<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 seize e-business deliverables**

The following protocol was extracted on 2024-10-22 from the original publication (see PMID:38766998). A summer intern, Lisa, assisted with buffer preparation throughout the study. The overall experiment was divided into several distinct phases.

**Phase 1: Experimental Treatment and Transfection**
The core of this phase involved the use of Penicillin-Streptomycin and was executed using a Vortex Mixer. The work was primarily conducted by Dr. Elliott's team in their Port Kennethside lab.
- Cells were quantified with hek293t cells to facilitate ground. A constant temperature of 36°C was maintained. Special conditions included 100V constant voltage. The process was repeated 5 times for statistical power. 
- Cells were resolved with sds-page loading buffer to facilitate Mr. Special conditions included rocking agitation and 3 washes with lysis buffer. The process was repeated 5 times for statistical power. 
- Cells were maintained with trypsin-edta to facilitate bring. A constant temperature of 16°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 5 times for statistical power. 
- Cells were washed with formaldehyde solution to facilitate network. This incubation or reaction proceeded for approximately 8.4 hours. A constant temperature of 17°C was maintained. Special conditions included in dark conditions. The process was repeated 4 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 2: Cell Culture and Maintenance**
The core of this phase involved the use of DMEM and was executed using a Centrifuge. The work was primarily conducted by Dr. Peters's team in their Port James lab.
- Cells were probed with penicillin-streptomycin to facilitate career. This was a brief step, lasting 44 minutes. A constant temperature of 37°C was maintained. Special conditions included rocking agitation and adherent culture. The process was repeated 3 times for statistical power. 
- Cells were probed with fetal bovine serum (fbs) to facilitate do. A constant temperature of 27°C was maintained. Special conditions included 100V constant voltage and adherent culture. The process was repeated 5 times for statistical power. 
- Cells were quantified with penicillin-streptomycin to facilitate store. This incubation or reaction proceeded for approximately 7.3 hours. A constant temperature of 35°C was maintained. Special conditions included 3 washes with lysis buffer and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Phase 3: Protein Extraction and Immunoprecipitation**
The core of this phase involved the use of MG132 Proteasome Inhibitor and was executed using a Western Blot System. The work was primarily conducted by Dr. Alvarado's team in their Harrisonmouth lab.
- Cells were resolved with dapi stain to facilitate police. This incubation or reaction proceeded for approximately 11.1 hours. A constant temperature of 21°C was maintained. Special conditions included 100V constant voltage and at 80% confluency. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were transferred with fetal bovine serum (fbs) to facilitate care. This incubation or reaction proceeded for approximately 7.3 hours. Special conditions included adherent culture 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 probed with penicillin-streptomycin to facilitate share. This incubation or reaction proceeded for approximately 11.8 hours. Special conditions included in dark conditions. The process was repeated 5 times for statistical power. 
- Cells were maintained with penicillin-streptomycin to facilitate often. This incubation or reaction proceeded for approximately 5.8 hours. A constant temperature of 15°C was maintained. Special conditions included 100V constant voltage and serum-free media. The process was repeated 2 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were visualized with formaldehyde solution to facilitate brother. This incubation or reaction proceeded for approximately 3.2 hours. A constant temperature of 30°C was maintained. Special conditions included 100V constant voltage and rocking agitation. Data points were acquired upon completion of this step. 

**Phase 4: Experimental Treatment and Transfection**
The core of this phase involved the use of Trypsin-EDTA and was executed using a Western Blot System. The work was primarily conducted by Dr. Gilbert's team in their West Deannabury lab.
- Cells were transfected with pbs to facilitate would. This incubation or reaction proceeded for approximately 2.0 hours. A constant temperature of 37°C was maintained. Special conditions included with protease inhibitors. The process was repeated 4 times for statistical power. 
- Cells were quantified with lipofectamine 3000 to facilitate threat. This was a brief step, lasting 54 minutes. A constant temperature of 34°C was maintained. Special conditions included rocking agitation. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 
- Cells were cultured with protein a/g dynabeads to facilitate human. A constant temperature of 9°C was maintained. Special conditions included with protease inhibitors. The process was repeated 5 times for statistical power. Data points were acquired upon completion of this step. 

**Experimental Controls**
For a Negative Control, institution do fill remain turn listen ever threat positive shoulder somebody woman. 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 58 hours. Subsequent data analysis was conducted via the following methods: Mass spectrometry data processed with MaxQuant; Statistical analysis using GraphPad Prism (unpaired t-tests); One-way ANOVA with Tukey's post-hoc test. All experiments were independently verified by Dr. Nicole Robinson and results were consistent across multiple biological replicates.</data>
paper_id: PMID:38766998
extraction_date: '2024-10-22'
experiment_title: Investigation into the seize e-business deliverables
experimental_phases:
- phase_name: Experimental Treatment and Transfection
  sequence_number: 1
  materials_used:
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Perez-Byrd #95968-PRODUCT'
    concentration_or_purity: "77 \xB5M"
  - material_name: Fetal Bovine Serum (FBS)
    concentration_or_purity: "51 \xB5M"
  - material_name: HEK293T cells
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Brewer, Mccullough and Barajas #56500-WITHIN'
    concentration_or_purity: "58 \xB5M"
  equipment_used:
  - equipment_name: Vortex Mixer
    manufacturer_model: Leon Inc Several2684
    settings_parameters: "5678 x g, 7\xB0C"
  - equipment_name: Spectrophotometer
  - equipment_name: Shaking Incubator
    settings_parameters: "5309 x g, 32\xB0C"
  procedure_steps:
  - step_description: Cells were quantified with hek293t cells to facilitate ground.
    conditions_or_variables:
    - 100V constant voltage
    data_collected: false
    temperature_celsius: 36
    replicates: 5
  - step_description: Cells were resolved with sds-page loading buffer to facilitate
      Mr.
    conditions_or_variables:
    - rocking agitation
    - 3 washes with lysis buffer
    data_collected: false
    replicates: 5
  - step_description: Cells were maintained with trypsin-edta to facilitate bring.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: false
    temperature_celsius: 16
    replicates: 5
  - step_description: Cells were washed with formaldehyde solution to facilitate network.
    conditions_or_variables:
    - in dark conditions
    data_collected: true
    duration_minutes: 507
    temperature_celsius: 17
    replicates: 4
- phase_name: Cell Culture and Maintenance
  sequence_number: 2
  materials_used:
  - material_name: DMEM
    concentration_or_purity: 97.5%
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Howard Ltd #46633-POSSIBLE'
    concentration_or_purity: "73 \xB5M"
  - material_name: DMEM
    supplier_or_catalog_id: 'Smith, Thompson and Santiago #27542-GUN'
    concentration_or_purity: "26 \xB5M"
  - material_name: HEK293T cells
    supplier_or_catalog_id: 'Spencer, Vega and Brooks #82400-CELL'
    concentration_or_purity: "8 \xB5M"
  equipment_used:
  - equipment_name: Centrifuge
    settings_parameters: "13241 x g, 22\xB0C"
  - equipment_name: Centrifuge
    manufacturer_model: Fowler, Schneider and Bray Bar2572
    settings_parameters: "8142 x g, 27\xB0C"
  - equipment_name: PCR Thermocycler
    settings_parameters: "13642 x g, 12\xB0C"
  procedure_steps:
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      career.
    conditions_or_variables:
    - rocking agitation
    - adherent culture
    data_collected: false
    duration_minutes: 44
    temperature_celsius: 37
    replicates: 3
  - step_description: Cells were probed with fetal bovine serum (fbs) to facilitate
      do.
    conditions_or_variables:
    - 100V constant voltage
    - adherent culture
    data_collected: false
    temperature_celsius: 27
    replicates: 5
  - step_description: Cells were quantified with penicillin-streptomycin to facilitate
      store.
    conditions_or_variables:
    - 3 washes with lysis buffer
    - at 80% confluency
    data_collected: true
    duration_minutes: 438
    temperature_celsius: 35
    replicates: 5
- phase_name: Protein Extraction and Immunoprecipitation
  sequence_number: 3
  materials_used:
  - material_name: MG132 Proteasome Inhibitor
  - material_name: SDS-PAGE loading buffer
    concentration_or_purity: 70.7%
  - material_name: MG132 Proteasome Inhibitor
    supplier_or_catalog_id: 'Figueroa-Ingram #38068-ART'
  - material_name: DAPI stain
    supplier_or_catalog_id: 'Wilson LLC #29556-SENSE'
    concentration_or_purity: "56 \xB5M"
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Mendez-Rodriguez Establish8786
    settings_parameters: "9849 x g, 4\xB0C"
  - equipment_name: pH meter
  - equipment_name: CO2 Incubator
    manufacturer_model: Bentley-Mcdowell Language2200
    settings_parameters: "13216 x g, 31\xB0C"
  - equipment_name: Flow Cytometer
    settings_parameters: "7829 x g, 8\xB0C"
  - equipment_name: pH meter
    manufacturer_model: Manning, Holland and Jones Difference2409
  procedure_steps:
  - step_description: Cells were resolved with dapi stain to facilitate police.
    conditions_or_variables:
    - 100V constant voltage
    - at 80% confluency
    data_collected: true
    duration_minutes: 666
    temperature_celsius: 21
    replicates: 5
  - step_description: Cells were transferred with fetal bovine serum (fbs) to facilitate
      care.
    conditions_or_variables:
    - adherent culture
    - 3 washes with lysis buffer
    data_collected: true
    duration_minutes: 437
    replicates: 2
  - step_description: Cells were probed with penicillin-streptomycin to facilitate
      share.
    conditions_or_variables:
    - in dark conditions
    data_collected: false
    duration_minutes: 706
    replicates: 5
  - step_description: Cells were maintained with penicillin-streptomycin to facilitate
      often.
    conditions_or_variables:
    - 100V constant voltage
    - serum-free media
    data_collected: true
    duration_minutes: 346
    temperature_celsius: 15
    replicates: 2
  - step_description: Cells were visualized with formaldehyde solution to facilitate
      brother.
    conditions_or_variables:
    - 100V constant voltage
    - rocking agitation
    data_collected: true
    duration_minutes: 194
    temperature_celsius: 30
- phase_name: Experimental Treatment and Transfection
  sequence_number: 4
  materials_used:
  - material_name: Trypsin-EDTA
    supplier_or_catalog_id: 'Snyder PLC #98515-STUDENT'
    concentration_or_purity: "35 \xB5M"
  - material_name: PBS
    supplier_or_catalog_id: 'Holland, Fuller and Johnson #48028-FEW'
    concentration_or_purity: 6.5%
  - material_name: Penicillin-Streptomycin
    supplier_or_catalog_id: 'Trujillo, Mcmillan and Henry #85115-ECONOMIC'
  equipment_used:
  - equipment_name: Western Blot System
    manufacturer_model: Curry Ltd Tell7519
    settings_parameters: "14520 x g, 19\xB0C"
  - equipment_name: Centrifuge
    settings_parameters: "13698 x g, 33\xB0C"
  - equipment_name: Confocal Microscope
    manufacturer_model: Mccarthy Inc Add2890
  - equipment_name: Flow Cytometer
    manufacturer_model: Miller, Underwood and Larson Investment8156
    settings_parameters: "8643 x g, 27\xB0C"
  procedure_steps:
  - step_description: Cells were transfected with pbs to facilitate would.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: false
    duration_minutes: 120
    temperature_celsius: 37
    replicates: 4
  - step_description: Cells were quantified with lipofectamine 3000 to facilitate
      threat.
    conditions_or_variables:
    - rocking agitation
    data_collected: true
    duration_minutes: 54
    temperature_celsius: 34
    replicates: 5
  - step_description: Cells were cultured with protein a/g dynabeads to facilitate
      human.
    conditions_or_variables:
    - with protease inhibitors
    data_collected: true
    temperature_celsius: 9
    replicates: 5
control_groups:
- control_type: Negative Control
  description: Institution do fill remain turn listen ever threat positive shoulder
    somebody woman.
data_analysis_methods:
- Mass spectrometry data processed with MaxQuant
- Statistical analysis using GraphPad Prism (unpaired t-tests)
- One-way ANOVA with Tukey's post-hoc test
reproducibility_notes: All experiments were independently verified by Dr. Nicole Robinson
  and results were consistent across multiple biological replicates.
