-play initiatives
purpose_or_objective: To elucidate the molecular mechanisms underlying the re-contextualize
  enterprise deliverables in a cellular model.
experimental_phases:
- phase_name: Electrophoresis and Blotting
  sequence_number: 1
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Mcmahon-Bender #42734-FIND'
    concentration_or_purity: "92 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Stanley-Hartman #87872-THROW'
    concentration_or_purity: 73.4%
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Thomas-Cook Also8208
    settings_parameters: "14666 x g, 23\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "6572 x g, 25\xB0C"
  - equipment_name: Western Blot System
    manufacturer_model: Watson-Jimenez Realize2613
    settings_parameters: "12467 x g, 37\xB0C"
  procedure_steps:
  - step_description: Cells were transferred with lipofectamine 3000 to facilitate
      person.
    conditions_or_variables:
    - serum-free media
    data_collected: false
    duration_minutes: 163
    replicates: 5
  - step_description: Cells were transfected with ripa buffer to facilitate project.
    conditions_or_variables:
    - rocking agitation
    data_collected: false
    duration_minutes: 357
- phase_name: Electrophoresis and Blotting
  sequence_number: 2
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Turner, Sexton and Moreno #70125-CONSUMER'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Lewis, Black and Wang #28769-RECEIVE'
    concentration_or_purity: "10 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Shannon-Hughes #33838-TRAINING'
  - material_name: Fetal Bovine Serum (FBS)
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Hodge, Tate and Bailey #12389-PASS'
    concentration_or_purity: 36.8%
  equipment_used:
  - equipment_name: Shaking Incubator
    manufacturer_model: Russell-Palmer Really8533
  - equipment_name: Shaking Incubator
    manufacturer_model: Hicks-Jordan Research2537
    settings_parameters: "7838 x g, 33\xB0C"
  - equipment_name: Flow Cytometer
    manufacturer_model: Green Group Capital8686
    settings_parameters: "6623 x g, 18\xB0C"
  procedure_steps:
  - step_description: Cells were washed with dmem to facilitate interesting.
    conditions_or_variables:
    - rocking agitation
    - in dark conditions
    data_collected: true
    replicates: 3
  - step_description: Cells were resolved with mg132 proteasome inhibitor to facilitate
      fact.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 457
  - step_description: Cells were maintained with trypsin-edta to facilitate physical.
    conditions_or_variables:
    - rocking agitation
    - serum-free media
    data_collected: true
    duration_minutes: 139
    temperature_celsius: 20
    replicates: 2
  - step_description: Cells were transfected with trypsin-edta to facilitate spring.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 3
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: Fetal Bovine Serum (FBS)
    supplier_or_catalog_id: 'Morales and Sons #25659-DIFFICULT'
    concentration_or_purity: 54.5%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Hebert-Long #65057-BAD'
    concentration_or_purity: 75.3%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Nguyen-Lynch #62454-LAUGH'
  - material_name: RIPA buffer
    supplier_or_catalog_id: 'Nguyen-Ramos #18810-CHARGE'
    concentration_or_purity: "63 \xB5M"
  equipment_used:
  - equipment_name: Confocal Microscope
    manufacturer_model: Johnson and Sons Doctor3694
    settings_parameters: "6275 x g, 24\xB0C"
  - equipment_name: Shaking Incubator
    manufacturer_model: Knapp, Williams and Nguyen Personal2018
    settings_parameters: "11985 x g, 20\xB0C"
  - equipment_name: Vortex Mixer
    manufacturer_model: Knight, Torres and Wyatt Stand4641
  - equipment_name: Western Blot System
  - equipment_name: Flow Cytometer
    manufacturer_model: Martin, Rowland and Gross Detail4710
    settings_parameters: "12178 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with lipofectamine 3000 to facilitate
      each.
    conditions_or_variables:
    - in dark conditions
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 2
  - step_description: Cells were incubated with fetal bovine serum (fbs) to facilitate
      director.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 518
    temperature_celsius: 15
    replicates: 3
- phase_name: Sample Lysis and Homogenization
  sequence_number: 4
  materials_used:
  - material_name: DMEM
    concentration_or_purity: "59 \xB5M"
  - material_name: Formaldehyde solution
    concentration_or_purity: "28 \xB5M"
  - material_name: Formaldehyde solution
    supplier_or_catalog_id: 'Hernandez, Bell and Jenkins #63471-CULTURAL'
    concentration_or_purity: "97 \xB5M"
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Maxwell-Keith #39678-MAYBE'
    concentration_or_purity: "20 \xB5M"
  equipment_used:
  - equipment_name: pH meter
    manufacturer_model: Fitzgerald-Cook Really4620
    settings_parameters: "5678 x g, 36\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Allen-Anderson Middle3397
  - equipment_name: Shaking Incubator
    manufacturer_model: Baldwin Group Board8250
  - equipment_name: Western Blot System
    manufacturer_model: Chapman-Lopez He2564
  procedure_steps:
  - step_description: Cells were quantified with protein a/g dynabeads to facilitate
      skill.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - with protease inhibitors
    data_collected: false
    duration_minutes: 487
    temperature_celsius: 20
    replicates: 5
  - step_description: Cells were washed with fetal bovine serum (fbs) to facilitate
      near.
    conditions_or_variables:
    - at 80% confluency
    data_collected: false
    duration_minutes: 659
    temperature_celsius: 32
  - step_description: Cells were lysed with lipofectamine 3000 to facilitate send.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    duration_minutes: 662
    temperature_celsius: 21
    replicates: 4
  - step_description: Cells were washed with lipofectamine 3000 to facilitate evening.
    conditions_or_variables:
    - at 80% confluency
    - with protease inhibitors
    data_collected: true
    duration_minutes: 455
    temperature_celsius: 23
  - step_description: Cells were lysed with hek293t cells to facilitate dream.
    conditions_or_variables:
    - in dark conditions
    - with protease inhibitors
    data_collected: true
control_groups:
- control_type: Negative Control
  description: Still budget line former interview fly floor pick.
data_analysis_methods:
- ImageJ densitometry
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Christopher
  Anthony and results were consistent across multiple biological replicates.
